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Key Points Question What genetic variants are associated with juvenile amyotrophic lateral sclerosis (ALS)? Findings In this family-based genetic study, exome sequencing was performed in 3 patients diagnosed with juvenile ALS and failure to thrive; this identified de novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient). Variants in SPTLC1 are a known cause of hereditary sensory and autonomic neuropathy, type 1A, and these data extend the phenotype associated with this gene. Meaning De novo variants in the SPTLC1 gene are associated with juvenile ALS, a fatal neurological disorder., This genetic association study identifies genetic variants associated with juvenile amyotrophic lateral sclerosis., Importance Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation. Objective To identify the genetic variants associated with juvenile ALS. Design, Setting, and Participants In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism. Main Outcomes and Measures De novo variants present only in the index case and not in unaffected family members. Results Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway. Conclusions and Relevance These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.

Background Age-related cognitive decline results in increased difficulty in performing tasks that require memory or rapid information processing. Cognitive resilience is the ability to withstand the negative effects of stress on cognitive functioning. The polygenetic contribution to cognitive resilience requires large data sets for analysis. In addition, longitudinal data is needed to identify individual differences in cognitive performance over time. The UK Biobank cohort of over 500,000 participants over the age of 40 offers the potential to advance research on the genetics and biology of cognitive resilience. Methods We created a longitudinal cognitive resilience phenotype by combining the phenotypic cognitive parameter of current reaction time with a proxy phenotype of education years (EY). We used this resilience phenotype, in genome-wide association studies (GWAS) to identify genes and gene sets that influence the biological pathways involved in resilience. To remove the influence of the EY on the analysis we compared genetic data on participants that displayed resilience to those that showed expected cognitive decline. Results GWAS outputs analysis showed 273 significantly enriched genes for participants that demonstrated resilience. Genotype–tissue expression was significant in brain tissue, particularly in the anterior cingulate cortex, frontal cortex, and hippocampus. Biological Pathway analysis includes synapse, post synaptic density and neuron guidance. Conclusion This analysis shows an association between cognitive resilience and enrichment of neuronal activity. Confirmatory examination of these findings in datasets with strong longitudinal cognitive data, such and the Health and Retirement Study, is ongoing., Introduction Type 1 diabetes (T1D) is a polygenic disease characterised by autoimmune inflammatory destruction of the pancreas and subsequent hyperglycaemia. Several GWAS have identified loci associated with T1D risk, but recent evidence suggests that epigenetic changes in DNA methylation may have a causal role in T1D. Methods To identify potential methylation-based biomarkers of T1D, blood-derived DNA from 250 individuals with ≥15 years duration of T1D was compared to 391 controls with no evidence of diabetes. All individuals were from the British Isles. DNA was bisulphite treated using the EZ DNA Methylation Kit (Zymo). The Infinium HD Methylation Assay MethylationEPIC BeadChips (Illumina) were used to determine the methylation status of >850,000 CpG sites, gene bodies and promoters. Results MethylationEPIC data was analysed using GenomeStudio v2011 and Partek Genomics Suite v7.0. Comparing T1D with controls identified 1,706 CpG sites with significantly different (p±2 fold change). Genes including HLA‐DRB1, HLA‐DQA1 and PLEKHA1 have been previously linked to T1D and contained >2 differently methylated CpG sites ≥p, Introduction Rare diseases (RDs) are a public health priority but their scarcity and diversity leads to a lack of knowledge and expertise. Accurate epidemiological information about RDs is necessary to inform public policy, but without an Irish rare disease registry, there is a dearth of primary data. Methods Collaborative work with Orphanet Coordination derived a global point prevalence of RDs from the ‘Orphanet Epidemiological File’ (http://www.orphadata.org) by selecting RDs described by ‘point prevalence’ from predefined geographic regions, and summing point prevalences. In the National Rare Disease Office, expert opinion and disease-specific publications were used to adapt a ‘high prevalence’ list for Ireland. Results Globally, ‘point prevalence’ describes 5,304 RDs ≥85.9%). The minimum cumulative point prevalence of RDs is 3.5‐5.9% of the population. While globally 84.5% RDs analysed ≥n=3585) had a point prevalence of 1/100,000. To construct a comparable Irish ‘high‐ prevalence’ list, 191 RDs with known prevalence >1/100,000 across all countries were drawn from the global list. A further 147 diseases with possible prevalence >1/100,000 in Ireland due to ethnic, environmental or founder‐effect are currently under consideration for inclusion. Conclusion 3.5%‐5.9% is the first evidence‐based estimate of the global population prevalence of RDs. Creation of an Irish list of high‐prevalence RDs permits development of care pathways and systems that address the needs of the majority of Irish people with RDs. Implementation of RD codification in eHealth Ireland will provide more accurate data., Introduction The acute hepatic porphyrias, including acute intermittent porphyria (AIP), variegate porphyria (VP) and hereditary coproporphyria (HP) along with familial Porphyria Cutanea Tarda (fPCT) are autosomal dominantly inherited disorders affecting key enzymes in the haem biosynthetic pathway. Clinically these disorders may manifest as photosensitive skin lesions (VP, HP and PCT) and/or acute neuropathic episodes (AIP, VP and HP). All demonstrate variable penetrance and expressivity. Thus, while biochemical investigations, including blood, urine and faecal porphyrin analysis, are critical for the diagnosis of active porphyric disease, these investigations may not be sensitive enough to identify presymptomatic variant carriers. Hence molecular genetic analysis has become an important component in kindred follow-up for identifying porphyria susceptibility. Methods The Biochemistry Department, St James’s Hospital, Dublin, has established a molecular diagnostic service based on direct nucleotide sequencing to facilitate diagnosis of genetic susceptibility to AIP, VP, HCP and PCT respectively. Results To date over 30 different genetic variants linked with a porphyria phenotype have been identified in different kindreds including non‐Irish. The spectrum of variants includes missense, nonsense, splice‐site and small insertions and deletions e.g. HMBS ≥R26C, R26H, IVS4+1G>A), PPOX ≥IVS4‐1G>A, Q435X, W427X, A150D, Q375X) and CPO ≥R332Q, R332W, c.1291‐1292 ins TG). In addition, novel variants have been identified in collaboration with Cardiff Porphyria Centre. Conclusion This unique insight into the molecular basis of porphyrias in the ROI indicates that acute porphyrias and fPCT are genetically heterogeneous. Furthermore, the variant scanning assay in St James’s Hospital has identified pathogenic variants in >93% of confirmed porphyria kindreds, Background The developmental and epileptic encephalopathies (DEEs) are a group of severe epilepsies which co-present with intellectual disability, and occur in cases without a family history of epilepsy. Their severe phenotype means that DEEs are thought to be primarily monogenic, caused by highly damaging rare mutations. Currently, analysis of exome sequence data can identify a causative mutation in around 40% of DEEs. Little is known about the genetic architecture of the remaining DEEs which screen-negative after genomic analysis. Here, we used a method known as polygenic risk scoring (PRS) to test whether the burden of common genetic variation is relevant to the development of the DEEs. Methods Exome and GWAS data on DEE cases (n=745), and population controls (n=75,000) were obtained from the DDD cohort and Ukbiobank, respectively. Damaging mutations in known epilepsy genes were bioinformatically inferred. PRS were calculated using the most recent ILAE GWAS of epilepsy and compared between i) DEE cases and the general population, and ii) DEE cases with and without damaging mutations. Results DEE cases with and without inferred damaging mutations were found to have elevated PRS for epilepsy. We did not detect a significant difference in PRS between DEE cases with and without damaging mutations. Discussion This research provides the first evidence that common genetic variation contributes to the development of the DEEs. Our results suggest common genetic variation contributes to DEE status irrespective of the presence of a highly damaging rare genetic variant. Further work in additional cohorts is required to extend these results., Rationale The phenotypic features in a person with epilepsy are often complex with regards to seizure presentations, which is acknowledged by the most recent revision of the seizure classification by the International League Against Epilepsy (ILAE). We provide updated seizure-related human phenotype ontology (HPO) terms to facilitate a deep phenotypic interpretation of heretofore unexplained genetic epilepsies. Methods The Epilepsiome project is a Task Force of the Genetics Commission of the ILAE and represent the link to the gene curation efforts within the ClinGen Epilepsy Clinical Domain Working Group (CDWG). Within the efforts to align terminology used in the diagnostic space, the Epilepsiome Project revised HPO terms for epileptic seizures. The updated classification was built through an online portal and consensus was achieved through biweekly conference calls. Results Focal, generalised and neonatal HPO seizure terminologies were constructed according to the most recent ILAE classification and aligned with the existing HPO structure. This ontology allows capture of clinical information at various levels of detail and aims to preserve the onset, awareness and motor/non-motor nature of each seizure type, using multiple parentages. We integrated other frequently observed seizures currently not included in the ILAE, which required a separate branch within the ontology due to biological peculiarity of their age of onset, their clinical significance or genetic architecture. Conclusions Improvements in HPO terms for epileptic seizures will enable a more versatile seizure ontology leading to deep phenotyping of people with epilepsy to improve associations with genomic data in both a research and diagnostic setting., Purpose Target5000 aims to genetically characterise approximately 5000 people in Ireland with an inherited retinal degeneration (IRD). Thus far, over 1,000 IRD patients have been sequenced for variants in 260 IRD genes. One arm of the project focuses on improving detection of candidate variants by whole genome sequencing (WGS), by analysing non-coding mutations and performing functional analysis. Approach IRD patients are clinically diagnosed by Target5000 ophthalmologists. When informed consent is given, the Target5000 study employs target capture next generation sequencing (NGS), with a positive candidate detection rate of 68%. To improve detection rates, whole-gene or WGS was employed on a case-dependent basis to identify pathogenic intronic variants not previously captured. Results One common form of IRD is ABCA4-associated Stargardt disease (STGD1), often caused by deep-intronic variants. Thus far, 36 ‘unresolved’ STGD1 and cone-rod dystrophy cases have undergone targeted ABCA4 whole-gene sequencing, positively identifying a candidate in ~50% of cases. A variant in intron 30 resulting in a pseudoexon inclusion was particularly frequent and found in 5/16 (likely) solved cases. Furthermore, 40 patient samples have undergone WGS. Conclusions An objective of Target5000 is to provide actionable outcomes empowering patients with genetic diagnoses and potentially future access to clinical trials or approved treatments, where appropriate. The results presented highlight the significant value of a target capture NGS strategy as a preliminary diagnostic measure, with remaining elusive cases undergoing more extensive genetic analysis. This methodology improves variant detection rates and progresses the goal of fully elucidating the genetic architecture of IRDs in Ireland., Background Copy Number Variants (CNVs) are large genomic deletions/duplications of >1kb, spanning regions that can encompass one or many genes. Though a common form of structural variation, pathogenic CNVs, of population freq., The Ladakhi people dwell in the Jammu and Kashmir regions of India, between the Karakoram and Himalayan mountain ranges, at ≥3400 meters altitude. The Ladakhi share similar linguistic, cultural and religious practices with Tibetans. However, relative to Tibetans, the Ladakhi are very poorly studied at the level of population structure and genetic selection. In this context, we set out to conduct a genomic survey of population structure in representative samples of the Ladakhi people. Methods We genotyped 310 Ladakhi DNA samples using the Illumina Global Screening Array gene chip. We merged the Ladakhi with data from 800 individuals representing different reference language groups including; Sino-Tibetan (Tibetans, Sherpa, Han), Indo-European (Indo-Aryan, Hazara), Austroasiatic (Munda) and Burusho (a linguistic isolate in Jammu-Kashmir). We performed ADMIXTURE, principal component analysis (PCA), fineSTRUCTURE and ChromoPainter analysis on the combined autosomal data. Results In PCA plots, the Ladakhi population cluster together with Sherpa and Tibetans, forming a distinct Himalayan group, different from other mainland populations of South and East Asia. ADMIXTURE analysis at k=4 suggests ancestry proportions in the Ladakhi to be approximately 50% Highlander (Tibetan/Sherpa) and 50% Indo-European. These results suggest contemporary Ladakhi people are the admixed of Tibetans and Indo-Europeans. Conclusions Our results suggests a considerable component of the Ladakhi genome descends from ancestral highlander populations residing on the Tibetan plateau for the last 35,000 years, with subsequent admixture with neighbouring Indo-European populations., Background The EU recognises rare disease (RD) as life threatening with delays in establishing a diagnosis and treatment. The Irish National Plan for RDs (2014) recommended epidemiological studies of RD prevalence to improve both cost efficiencies and care of patients with RD’s. Objective To derive the incidence of paediatric RD and the number of paediatric RD mortality cases through analysis of records held at two major tertiary paediatric hospitals, for children born in the year 2000. Methods Cases were identified using electronic/manual records from: the National Paediatric Mortality Registry office; Clinical, Cytogenetics and Molecular genetics database; Radiology and the Hospital In-Patient Enquiry system (HIPE). In addition a detailed analysis of national death registration information for RDs from 2006-2016 was undertaken along with a 2year study (2015-2016) of inpatient RD deaths. Results There were 54,789 livebirths in 2000. Genetics records identified 801 cases of RDs Ongoing HIPE searches identified 1381 cases. Mortality data revealed that of all deaths on the Register (2006-2016), (n=4044) aged 0-14, 58.56% (n=2368) had a RD diagnosis with age distribution; Neonates, 56% (1140/2050), Post-neonates, 58% (450/778), Children aged 1-14 years, 64% (778/1216). Of the total (n=234) inpatient deaths with a RD from 2015-2016, 52.6% (n=123) were cared for at the two major centres. Conclusion This study to-date has identified > 2,200 RD patients presenting by age 17 giving a minimum incidence of 4% for paediatric RDs. We expect the final figure to be higher when we complete analysis of all the HIPE and sub-specialty data from these major centres., Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disease. ADPKD is primarily caused by variants in PKD1 and PKD2. Sequencing of PKD1 is difficult due to multiple pseudogenes. There is unexplained variance in the age-of-onset of PKD, even within families. Aim 1) Establish a targeted NGS panel to improve molecular diagnosis of PKD and 2) characterize large ‘super-families’ for the study of new ADPKD genes and genetic modifiers. Methods NGS was performed using a custom Roche SeqCap targeted panel (273 genes) and Illumina NextSeq. Bioinformatics was performed using an in-house GATK pipeline. Pathogenicity was assigned using American College of Medical Genetics and Genomics guidelines and Mayo Clinic PKD in-house methods. Gap-filling Sanger sequencing was utilized in unsolved cases Results 172 PKD patients were sequenced with average coverage 189X. A molecular diagnosis meeting pathogenicity criteria was obtained in 82% (141/172) of patients following gap-filling Sanger of PKD1 and PKD2 (n=41). 46 of the PKD-causing variants we detected were novel. We identified 13 rare, diagnostic PKD variants shared across multiple affected individuals recorded clinically as having no known familial relationship. Second-degree relatedness was confirmed via clinical follow-up. These families form the basis for the assembly of PKD ‘super-families’. Conclusions NGS is suitable for sequencing of PKD genes including PKD1, although some gap filling by Sanger is required for complete coverage. We have identified 13 potential ADPKD ‘super-families’ using genomic data for further study. These results are improving diagnostics of ADPKD in the Irish renal clinic., Purpose Target5000 is a genetic study to detect and characterise variants associated with inherited retinal degenerations (IRD). Choroideremia is an X-Linked recessive chorioretinal degenerative condition with progressive atrophy of several key cells of the retina and the surrounding blood retinal barrier. Here we describe a novel deletion in the CHM gene found in two Irish pedigrees. This 500kb deletion represents the largest yet detected IRD-associated deletion in Ireland. Approach As part of the Irish IRD registry, Target5000, patients with inherited retinal degenerative conditions are recruited. Target capture sequencing was employed to investigate variation in 254 IRD-associated genes. Upon detection of the deletion in CHM, PCR analysis was used to elucidate the full extent of the deletion. Results Two members of a large X-linked Retinitis Pigmentosa pedigree clinically presented with choroideremia and tested negative for the segregating RPGR variant found in other affected members of this pedigree. Both males were sequenced and found to possess large deletions spanning the CHM gene, totalling 500kb. This deletion has also been detected in a second Irish pedigree since its discovery. Two additional males and two carrier females from this second pedigree were all found to be severely affected with progressive choroideremia. Conclusions Typically, female carriers of CHM mutations show mild stationary signs with no symptoms, while males are severely affected. In this instance, females were more severely affected than expected with advanced signs of degeneration and progressive visual decline. This is possibly due to random X-inactivation and the severity of CHM gene deletion., Introduction The largest cohort of patients at The National Centre for Adult Inherited Metabolic Disorders (NCIMD) have Phenylketonuria (PKU). The NCIMD manages patients transitioned from Paediatric services upon reaching adulthood. Improved treatments have extended life expectancy and increased quality of life for patients with PKU; however diet and supplements remained the only means of treatment for life until the recent introduction of Sapropterin dihydrochloride. Aim To analyse the genotype of the PKU cohort in attendance at The NCIMD with a focus on responsiveness to Sapropterin dihydrochloride. Method The data are collated from when the Adult unit was first established in 2013 until the end of May 2019. Exclusion criteria include patients over the age of 53 and patients who have two negatively indicated genotypes for the use of Sapropterin dihydrochloride. Genotypes are recorded in a secured database onsite and descriptive analyses were performed. Results The total number of patients examined is 282; 104 were male (36.8%) and 178 were female (63.1%). The total samples processed and available for analysis were 148 (male= 46, 31%; female= 102, 68.9%). The frequency of Saptopterin dihydrochloride responsiveness in both alleles was observed (responsive= 15, 10%; unresponsive= 48, 48.33%; uncertain= 85, 57%). The most common alleles recorded were R408W (41.1%), F39L (13.8%), 165T (11.2%), and L249F (3.8%). Conclusion Due to the uncertainty surrounding Sapropterin dihydrochloride responsiveness for various common mutations in the Irish PKU cohort, there is a need for greater genetic and metabolic collaboration. Analysis and treatment may be impacted by time elapsed from sending samples to receiving results., Introduction The Department of Clinical Genetics at CHI provides services for individuals affected by or at risk of a genetic condition in the Republic of Ireland. There are currently 3,283 referrals waiting to be seen, of whom 930 are waiting longer that the HSE standard of 18 months. A negative consequence of a long waiting list is that patients die whilst waiting. Resulting harm includes: 1) no diagnosis 2) no genetic testing, no DNA stored, 3) family unaware of a hereditary disorder, denied screening, 4) relatives having unnecessary screening as no predictive test for family, 5) future pregnancy options limited if paediatric proband undiagnosed. As of 13/06/2019, we have recorded 33 deaths on our waiting list. We began to systematically collect data on deaths since March 2018. This study concentrates on these cases; n=15/33. Aims To identify the consequences to the relatives of these 15 referrals. Results Nine were adult cancer genetic referrals, 5/9 diagnostic, 3/9 predictive, and a further case had NF2. Only 1/9 had DNA stored. Two adult patients had a cardiac family history (Marfan syndrome, cardiomyopathy) respectively. Neither had DNA stored. Four paediatric patients had multiple malformations secondary to a chromosomal or genetic syndrome. In 3/4 a diagnosis had already been reached. The fourth case, who died unexpectedly of unrelated causes, had no DNA stored. Summary 11/15 patients who died did not have DNA stored, precluding diagnosis and risk calculation for their relatives. As each extended 3 generation Irish family has ~64 relatives, lack of diagnosis has far reaching consequences., Background Women who carry a pathogenic variant in either a BRCA1 or BRCA2 gene have a high lifetime risk of developing breast and tubo-ovarian cancer. To manage this risk, women may choose to undergo risk-reducing surgery to remove breast tissue, ovaries and fallopian tubes. Surgery should increase survival, but can impact women’s lives adversely at a psychological and psychosexual level. Interventions to facilitate psychological adjustment and improve quality of life post risk-reducing surgery are needed. Aim of Review To examine psychosocial interventions in female BRCA carriers who have undergone risk-reducing surgery and to evaluate the effectiveness of such interventions on psychological adjustment and quality of life. Methods We searched the Cochrane Central Register of Controlled trials (CENTRAL) in the Cochrane Library, MEDLINE via Ovid, Embase via Ovid, CINAHL, PsycINFO, Web of Science and Scopus up to April 2019. Results We identified two studies; one randomised controlled trial and one nonrandomised study. Conclusions The effect of psychosocial interventions on quality of life and emotional well-being in female BRCA carriers who undergo risk-reducing surgery is uncertain given limited high quality evidence. Next Generation Sequencing, along with targeted cancer treatments, increasing knowledge around the biology of cancers and the results of the 100K Genome Project will open up genetic testing to many more women. For as long as surgical interventions remain the dominant risk-reducing option for management of women with a deleterious BRCA gene, health professionals have a responsibility to ensure there is provision to holistically manage the outcomes of such surgery., Introduction FATCO (Fibular Aplasia, Tibial Campomelia and Oligosyndactyly) syndrome is a rare descriptive diagnosis first defined by Courtens et al. in 2005, who recognised a comparable pattern of malformations with his own case and 4 others described in the literature. Aetiology remains unknown, however defects involved in SHH (Sonic hedgehog) gene expression have been proposed. Case Description We report on a term male infant born with severe malformations. On examination, there was absence of the left radius and ulna, bilateral anterior angulation of lower limbs with skin dimpling overlying. Both ankle joints were dysplastic and there was oligosyndactly of both feet. Right upper limb was normal. X-rays of the limbs revealed dysplastic tibiae, absence of both fibulae, a right foot containing 3 ossified metatarsals with 2 formed digits, and a left foot with a single ossified metatarsal and two soft tissue digits with small bony elements. The infant had no other associated anomalies, and is developmentally appropriate at 1 year. Management included Symes amputation, prosthetics and following genetic referral FATCO syndrome was suggested as the best fitting diagnosis. Whole genome sequencing of the infants blood is currently being performed. Discussion This is an important case to report as there are very few descriptions in the literature, In keeping with the majority of reports, this case appears to be sporadic and development is normal. Our case is male, keeping with preponderance. Treatment aims at optimising functionality of limbs and stabilisations of joints., Introduction Fibrous cephalic plaques (FCP) are a characteristic manifestation of tuberous sclerosis complex (TSC) and occur in one third of cases. Their natural history and long term course is unknown, as is the outcome of long term follow-up of TSC cases in old age. Phenotype and methods We describe an 80 year old with TSC due to a c.2784dupC TSC2 mutation, who was diagnosed in infancy with an FCP and was regularly followed up at the TSC clinic over 8 decades with regular epilepsy treatment and renal monitoring. Results Regular clinical photography and clinical records document the plaque at different ages. The FCP naturally resolved at 74 years. Facial angiofibromas also faded with time in the last decade. His epilepsy and renal abnormalities remained under control with careful surveillance and monitoring. Discussion Natural aging in the eighth decade causes progressive laxity of collagen and leads to natural resolution of FCPs. This novel finding with a unique 80 year follow up yields valuable insights into the aging changes within FCPs and facial angiofibromas as the pathways linking facial angiofibromas and FCP’s through the TGF-β1 pathway are now being elucidated. Conclusion We present a clinical odyssey showing the natural progression and history of FCPs in TSC and comment on the mechanistic pathways allowing potential interventions in this disfiguring condition. TSC cases can be successfully managed and complications – particularly in the brain and kidney, can be avoided over an entire lifetime. This is encouraging for long term prospects for patients with TSC., Introduction Fabry disease is an X-linked inherited disorder due to deficient activity of the enzyme alpha-galactosidase A and progressive lysosomal deposition of globotriaosylceramide in cells. Aim To report the genotype/phenotype landscape of the adult Fabry disease cohort attending The National Centre for Adult Inherited Metabolic Disorders (NCIMD). Method All Fabry patients (N=70) attending NCIMD until end of May 2019 were included in this analysis. Genotypes and phenotypes were recorded by chart review. Descriptive analyses were performed. Result 26 (37.1%) were male (median age 43 [32:54]) and 44 (62.9%) were female (median age 46 [25:61]). The AGAL pathogenic variants were missense (52, 74.3%), deletion (9, 12.9%), nonsense (8, 11.4%) and duplication (1, 1.4%). Most missense variants occurred in exon 2 (25%), exon 3 (19.2%), exon 5 (23.1%) and exon 6 (21.2%). 21.2% of missense variants were N215S. 28 patients were on enzyme therapy and 2 were on oral chaperone therapy. The incidence of cardiac (M=18/26; F=18/44; p=0.021), renal (M=14/26; F=18/44; p=0.304), neurological (M=17/26; F=20/44; p=0.107) and hearing (M=14/26; F=19/44; p=0.399) involvement were observed. Within N215S cohort, 2 had hypertrophic cardiomyopathy and 5 with a degree of left ventricular hypertrophy. Conclusion Pathogenic variants were observed across the AGAL gene in the cohort. Incidence of cardiac involvement in both genders is similar. Females had more frequently observed renal, neurological and hearing involvement. N215S AGAL variant is the most common variant which is associated with a predominant cardiac phenotype, thus collaboration between clinical geneticists and cardiovascular physicians are important when establishing diagnosis and management., Background Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disease with a worldwide prevalence of 1:500. Genetic etiology is suspected in up to 50% of HCM patients. To gain insight into the diagnostic yield and mutation spectrum of HCM, a retrospective review was performed for 114 consecutive cases with a clinical suspicion of HCM who underwent multigene panel testing at our laboratory between 2014 and 2019. Method Data was manually extracted from laboratory reports with respect to indication for testing, number of genes on panel, variants identified and classification at the time of testing. Results A total of 114 patients with a diagnosis of HCM had samples submitted for diagnostic testing using a multigene panel of between 16 and 20 genes, depending on the year of testing. 56 patients had no genetic variant identified, 33 patients had a pathogenic or likely pathogenic variant identified and 25 had a variant of uncertain significance identified. One 11 year old patient had a normal result from an 18 gene panel for HCM, but was later diagnosed with Friedrich ataxia. One adult female patient had a normal result from a 19 gene panel but was later diagnosed with Fabry disease. Conclusion Clinically actionable ‘Pathogenic’ or ‘Likely pathogenic’ variants were identified in 29% of patients with a Clinical diagnosis of Hypertrophic Cardiomyopathy with VUS being identified in 22%. The most common 2 genes in which clinically actionable variants were found were MYH7 (47%) and MYBPC3 (31%)., Huntington’s disease (HD) is an inherited progressive neurodegenerative condition. In the Republic of Ireland genetic testing for HD is available via two routes. Symptomatic individuals can access testing via a Neurologist. Asymptomatic individuals with a known family history of HD can seek testing via a genetic counselling multi-step process. Aim The aim of the audit was to review the activity of the HD specialty clinic. Methods Retrospective chart, laboratory and clinical database review for HD referrals received for 2016, 2017 and 2018 was carried out. Parameters examined included: number of referrals, age profile, motivation for testing, results. Results Over this 3 year period 93 referrals were received. 80 referrals were for predictive testing and 13 for genetic counselling post testing through neurology. The youngest person was 18 years of age at time of referral. More females requested a referral for predictive testing than males, 48 (60%) and 32 (40%) respectfully. The most common motivation given for predictive testing was with regard to family planning and concerns for children and to help them plan for the future. Of the 30 tests carried out to date, 52% were mutation positive and 42% were mutation negative. The average age of those who proceeded with testing was 37yrs. Conclusion These findings reflect data published from the UK with regard to age of presentation and female to male bias. The most common motivation for testing was family planning unlike the UK where the most common reason provided was to reduce uncertainty.

Myocyte enhancer factor 2 C (MEF2C) is a transcription factor that plays a central role regulating cell differentiation, proliferation, survival and apoptosis. MEF2C has been implicated in each of the most recent GWAS of cognitive ability (CA) and educational attainment (EA). Animal studies have indicated that knockout of Mef2c interferes with healthy development of brain regions associated with cognitive function, e.g. hippocampal dentate gyrus, neocortex. Furthermore, mutation/deletion of MEF2C can cause severe intellectual and developmental disability. We therefore hypothesised that genes regulated by MEF2C would be associated with cognitive function. We created a set of differentially expressed genes (DEGs) based on an RNA-seq study that captured the transcriptional changes in mouse adult brain that result from early embryonic deletion of Mef2c in cortical and hippocampal excitatory neurons. This mouse DEG list was converted to human orthologues (n=1052) and tested for enrichment of genes associated with 1) CA, and 2) EA, using MAGMA and recent GWAS summary statistics for each phenotype. We also performed hypergeometric tests to investigate if the DEGs were enriched for current primary intellectual disability (ID), autism, and loss-of-function (LoF) intolerant (i.e. highly constrained) genes. We then used Ingenuity Pathway Analysis (IPA) to explore functional pathways implicated by the MEF2C DEGs. The DEGs were significantly enriched for CA (p=1.08e-07) and EA (p=9.88e-09) genes; along with ID (p=0.008), autism (p=0.001) and LoF intolerant (p=5.55e-21) genes. The top functions IPA predicted to be decreased from these DEGs are ‘development of neurons’ (p=5.41e-38, z-score=-2.0) and ‘formation of cellular protrusions’ (p=1.02e-28, z-score=-2.1). These findings indicate that genes influenced by MEF2C are highly constrained and contribute to cognitive function and neurodevelopmental disorders with severe cognitive deficits., Nearly 50% of all colorectal cancer patients progress to develop metastatic lesions (mCRC) and despite ongoing efforts the survival rates for these patients remains significantly low (90% CRC-specific enhancer regions, which was subsequently integrated with RNAseq derived gene expression in order to identify gene-enhancer pairs. Applying motif and transcription factor identification algorithms to the methylation signature, showed intricate networks of disease-associated transcription factors whose binding sites are significantly impacted as a result of the altered methylation within these enhancer regions. Utilization of deep machine learning approaches to the methylation data, demonstrates specific methylation patterns that allow stratification of patients independent of their clinical features. Finally, we show that two methylation derived patient clusters overlap significantly with expression derived consensus molecular subtype (CMS) -2 (WNT-p53 cluster) and CMS-4 (EMT-like). This study for the first time presents a critical insight into an enhancer driven epigenomic landscapes, which potentially regulates disease-associated phenotype within mCRC., Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory aetiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n=100) and individuals without a history of depression (n=100) using the Illumina 450K microarray. Our analysis identified 6 significant (Sidak corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Sidak corrected P = 1.27 x 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype., Mutations in RP2 are responsible for approximately 15% of X-linked Retinitis Pigmentosa cases. RP2 is ubiquitously expressed and involved in ciliary trafficking of lipid-modified proteins. A patient harbouring the most common nonsense RP2 mutation, R120X, was identified through the Target 5000 programme. This enabled the generation of a patient-derived primary fibroblast disease model. The aims of this study were (i) to identify a vector capable of effectively transducing primary fibroblasts, (ii) to rescue RP2 expression in the R120X cell model and (iii) to explore potential assays for evaluating rescue of RP2 function in these cells. Transduction efficiencies were determined by treating normal fibroblasts with a CAG.EGFP construct packaged in AAV2/2, 2/5 and 2/8 capsids. The results were 55.5% ± 2.5, 17.5% ± 15.4 and 2.2% ± 1.0, respectively. The expression level of RP2 mRNA in untreated R120X fibroblasts was 7.5 fold ± 3.2 lower than that of wild type fibroblasts, while RP2 protein was absent in R120X cells. Transduction of mutant cells with AAV2/2.CAG.RP2 resulted in overexpression of RP2 protein by 1.19 fold ± 0.67. The R120X cell line was evaluated for phenotypes associated with absence of RP2, including Golgi fragmentation and mislocalisation of an intraflagellar trafficking protein, IFT20.The areas of both GM130 and IFT20 were significantly larger in mutant fibroblasts compared to control cells. Treatment with AAV2/2.CAG.RP2 was beneficial in reversing Golgi fragmentation, as the Golgi area in transduced R120X fibroblasts was reduced by 1.5 fold ± 0.5 when compared to untreated cells (p < 0.0001)., Background: Genome-wide association studies (GWAS) identify associations of individual SNPs with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes. Methods: we conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product (sARTP) method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9,040 cases and 12,496 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes contributing to the top associated pathways and gene sets. Results: We identified 14 pathways and gene sets associated with PDAC at FDR < 0.05. After Bonferroni correction (P-value ≤ 1.3x10-5), the strongest associations were detected in five pathways and gene sets, including maturity onset diabetes of the young (MODY), regulation of beta cell development, role of epidermal growth factor (EGF) receptor transactivation by G-protein-coupled receptors in cardiac hypertrophy pathways, and the Nikolsky breast cancer chr17q11-q21 amplicon and Pujana ATM Pearson correlation coefficient (PCC) network gene sets. We identified and validated rs876493 and three correlating SNPs (PGAP3) and rs3124737 (CASP7) from the Pujana ATM PCC gene set as eQTLs in two normal derived pancreas tissue datasets. Conclusion: Our agnostic pathway and gene set analysis integrated with functional annotation, eQTL analysis and experimental validation provides insight into genes and pathways that maybe biologically relevant for risk of PDAC, including those not previously identified., We carried out a detailed genetic study of the population structure, local migration rates and population changes across in the Netherlands using cutting edge methods. Our dataset couples genome wide SNP data and geographic information (N=1422), which together allow us to investigate the interplay between genetics and local geography. To interrogate fine scale population structure we applied the haplotype-based method Chromo Painter/fineSTRUCTURE, which partitions data based on patterns of haplotype sharing. FineSTRUCTURE identified 16 genetic clusters which correlate closely with regional geography. At the finest level, this clustering has the resolution to distinguish subtly different eastern and western genetic groups within the North-Brabant province. At the coarsest level, clustering delineates a clear north/ south split in the Netherlands, reflecting deeper differences. We investigated whether our clustering reflects barriers to gene flow using the “Estimating Effective Migration Surfaces” (EEMS) method, and observed a strong migrational cold spot splitting the country, broadly overlapping the course of the Rhine. We also estimated recent changes in the effective population size (Ne) using the IBDNe method, observing super-exponential population growth across the past 50 generations. This expansion rapidly increases in rate from ~1650 CE onwards, potentially driven by the Dutch Golden age of the 17th Century. Notably our Ne estimates are systematically lower in northern populations than southern suggesting lower diversity in the north, which is consistent with reported ROH and IBD analysis. Combined our results paint a picture of the dynamic population genetics of the Netherlands that are strongly linked to geography., We present here a demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island’s human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras. Large scale migrations into the island are implied during the transitionary periods carrying with them ancestry ultimately derived from Anatolia and later the Russian steppe. Patterns of haplotypic-sharing and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no major population replacement has occurred on the island since this point in time. We further dissect the genetic affinities of each Irish population with reference to wider palaeogenomic datasets, using both allele and haplotype-sharing methods, the latter made possible through genotype imputation., Background: Rare diseases (RDs) affect at a minimum 5 per 10,000 people. Although individually rare and under-recognised in healthcare systems, collectively RDs are common with up to 8,000 diseases now described. The National Plan for RDs (2014), recommended the need for epidemiological studies, highlighting the requirement for RD coding to identify RD patients and thereby improve both cost efficiencies and care of patients with RDs. Objectives: To derive an estimate of the number of childhood onset RDs through analysis of records held at TSCUH & OLCHC. Methods: Reports of patients born in the year 2000 were extracted from: the National Paediatric Mortality Registry office; clinical, cytogenetics and molecular genetics databases, and the Hospital In-Patient Enquiry system (HIPE) TSCUH/OLCHC. RD cases were identified using electronic/manual results and assigned orpha-codes. Results: 54, 7893 livebirths, census 2000. National Paediatric Mortality Register, 73 deaths of children born in year 2000 of these 60 had a RD (82%). Clinical, cytogenetic and molecular genetics from TSCUH/OLCHC identified 603, 121 and 77 cases of RD respectively. HIPE TSCUH/OLCHC searches to-date have identified 202 and 242 cases of RD respectively. Conclusions: RD epidemiological data is difficult to acquire in the current structure of the Irish health service, requiring multiple sources and an inordinate amount of time accessing manual records. This study to-date has identified over 1,000 RD patients presenting by age 17 to OLCHC/TSCUH giving a minimum incidence of 2% for paediatric RDs. In the coming year records from TSCUH specialties will be accessed for inclusion in the study., Background & Aims: Newborn screening for Cystic Fibrosis (CF) commenced in the Republic of Ireland in July 2011. The aim of this study was to do a comprehensive review of the first five years, focusing on those who had CFTR genetic testing following an elevated IRT. Methods: This study included all neonates screened from July 2011 to June 2016. Data was expanded by cross-referencing patient charts, clinical and lab databases with the Non-NBS database to track down cascade tested relatives. Results: In this period a total of 342,424 infants were screened. 141 CF and 19 CF-SPID cases were identified in addition to 238 healthy carriers. 2 babies died from unrelated illnesses, before their Sweat Test. A total of 300/400 (75%) couples with a CF/CF-SPID/Carrier child were seen by a Genetic Counsellor. Phe508del was the most common mutation (79.9%) followed by Gly551Asp (8.7%). Consequently, 185/238 Carrier parents (78%) underwent genetic testing, identifying 1 carrier couple. 101/160 (63%) CF/CF-SPID parents were tested. 255 additional relatives came forward for cascade testing - 184 from 68/162 CF affected/CF-SPID/RIP families (42%), resulting in 3 new CF cases, 3 new CF-SPID cases and 64 additional carriers. Two cases were siblings born prior to NBS. One case was missed though NBS. 71 relatives from 33/238 Carrier families (14%) came forward for cascade testing, identifying a further 18 carriers. Conclusion: Through early detection of CFTR mutations, NBS provides the opportunity of early intervention and complication prevention as well as improvements in prenatal diagnoses and availability of cascade testing., Background: Multi-gene testing is useful in genetically heterogeneous conditions, including inherited cardiac pathologies. Extended panels increased diagnostic yield of variants where pathogenicity is certain (class 5), likely (class 4) and uncertain (class 3). Concerns exist regarding management of class 3 and 4 variants in conditions of oligogenic inheritance or variable expressivity. Aim: 1. To review diagnostic yield of genetic tests performed in families with inherited cardiac pathologies 2. To assess management of different classes of variants by clinicians internationally. Methods: A retrospective cohort analysis was undertaken. Patients in whom “cardiac” genetic tests were requested between 2015 and 2017 were identified from a prospectively maintained departmental patient database. Data regarding indication for testing, diagnostic yield, and classification of variants were retrieved by manual chart review. An electronic survey regarding clinical management of variants (http://www.surveymonkey.com/r/cardiacvariants) was distributed to colleagues internationally via professional bodies and direct email. Results: 636 tests (630 patients) were performed between 2015 and 2017 in our centre (183 diagnostic; 453 predictive). At least one variant was identified in 71(39%) patients (28(15%) class 5; 9(5%) class 4; 38(21%) class 3. 135 respondents (23 countries) completed the survey. Considering class 4 variants, 110(81%) counselled patients about the possibility of variant reclassification. In the case of a negative predictive test, 17(13%) were fully reassuring that the patient would not develop the familial phenotype. Conclusion: Considerable variability in management of class 3 and 4 variants exists. Decision-making relies on interpretation of the phenotype, family history and genotype. Close multi-disciplinary working between cardiology and clinical/molecular genetics teams is critical., Familial hypercholesterolaemia (FH) is an autosomal dominant disorder due primarily to mutations in LDLR, APOB and PCSK9, which causes marked increases in LDL cholesterol levels and predisposes to premature CVD. Given a prevalence of 1:250, there are approximately 23,000 FH sufferers in the Republic of Ireland, most of whom are as yet undiagnosed. The most cost-effective strategy for identifying FH is genetic cascade screening in kindreds with an identified proband. We report interim outcomes of a FH genetic diagnostic service configured around an initial screen of 40 known FH variants followed by either a confirmatory analysis or a full variant scan using PCR and direct nucleotide sequencing, in positive and negative screens respectively. To date our service has genetically diagnosed 69 patients with FH, including 50 index cases and 19 positive cascade screens. In total, 30 disease-associated variants in LDLR and APOB have been identified including four due to copy number variation using MLPA. Based on phenotypic classification by Dutch Lipid Clinic Network scoring 75% of those designated “Definite/Probable FH” were genetically confirmed compared with, Hereditary Breast & Ovarian Cancer syndrome (HBOC) is caused by mutations in BRCA1/2 genes and is associated with a high life time risk of breast cancer and ovarian cancer. Ovarian tumours with inherited (germline) or acquired (somatic) BRCA1/2 mutations respond to drugs that inhibit poly ADP-ribose polymerase (PARPi). Currently, mutation screening for HBOC patients are ‘sent away’ to the UK, with a predictive (pre-symptomatic) service for known familial mutations offered at DCG. At this time, there is no service for tumour BRCA testing for potential PARPi treatment. Supported by the National Cancer Control Programme, DCG & CMD have collaborated to assess next generation sequencing BRCA gene panels & platforms to establish a pathway for germline & tumour mutation analysis and validate an optimal clinical testing method for diagnostic and therapeutic use. The ThermoFisher Oncomine panel with the Ion Torrent PGM/S5 was used to target and sequence 64 unique germline samples with a wide range of known BRCA mutations. These were analysed using JSI SeqNext software and others. After optimisation, 99.84% (624/625) variants were detected at some level. However, there were 117 false positive calls, all in homopolymer regions. Distinguishing false positives from some true positives with a low variant fraction was challenging. Subsequently, the Nimagen EasySeq kit (employing single molecule Molecular Inversion Probes, smMIPs) with the Illumina MiSeq was used for 32 samples. There was a 100% variant call rate (376/376) with no false positive calls. Initial tumour results are also very convincing. Now proceeding to a full clinical validation., Establishing the pathogenicity of missense variants detected in Lynch syndrome / Hereditary Non Polyposis Colorectal Cancer (HNPCC) families is a challenge for diagnostic laboratories. Here we consider two families from Northern Ireland who meet Amsterdam II Criteria for HNPCC, in whom the presence of a PMS2 gene missense variant c.137G>T p.(Ser46Ile) rs121434629 has been shown. This variant occurs within a conserved ADP/ATP binding region of the PMS2 protein. Disruption of this domain is predicted to result in reduced mismatch repair efficiency and has previously been reported in the literature as a recurrent and founder variant in the PMS2 gene. However, no co-segregation data has been published for this variant. Adoption of the ACMG Standards and guidelines (Richards et al Genetics in Medicine 2015) along with the release of ACGS best practice guidelines for the interpretation of sequence variants has initiated a review of the classification of variants detected within the region against these standards. Bioinformatic analysis and evidence available in the published press, had led to a classification of likely pathogenic for this variant. However, addition of the co-segregation evidence provided by local families, at the strong level, enables the variant to be re-classified as pathogenic. In conclusion, we have shown co-segregation of the PMS2 c.137G>T p.(Ser46Ile) variant with Lynch syndrome associated phenotype to a Path P1 strong level of significance through family studies., The C677T polymorphism in the folate metabolising enzyme methylenetetrahydrofolate reductase (MTHFR) is associated with hypertension. Riboflavin is a cofactor for MTHFR in one-carbon metabolism, for generating methyl groups important in DNA methylation. Supplementation with riboflavin has been shown to lower blood pressure in MTHFR 677TT genotype individuals. The mechanism regulating this gene-nutrient interaction is currently unknown but may involve aberrant DNA methylation also implicated in hypertension. This study examined DNA methylation of hypertension-related genes in adults stratified by MTHFR genotype and the effect of riboflavin supplementation on methylation of these genes in the MTHFR 677TT genotype group. We measured DNA methylation using pyrosequencing in a set of candidate genes associated with hypertension including angiotensin II receptor type 1 (AGTR1), G nucleotide binding-protein subunit alpha 12 (GNA12), insulin-like growth factor 2 (IGF2) and nitric oxide synthase 3 (NOS3). Stored leukocyte samples from participants with the MTHFR C677T genotype who had participated in targeted RCTs (1.6mg/d for 16wks) at Ulster University were accessed for this analysis (n=120). Baseline methylation differed between MTHFR C677T genotype groups at NOS3 (p=0.026) and AGTR1 (p=0.045). Riboflavin supplementation in the MTHFR 677TT genotype group resulted in altered average methylation at IGF2 (p=0.025) and CpG site specific alterations at the AGTR1 and GNA12 loci. This study demonstrates an interaction between DNA methylation of hypertension-related genes and riboflavin supplementation in adults with the MTHFR 677TT genotype. Further work using a genome-wide approach is required to better understand the role of riboflavin in altering DNA methylation in these genetically at-risk individuals., Chronic kidney disease (CKD) is considered a major public health problem, affecting approximately 10% of the global population. While a comprehensive review of known CKD biomarkers yielded many results, it also highlighted a lack of research in chromosome Y. Single nucleotide polymorphisms (SNPs) on chromosome Y have previously been associated with a 50% increase in risk of developing coronary artery disease, a condition with close links to CKD. Therefore, Y chromosome SNPs may also impart increased risk of developing CKD. Individuals from the Genetics of Nephropathy: an International Effort (GENIE) consortium (n=791) and the Northern Ireland Cohort for the Longitudinal Study of Aging (NICOLA; n=1241) were genotyped using the Illumina HumanOmni1-Quad array and the Illumina CoreExome-24 array, respectively, to determine if any association exists between Y chromosome SNPs and CKD, or estimated glomerular filtration rate (eGFR), a measure of kidney function. However, poor coverage of chromosome Y resulted in only 3 SNPs in the GENIE cohort and 421 SNPs in the NICOLA cohort passing quality control. Association analysis of both datasets did not reveal any significant associations. Due to limitations of this study, further analysis is required to determine whether SNPs on chromosome Y are associated with CKD and/or eGFR. An array with greater Y chromosome coverage will be selected and be used to re-genotype these individuals, and individuals from additional cohorts, allowing greater SNP coverage and direct comparison of SNPs between these cohorts. Increased SNP coverage and increased participant numbers will allow meta-analysis to be performed with sufficient power., Background: Tumour hypoxia is a major driver of prostate cancer progression and metastasis. miR-21 is a microRNA which has been previously linked to hypoxia, but this relationship remains poorly characterised in a prostate cancer setting. Therefore, in this study, we investigate the link between hypoxia and miR-21 in prostate cancer cells. Methods: We have used 2D and 3D cell prostate cell models of hypoxia to investigate the functionality of miR-21. Expression levels of miR-21 have been measured by qPCR and functional bioassays used to examine its effect on prostate cell behaviour. Target genes have been identified and bioinformatic analysis has been employed to investigate a clinical significance for miR-21 in prostate cancer. Results: miR-21 is induced by hypoxia in prostate cancer cell-lines. Over-expression of miR-21 impacts upon target genes which in turn affects cell behaviour. Data-mining of online repositories of clinical data and bioinformatic analysis of miR-21 cellular networks reveal that miR-21 exerts a wide influence on several important cell processes, the dysregulation of which can lead to development of prostate cancer. Conclusions: We propose that miR-21 could be an important microRNA in the pathogenesis of prostate cancer and has potential as a biomarker in this disease., The Neolithic period begins in Europe around 8500 years before present (BP) and is characterized by the adoption of farming and domestication of various types of animal. In our project we focus on the structure of the Maltese population during the latter part of the Neolithic period. Nine individuals, from 4900 to 4350 years BP, collected from the Xaghra Circle site in the island of Gozo, were sampled. DNA was extracted from both teeth and the inner part of petrous bones giving an average endogenous DNA respectively of: 1.7% for 4 teeth and of 21% for 5 petrous bones. We then used a median of 363,579 SNPs from the Human Origin dataset to compare our samples with 37 ancient individuals from Neolithic and Bronze Age period and 604 present-day European individuals already published. PCA analysis shows, for the 5 high coverage samples, places the Maltese individuals with the early European farmers (EEF) from Germany and Hungary. Further analysis with D-statistics depict that the Maltese population do not resemble any hunter-gatherer population from Caucasus or Eastern Europe, while they show a higher affinity with Western European hunter gather individuals (WHG)., According to the WHO, glaucoma is the second leading cause of blindness in the world and is the leading cause of irreversible blindness. The total number of suspected cases of glaucoma is estimated to be over 60 million worldwide, increasing to 79.6 million by 2020. Commonly, glaucoma is treated using eye drops containing prostaglandin analogs, including latanoprost and bimatoprost. However, these treatments come with ocular adverse reactions including ocular surface irritation, acute iritis, conjunctival hyperemia, thickening and elongation of eyelashes, induced iris darkening as well as periocular skin pigmentation. Patient compliance has been shown to be affected by these side-affects including non-compliance for cosmetic reasons with thickening and lengthened eyelashes and the occurrence of pigmentation. This study aimed to identify whether there are differences in gene expression between those prostaglandin treatments containing preservatives and those without preservatives. Primary human trabecular meshwork cells were stained with phalloidin to determine morphology. The cells were treated with prostaglandins either with or without preservatives, gene expression analysis was performed by PCR to determine differences between preservative containing and preservative free treatments. Differences in gene expression were shown at different time-points after treatment. Differences were also shown between treatments which were preservative free and those treatments which contained preservative. With the significant differences in gene expression levels between prostaglandins containing preservatives and those without preservatives, it indicates that prostaglandins without preservatives are likely to produce less side effects in glaucoma patients., For the majority of its history the field of ancient population genetics was restricted to non-human samples due to the difficulties with modern contamination and the nature of ancient DNA (aDNA) sequences: short, highly degraded, chemically modified and present in low concentrations with high concentrations of microbial contamination. The development of efficient extraction techniques, the discovery that the petrous part of the temporal bone is a rich reservoir for aDNA and the development of high-throughput next-generation sequencing (NGS), have resulted in the rapid expansion of the field, with sequences from over 1000 ancient individuals published to date. Portugal occupies a unique position in Europe; facing both the Atlantic and the Mediterranean it was connected to two major maritime trade and migration routes, as well as experiencing influx from central mainland Europe throughout its prehistory. Many open questions remain about population changes in the Iberian Peninsula at major transition periods in European prehistory, such as the transition to the Bronze Age involving migrations from the Pontic Steppe, the source for the R1b Y-chromosome haplotype now dominant in European populations. In this study we present high quality whole genome sequences (0.052.9X, 13 samples at ~1X) from 25 ancient Portuguese individuals, covering a period of over 3000 years, to examine the demographic and selection processes acting on prehistoric Portuguese populations. We use principal component analysis (PCA), outgroup f3 statistics, Patterson’s D-statistic and ADMIXTURE analysis to investigate questions such as hunter-gatherer admixture in the Neolithic and Steppe introgression in the Bronze Age., Background: Epilepsy is a neurological condition affecting an estimated 50 million people worldwide and roughly 40,000 people in Ireland. Levetiracetam (LEV) is an effective anti-epileptic drug, but 10-20% of patients exposed to LEV report behavioural side-effects and up to 1% of those treated experience acute psychosis. We set out to determine contribution of common genetic variation to these adverse drug responses (ADRs). Methods: Individuals from the EpiPGX study cohort were screened for European ancestry and matched to predefined phenotypic criteria. Controls were exposed to LEV, but without any adverse reactions. GWAS were carried out on patients who experienced behavioural disorders (n=149), acute psychosis (n=19), or any affective symptoms in response to LEV treatment (n=90). After identification of a genome-wide significant hit in the affective disorder analysis, a further GWAS was performed in a replication cohort (n=68). Following this, polygenic risk scores (PRS) for all cases and controls were calculated using the results from the Psychiatric Genomics Consortium’s GWASes of Schizophrenia (SCZ) and Bipolar Disorder (BIP). Results: A genome-wide significant result was found in SNP rs7500119 in the CALB2 gene. Upon replication the SNP lost genome-wide significance but maintained nominal significance. PRS analysis for both SCZ and BIP were predictive of LEV-induced psychosis. Discussion: The univariate analysis did not identify a genome-wide significant signal for neurological ADRs to LEV that survived replication in an independent cohort. Further work with larger sample sizes may identify such variants. Increased PRS for SCZ and BIP are associated with LEV-induced psychosis, this analysis will also benefit from a larger sample, The impact of natural selection on beneficial alleles can be observed in modern human genetic variation; however deciphering the origins of these alleles is complicated by the vast complexity of human history, in which many population splits and admixture events have occurred. Here we describe a new statistical framework of Approximate Bayesian Computation (ABC) that can detect which ancestral group an allele undergoing selection first appeared. We assume a specific model in which a source population splits into two groups that later undergo admixture to form the lineage leading to the contemporary population and simulate the origin of beneficial alleles at different stages of the population’s history. Using genetic variation observed at the allele at the present time, as well as the knowledge we have of the timing of demographic changes and admixture events, we test if our approach can accurately predict the time the allele arose, and in which ancestral population it first emerged in. In this presentation, we will show preliminary results from our simulation study and discuss a potential application of the method for whole-genome data from an admixed human population., There are over 12000 people in Northern Ireland living with rheumatoid arthritis (RA); a painful, systemic autoimmune disease, causing swelling, stiffness, loss-of-function in joints, disability and significantly lowering ones quality of life. Various medication options are available; low-dose (10 to 25 mg/wk.) methotrexate (MTX), a small-molecule disease-modifying anti-rheumatic drug (DMARD), is a first-line therapy, due to its affordability, cost-effectiveness and efficacy. Other DMARDs used in RA are sulfasalazine, chloroquine, hydroxychloroquine, azathioprine, and leflunomide. However, there is significant person-to-person variability in treatment responses with nearly 50% of patients indicating poor or no-response to any of these medications. Serum drug metabolite concentration of 100 RA patients treated with DMARDs were determined using tandem mass-spectrometry. Allelic discrimination analysis using Taqman probes was performed on the following SNPs; rs246240 (ABCC1), rs1476413 (MTHFR), rs2231142 (ABCG2), rs3740065 (ABCC2), rs4149081 (SLCO1B1), rs4846051 (MTHFR), rs10280623 (ABCB1), rs16853826 (ATIC), rs17421511 (MTHFR) and rs717620 (ABCC2). Demographic analysis, clinical parameters and disease scores (e.g. DAS28) were also recorded. These SNPs are located within the genes involved in the metabolism of DMARDS and anecdotal evidence has been reported in the literature of their participation in modulating normal metabolism and function of DMARDs. Correlation statistics was used to determine if the genetic profiles associate with the emergence of drug metabolites responsible for poor or non-response to DMARDs. Our findings suggest that genetic-profiling studies may help predict future treatment responses of patients to certain DMARDs. A stratified medicine strategy can help prioritise treatments to those patients most likely to respond while avoiding ineffective treatments. Abbreviations: single nucleotide polymorphisms (SNP); rheumatoid arthritis (RA), disease-modifying anti-rheumatic drug (DMARD), methotrexate (MTX), Rare mutations in genes that encode centrosomal or ciliary proteins cause disorders that present with severe cognitive deficits and variable neuropsychiatric phenotypes. We set out to explore the involvement of centrosomal/ciliary genes in schizophrenia, a neuropsychiatric disorder that affects 1% of adults and is a major global health issue. Our analysis of publicly-available genome-wide association study (GWAS) data revealed that seven schizophrenia risk genes encode proteins with centrosomal functions. Of these, SDCCAG8 is also associated with educational attainment. To analyse the molecular function of SDCCAG8, we used genome editing to ablate it in SHSY5Y neuronal and hTERT-RPE1 retinal epithelial cells. Loss of SDCCAG8 impairs cells’ ability to make primary cilia and the signalling capacity of residual cilia, although centrosome structure appears normal by immunofluorescence microscopy. Recent RNA-Seq analysis on RPE1 SDCCAG8 deficient cells compared to wildtype cells revealed a large number of differentially expressed genes (DEGs; n=2,045) in the absence of SDCCAG8. Pathway analysis of DEGs revealed that there is enrichment in axonal guidance signalling (p=2.51-15). There were also significant enrichments for several pathways that are involved in the production and turnover of extracellular matrix (ECM). Previously, many components of the ECM have been shown to be perturbed in patients with schizophrenia. Using MAGMA gene-set analysis, we found that set of DEGs were enriched for genes associated with schizophrenia (p=0.03) and cognitive ability (p=0.03). This study shows that a combination of gene editing and genomic analyses can help uncover the processes that implicate centrosome/ciliary genes in neurodevelopmental phenotypes., Scotland and Ireland are separated in places by less than 20 kilometres of sea. They share the Gaelic language and similar frequencies of particular alleles and phenotypes, hinting at shared ancestry. The population structure within England and Ireland have recently been described. However, the extent of structure within the majority of Scotland, its surrounding islands, and their links to Ireland are currently unknown. We present an analysis of the British Isles and Ireland using a combined and comprehensive sample (n=2,556) of all major regions – expanding coverage in mainland Scotland (n=567), the Hebrides (n=57), the Isle of Man (n=40), Orkney (n=111) and Shetland (n=172). By analysing individuals with extended ancestry from specific regions, we demonstrate extensive structure in all regions of the British Isles and Ireland, as well as some of the finest scale structure observed worldwide within Orkney. We resolve the shared genetic history between Ireland and Mainland Scotland, confirm the strongest differentiation of Orkney and Shetland from other populations, show the major differentiation in Mainland Scotland is between the south-west and the north-east, and reveal the distinctiveness of the Hebrides and the Isle of Man. We additionally show decreasing cline of Norwegian ancestries across northern Britain, following the spread of the Norse Vikings. Our work represents a comprehensive description of genetic structure in the British Isles and Ireland and greatly expands the knowledge of genetic stratification within the north of the British Isles, informing on the study of rare genetic variants and genetic trait associations in these populations., The Savage et al. (in press) GWAS meta-analysis of intelligence of healthy controls supports increasing findings on variability in intelligence and evidence of overlap with schizophrenia. Utilising convenience sample of pre-existing Irish dataset of broad psychosis cases (916 cases and 330 controls), wherein the controls participated in the Savage et al. (in press) meta-analysis, the present study functioned as secondary analysis of said meta-analysis findings regarding the broad psychosis cases. With the five most significant single nucleotide polymorphisms (SNPs) as identified by Savage et al. (in press) and patient diagnosis as independent variables, this statistical regression analysis focused on the extent to which these genetic variances were of importance in a clinical population by examining the effects in schizophrenia of previously identified genetic variation associated with intelligence (IQ) in healthy controls. Further objective was to extend the Savage et al. (in press) findings to investigate the effects in schizophrenia of genetic variation on memory (working memory and episodic memory). As hypothesized the present study observed nominal trend association for SNP rs2726491 with decreased errors in performance IQ, and a nominally significant association with decreased errors in working memory for rs2726491 across both healthy and clinical population samples. These nominal associations would be suggestive of stronger effects in psychosis, however, the present study was underpowered to observe an association at the corrected level. Nevertheless, future research building on these suggestive findings could further our understanding of the biological psychopathology of schizophrenia, and crucially bring about improved cognitive function in schizophrenia patients., We present a model, algorithm, and results for multiway admixture events. This is where two or more genetically differentiated groups come together. Data from such events can inform us of the demographic history of a species, carry signatures of natural selection, and may increase the power of genome wide association studies. Our model is based on Li and Stephens style haplotype copying and delivers accurate local ancestry estimation along the genome for each admixed individual. Unlike existing methods that return local ancestry, we do not assume knowledge of the relationship between sub-groups of donor reference haplotypes and the unseen mixing ancestral populations. Instead, our approach infers these in terms of conditional copying probabilities. We also infer admixing proportions, timings, and recombination rates. Furthermore, we can estimate drift between modern reference populations and the unseen mixing groups using a version of Fst that is computed on putative partial genomes derived by assignment of chromosome segments to ancestral backgrounds. We demonstrate compelling results using the Human Genome Diversity Panel, including replication of some known admixture events, and we detail novel findings such as a recent 4-way admixture in San-Khomani individuals. Keywords: Population Genetics, admixture, demography, local ancestry estimation., Sibling transplant pairs have better transplant outcomes than unrelated donor-recipient (DR) pairs suggesting shared genetic ancestry between donors and recipients has potential for predicting transplant outcome. We set out to evaluate methods to detect and quantify shared ancestry using GWAS data, to see which could best predict renal-transplant outcome. We tested three different methods for estimating shared genetic ancestry on deceased donor DR pairs of European ancestry. Method 1 calculated identity by descent (IBD) which was then used to estimate the degree of relationship. Method 2 calculated genetic distance using identity by state which examines the number of shared alleles across the genome. Method 3 created a mosaic of an individual’s genome from the haplotypes of the other individuals in the dataset. The similarity of mosaic genomes in a given DR pair was used as a measure of shared ancestry. These measures were then tested against estimated glomerular filtration rate (eGFR) at 1 year (DR pairs, n=1,450) and 5 years (DR pairs, n=1,309) post-kidney transplant, change in eGFR between 1 and 5 years (Δ eGFR; DR pairs, n=982) and time to graft failure (DR pairs, n = 1,806). We did not find significant correlations between any of the measures of shared ancestry in the European ancestry deceased-donor DR pairs and graft function. The genetic relationship between the vast majority of our donor-recipient pairs was distant, and not detectable via IBD. The effect size of shared ancestry at the genomic level on eGFR is limited, and not detectable in our analysis., Background: The treatment of comorbidities remains costly and represents a major priority in Evidence Based Medicine (EBM). Determining genetically the molecular-subclasses of pro-inflammatory comorbid conditions is important to stratify patients that may more effectively respond to specific treatment interventions. The objective of this study is to develop a Machine Learning (ML) based classifier to stratify patients with Type-2-Diabetes and different comorbidities. Methods: A preliminary dataset of samples from 254 people with Type-2-Diabetes recruited at NICSM were genotyped with an Affymetrix UKBioBank Axiom Array. SNP results for 80 patient samples of class DCM1 (i.e. Type-2 Diabetes associated with comorbidities of circulatory system) and 90 patient samples of class DCM2 (i.e. Type-2-Diabetes associated with comorbidities of digestive system) were filtered through feature selection using ANOVA, Chi-square and Fast Correlation Based Filter. The top-10 SNPs along with information from Electronic Care Records (ECR), were selected for building 5 ML binary classifiers, using Support Vector Machine, Random Forest, Artificial Neural Network, Decision Tree and Naive Bayes algorithms, and their performances were tested with a 10-fold cross validation. Results: Of the 5 classifiers, the Naive Bayes algorithm outperformed all others with an Area under the Curve score of 0.681, overall Classification Accuracy of 65.68% and Mathews Correlation Coefficient of 0.316. Conclusion: Further improvement in the performance of our ML classifier is currently in-progress. With the inclusion of further data from ECR, as well as data from public repositories, we hope to build a better classifier., This project aims to investigate the relationship between folate status and the accumulation of mutations within the human mitochondrial genome. Folate is an essential B vitamin that is required for DNA synthesis, methylation reactions and is a major contributor to NADPH production through the folate one-carbon metabolism (FOCM) pathway. As a diet with a suboptimal level of folate can impact on DNA precursor availability, there is a strong biological plausibility that this will cause an increased occurrence of mutations within a cell’s genome due to errors in DNA replication. Mitochondrial dysfunction has been linked to many age-related conditions such as cardiac myopathies, neurological disorders and muscular wastage. The accumulation of mutations within the mitochondria over one’s lifetime may increase the level of mitochondrial dysfunction thus increasing the likelihood of developing such diseases. This project will look at the potential relationship between folate-status and the frequency of mutations occurring within the mitochondrial genome using a combination of both cell line and animal models plus a human cohort with known folate status and age ranges., Common variants associated with schizophrenia are enriched among highly constrained (HC) genes. As schizophrenia and cognition are genetically correlated, we hypothesized that genes associated with cognitive function are enriched for HC genes. Using MAGMA to perform gene set analysis of the largest available GWAS datasets, we found that HC genes (n=3,230 (loss-of-function intolerant)) are strongly enriched for genes associated with educational attainment(EA; p=1.27E-09) and cognitive ability(CA; p=5.64E-09) in comparison to genes under lesser or weak constraint (p>0.05 for both EA and CA). This signal remained significant following conditional analysis to co-vary for ‘brain-expressed’ (n=14,243) and ‘brain-specific’ (n=1,424) gene-sets. In schizophrenia, evidence shows that common variants are likely to persist in the population due to background selection (BGS) mechanisms. BGS refers to the phenomenon by which selection against deleterious variants reduces genetic diversity, impairing the overall efficiency of selection and allowing alleles with small effects to rise in frequency by drift. We ran a stratified linkage disequilibrium score regression (LDSR) analysis to test for heritability enrichment in EA and CA for SNPs within genomic regions that are under various types of selection. The heritability of EA and CA is enriched for SNPs in regions under background selection(p=0.028 for EA and p=0.002 for CA) and depleted for SNPs in regions under positive selection. Recent studies suggest that natural selection is acting against phenotypes such as EA or CA. This study suggests a mechanism by which variants contributing to these phenotypes are not removed by negative selection and are maintained in the population., Mutations in the photoreceptor-specific tubby-like protein 1 (TULP1) are associated with recessive retinitis pigmentosa 14 and Leber congenital amaurosis 15; severe, early-onset forms of retinal degeneration. We have explored an adeno-associated virus (AAV)-mediated gene replacement therapy in a murine model carrying a targeted disruption of the Tulp1 gene (Tulp1 -/- mice). The human TULP1 cDNA driven by the chicken beta-actin promoter (CBA) promoter was generated in an AAV serotype 5 (AAV-CBAP-TULP1). 1x10e11 vg of AAV-CBAP-TULP1 (+1:600 of an AAV-EGFP vector for tracing) was delivered to TULP1-/- mice at postnatal day 2 via sub retinal injection. Immunoblotting and qPCR demonstrated that the replacement TULP1 protein had the correct molecular weight and that the level of expression of protein achieved was ~55 % (n=8; p, Background: Diabetic kidney disease (DKD) is the most frequent cause of end stage renal disease. There is a need for improved biomarkers for the early detection of DKD. MicroRNAs (miRNAs) are short, non-coding regulatory RNA molecules commonly found in urinary exosomes that may be differentially expressed during renal dysfunction. Therefore, we profiled urinary exosomal miRNA expression in type 2 DKD (T2DKD). Methods: Qiagen Human Urine Exosome Focus miRNA Panel was used to profile 87 miRNAs in a discovery cohort of 14 T2DKD and 15 age and gender matched type 2 diabetic patients with normal renal function (T2NC). Differentially expressed miRNAs were validated in a second cohort of 22 T2DKD, 18 non-diabetic patients with poor renal function (CKD), and 22 T2NC. Results: Three urinary miRNAs (miR-21-5p, let-7e-5p and miR-23b-3p) were significantly upregulated (P, Werner syndrome (WS) is a rare genetic disorder due to mutations in the WRN or LMNA genes, with an estimated global incidence of 1 in 1,000,000 - 10,000,000. It is a segmental progeroid disorder characterised by an array of clinical features consistent with accelerated aging. We report the case of a 28 year old female patient, the offspring of a consanguineous union, who was referred to our metabolic clinic for review. She reported a history of vocal cord paralysis aged 19 years and subcapsular cataracts aged 24 years. Moreover, she had been diagnosed with primary hypothyroidism, primary hyperparathyroidism and subfertility despite normal menstruation. Further diagnoses included NAFLD with mild fibrosis. On examination, she had skin atrophy, hyperkeratosis, a loud S2, scalp alopecia, axillary acanthosis nigricans, and marked visceral adiposity with lipodsytrophic upper and lower limbs. Echocardiography confirmed trace regurgitation in aortic, mitral and tricuspid valves and DEXA confirmed osteoporosis. HOMA score was > 11 confirming severe insulin resistance and AMH levels were low. Phenotypically the patient had a diagnosis of definite WS but genetic confirmation was sought. Analysis of LMNA did not identify pathogenic variants. An RT-PCR method with direct sequencing was developed in-house to examine the extensive coding region of WRN. This revealed a homozygous genotype for the nonsense variant g.129, 248C>T, c.3961C>T, p.Arg132Ter. To our knowledge this is the first reported case of WS in the Republic of Ireland. In cases with multiple early-onset morbidities a genetic basis should be considered, particularly if there is a risk of consanguinity., Hyperlucent zones within areas of pulmonary consolidations may represent cavitatory lung lesions on CT imaging, from multi-factorial causes such as TB, pulmonary infarction, pyogenic lung abscess, pneumocystis pneumonia, Klebsiella pneumonia and less frequently due to necrotic processes from fungi. We were presented with this clinical conundrum in a patient against a background of refractory asthma, chronic cough, worsening dyspnoea, poor spirometry results and becoming progressively unwell. Due to a strong history of cancer in the family, EBUS-TBNA was carried out to obtain lung-biopsy samples. Laboratory histological analysis and ROSE revealed hyphae and fungal spores within the tissue samples biopsied, no malignant cells were recovered from the lymph node biopsy samples in all stations. We initiated anti-fungal treatment; itraconazole, 200mg once daily for 2 days after which the patient began to show signs of improvement. Seven family members with prior history of fungal-lung disease had developed lung-cancer later in life, and anecdotal prior research had shown that a premature stop-codon mutation at the tyrosine-238 residue of the dectin-1 gene in a Dutch family had predisposed patients to risks of contracting fungal-lung disease and subsequently developing lung-cancers in the long-term. We carried out Sanger-sequencing of all the exons of the dectin-1 gene as well as whole-exome sequencing on the HiSeq (Illumina) platform to identify candidate markers that may explain the heritability in this Kent family of Irish descent. We highlight the results of this study in this presentation. Abbreviations: endo-bronchial ultra-sound transbroncial-needle-aspiration; EBUS-TBNA, Rapid-OnSite-Examination; ROSE, tuberculosis; TB, Lynch syndrome (LS) (previously Hereditary Non-Polyposis Colorectal Cancer syndrome) is a cancer predisposition syndrome conferring variable risks of endometrial, colorectal, upper gastrointestinal, urinary and biliary tract cancers. Lynch syndrome is a dominantly inherited trait, caused by pathogenic germline variants in one of the mismatch repair (MMR) genes MLH1, MSH2, MSH6, or PMS2; and more rarely by deletions in EPCAM causing hypermethylation of the MSH2promoter. A recent report suggested that germline variants in MSH6 or PMS2 are associated with an increased incidence of breast cancer. Other data with respect to this association is conflicting, and prospective studies have not shown evidence for this association. Here, we report a case of a 37-year old female patient with multifocal breast cancer demonstrating defective MMR, associated with a germline variant in MSH2. This prompted us to undertake a respective cohort study to assess the prevalence of breast cancer in patients with Lynch syndrome managed in our centre. We report on 60 consecutive patients (including the case described here above) tested and found to carry germline pathogenic/likely pathogenic variants in MMR genes were identified from a prospectively maintained departmental database. Pedigrees from these patients were analysed, and number of breast cancers in probands and first and second degree relatives were recorded. Age at diagnosis, phenotypic data and genotype were noted., Amyotrophic lateral sclerosis (ALS), usually23 known as a motor neuron disease, is a fatal neurodegenerative disorder which causes death of neurons controlling voluntary muscles. ALS has no cure, and its underlying cause is mostly unknown, although a strong genetic component is known to play a role. The gene ATXN2 normally has a repeat structure of around 22-23 triplets encoding for glutamine (CAG) within the reading frame of the gene encoding the ataxin two protein. Studies have shown that harbouring more than 40 repeats causes spinocerebellar ataxia type 2 (SCA2). Recently, it was discovered that intermediate-length repeat expansions (27-33 repeats) in ATXN2 are significantly associated with the risk of ALS. The aim of this study is to genotype the ATXN2 gene in a cohort of controls and patients from the Irish ALS bank in order to assess the association between this genotype and ALS. The most common alleles in this cohort were 22, 23, and 27 repeats, at frequencies (cases and control combined) of 87.0%, 8.3% and 1.9%. Trinucleotide repeat counts ≥27, ≥29 and ≥30 for the larger allele were significantly associated with ALS (p < 3.6×10-3, corresponding to α = 0.05) and the odds ratio for ALS in the established ALS risk range was 1.90 (95% CI 1.03-3.51). This study further exemplifies the correlation between this gene and ALS in the Irish population, contributing to the research of causative genes for this devastating disease. Currently, our research is assessing the length of repeat expansions in other ataxia-associated genes, including ATXN1., Introduction: Huntington’s disease (HD) is a progressive, incurable, autosomal dominant, neurodegenerative disease. Genetic testing for HD has been available in the Department of Clinical Genetics since 1995. This clinic employs the gold-standard multistep approach to genetic testing, involving pre-test counselling, two blood draws and psychiatric review, allowing patients time to consider the consequences of testing and to withdraw at any time. Aims: To establish the uptake of predictive testing among first-degree relatives of patients diagnosed with HD. Methods: Families with at least one relative referred for genetic counselling between 2014 and 2016 were identified from a prospectively maintained departmental database. Familial pedigrees were analysed to identify at-risk relatives. Data was collected by retrospective chart review regarding number of first-degree relatives of the family proband attending clinical genetics for predictive testing, number who completed testing, diagnostic yield and patient demographics. Results: 241 asymptomatic adult first-degree relatives of the proband in 35 families were identified. 125 of these were children of the proband and 106 were siblings. 41 (17.4%) self-referred for predictive testing and 26 (10.8%) completed testing (9 positive; 17 negative). The median age for those seeking genetic testing was 36y (23-69). Patients completing testing were younger than those withdrawing from process (median 35 (23-55)-vs-40 (33-69y)). Conclusion: Uptake of genetic testing among relatives of patients affected by HD is currently low, in-keeping with rates reported in international literature. However, this may change in time with increasing advent of therapy. Decision-making in an incurable disorder is complex and may explain this low figure., Introduction: Over recent decades the life expectancy of those with Down Syndrome (DS) has increased dramatically. Much of this improvement can been attributed to early intervention, and the research which supports these interventions. Despite medical advancements, individuals with DS still have a greater mortality and morbidity compared with individuals from the general population and those with other forms of intellectual disability. Demonstrably there is a need for ongoing research to improve the quality and duration of life for those with DS. In modern academia there have been significant developments in the prenatal diagnosis of DS (e.g. Non-Invasive Prenatal Testing). Some of these developments have been met with controversy from members the DS community. Methods: A structured PubMed search was performed utilising comprehensive terms to identify publications focusing on DS, childhood and the prenatal period. This was compared to the total number of publications available on PubMed per year (1990-2017). Results: Since 1990, there are has been a general increase in the number of publications focusing on DS. However, the proportion of publications focusing on DS, compared to total PubMed publications, has decreased. Among those publications focusing on DS there has been a decline in the proportion of studies focusing on childhood and a proportionate increase in those focusing on the prenatal period. Conclusion: The results of this preliminary review of the literature suggest a general decline in the proportion of academic publications focusing on DS and a shift in focus away from childhood and towards prenatal studies, Introduction: Interstitial deletions of 12q are rare with around 6 cases including 12q21 deletions described in the literature. We identified a male infant with 12q21.1-q21.33 deletion with phenotypic features including wide sandal gap and longitudinal plantar creases, short upturned nose, low set ears, feeding difficulties and delayed development. Methods: Array-CGH using the Agilent (ISCA*v2) 8x60K oligo array (genome assembly Build GRCh37) was undertaken on a chorionic villus sample at 13 weeks gestation due to raised nuchal translucency, and confirmed on venous blood after birth. A comparison of a-CGH microarray profiles was undertaken on the existing described cases. Results: Array-CGH confirmed a ~16Mb deletion containing nine OMIMMorbid genes ALX1 (OMIM *601527), BBS10 (OMIM *610148), CEP290 (OMIM *610142), DUSP6 (OMIM *602748), KITLG (OMIM *184745), MYF6 (OMIM *159991), OTOGL (OMIM *614925), PTPRQ (OMIM *603317) and TMTC3 (OMIM *617218). Using overlapping features of different 12q21 cases allowed microarray profiles to confirm a common deletion region including a non-morbid gene LIN7A. Its role encodes a scaffold protein within the CASK pathway which is important in synaptic function and is a possible responsible gene for the intellectual disability and cortical development present in all described cases. Parental a-CGH was normal confirming our case is de-novo. Conclusion: We delineate a 12q21 deletion syndrome with characteristic phenotypic features. LIN7A is a consistent deleted gene in this region and may be responsible for the intellectual disability due to cortical maldevelopment in this syndrome., Trisomy 18 (T18) is a relatively common chromosomal disorder with a prenatal prevalence of ~1/2,500. Features associated with T18 include congenital heart defects (CHD), microcephaly, overriding fingers and rocker bottom feet. Radial ray anomalies (RRA) occur in ~ 1/10,000 pregnancies. RRA are associated with prenatal teratogen exposure, abnormal glycaemic control in pregnant women and syndromic disorders. To date there are few reported cases of T18 and bilateral RRA in the literature. We describe two cases of T18 with bilateral RRA: Case A: Male infant who passed shortly after delivery at 31 weeks gestation to 37 year old mother with a history of Crohn’s disease. PM identified CHD, significant growth restriction, overlapping fingers, bilateral talipes equinovarus and bi-lateral absent radii and thumbs. Case B: Male infant born at 16+4 weeks gestation to a 44 year old mother. PM examination identified significant growth restriction, an omphalocele, absent left radius, dysplastic right radius and absent thumbs, among other anomalies. For Case A and B karyotype and FISH analysis performed at post mortem confirmed T18. In both cases the diagnosis of T18 was not made antenatally. Here we discuss the importance of antenatal assessment which combines the use of ultrasound, clinical, genetic, cytogenetic and molecular testing in order to obtain the correct diagnosis from a wide spectrum of differentials. Foetal karyotype analysis should be considered in cases of RRA, especially if other malformations are detected. Cases with bilateral lesions have a significantly higher association with aneuploidy, in particular T18., Background: Clinical Genetics services provide a diagnostic, counselling and genetic testing service for children and adults affected by, or at risk of, a genetic condition, most of which are rare, or genetically heterogeneous. Appropriate triage of referrals is crucial to ensure the most urgent referrals are seen as quickly as possible, without negatively impacting the waiting times of less urgent cases. Aim: To examine triage practice in 6 Clinical Genetic centres across the UK and Ireland. Method: Thirteen simulated referrals were drafted based on common referrals to Clinical Genetics. Copies of each referral were forwarded to each centre, where 10 nominated clinicians were asked to triage each referral. Triaged referrals were returned to the coordinating author for analysis. An electronic questionnaire was contemporaneously completed by clinical leads in each unit to gather local demographic details and local operating procedures relevant to triage. Results: Widespread inconsistencies were noted both within and between units, with respect to acceptance of referrals to services, prioritisation, and designated clinic type. Referral rates, staffing levels, and waiting lists varied widely between units. Conclusion: Inconsistencies observed between units are likely influenced by a number of factors including; staffing levels, referral rates, and average family size. Inconsistency within units likely reflects the complex nature of many Clinical Genetic referrals and triage guidelines should help improve decision making in this setting., Ireland’s breast cancer(BC) incidence is 122.6/100,000. 3% of BCs are attributed to variants in BRCA1/BRCA2. Knowledge of pathogenic variants drastically changes the risk management of patients. Variants in other genes(CHEK2, ATM) confer moderate-risk; up to 50% of inherited BC risk is unexplained. Analysing multiple genes in a cost-effective manner is possible through next-generation sequencing(NGS). We aimed to identify variants contributing to Irish BC susceptibility using NGS. A custom gene-panel was designed; genes were primarily selected from clinical panels (BC, BC and ovarian cancer, broad cancer) and candidate genes identified through GWAS. Captured libraries from 90 BCs and 77 controls were sequenced using Illumina’s NextSeq. Variant calling was performed following GATK best practices. Following variant annotation (VEP, ANNOVAR, SnpEff), loss-of-function(LOF) and missense variants were analysed. Missense deleteriousness prediction scores were obtained from five sources. Clinvar reports were considered. Frequencies were obtained from ExAC/gnomAD. LOF variants were identified in BCs/controls in known BC risk genes BRCA1, ATM, CHEK2, and MSH6(candidate risk gene). A splice-region LOF variant in PBRM1 was identified (4 BCs:1 control). 22 novel LOF variants were identified. Deleteriousness prediction tools unanimously scored 40 missense variants “damaging”; three in BRCA1, BRCA2, ATM had opposing Clinvar reports. Rare missense variants were identified in FANCD2, SFN, ARID1B. Novel missense variants were identified in genes appearing on clinical panels(XPC, FANCA) and reported in GWAS(PTGS2, NOTH2, CYP1B1). These results demonstrate the challenges of accurately predicting variant pathogenicity, and highlights the need for caution when considering the use of broad panel testing on an unselected population., Background: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with a population frequency of ~1 in 88, frequently co-occurring with other psychiatric disorders. While it is accepted that ASD is a highly heritable disorder (h2 >0.8), much of the effect of genetic variation on autism remains unclear. A major search is currently underway to seek out the variation underpinning this disorder. Methods and Results: A family was enrolled comprised of unaffected parents and 4 ASD-affected offspring. DNA was extracted from saliva samples using Perkin Elmer Prepito D cyto kit. All six samples were sequenced using SOPHiA GENETICS Whole Exome Panel covering 26,000 genes, run on HiSeq 4000 (2x250). QC was performed as standard. Data analysis was carried out using SOPHiA DDM. The identification and annotation of variants implicated in ASD will be reported. Discussion: This study will contribute to the autism genomics field with the most up to date technology in a clinically relevant family based study. The genes identified will add to those already associated with ASD, giving a deeper understanding of the genomics of the disorder. In turn, this genomic understanding will bring a clearer picture of the mechanism of disease, both on an individual level and on a global level. This gives the opportunity to develop personalised therapies and management strategies, improving patient outcomes. Genomics is certain to play a crucial role in the diagnosis and intervention of ASD in the future., Background: Little is known of the true epidemiological burden or character of mitochondrial disease in Ireland. Yet such information is important for provision/planning of evidence-based health policies/future services. Aim of study: 1) to characterise the cohort of patients with mitochondrial disease attending the National Centre for Inherited Metabolic Disease(NCIMD)/Adult Metabolic Service in reference to phenotype (clinical and biochemical), genotype, treatments/management and outcomes. Methods: A retrospective study was conducted on all patients attending the NCIMD/Adult Metabolic Service with a diagnosis of mitochondrial disease. Results: Fifty five patients (33/55 (60%) male and 22/55 (40%) female) have a mitochondrial disease diagnosis. Pathogenic variants were identified in 39/55 (71%), testing pending in 5/55 (9%) and no pathogenic variants were identified in 11/55 (20%). 31/55 (57%) patients have MELAS; 2/55 (4%) have Kearns-Sayre syndrome and 1/55 (2%) have leber hereditary optic neuropathy or pyruvate dehydrogenase deficiency (PDD) deficiency or neuropathy, ataxia and retinitis pigmentosa. 19/55 patients (34%) have another mitochondrial disorder with only 9/19 (47%) having a confirmed genetic diagnosis. Conclusions: MELAS, due to m.3243A>G, is the most common mitochondrial disorder which is in keeping with international studies. 30% of patients have a mitochondrial diagnosis due an abnormal biochemistry. Mitochondrial disease criteria (Wolf NI et al., 2002) will be applied to identify those for further genetic testing. Low numbers of patients suggest there is a large cohort of mitochondrial patients not yet captured by this clinic. The study will be expanded to calculate the prevalence of adult mitochondrial disease in the Irish population., Abnormal methylation affecting allele-specific expression of the H19, IGF2, KCNQ1 and CDKN1C genes at the 11p15.5 locus are variably associated with congenital disorders of growth including Beckwith Weidemann syndrome (BWS), Silver Russell syndrome (SRS), and isolated lateralizing overgrowth. Methylation defects causing isolated hemi-hypertrophy commonly overlap with those causing BWS. At the 11p15.5 locus, hypomethylation of the H19 DMR (differentially methylated region) (IC1) on the paternal allele, or hypermethylation of the KCNQ1OT1: TSS – DMR (IC2) on the maternal allele are mechanisms underlying SRS. We present atypical cases related to SRS methylation abnormalities at the 11p15.5 locus. Patient 1 is a 2y-old girl with leg-length discrepancy, and asymmetric facies. Relatively small at birth (5lb 4oz), post-natal growth velocity was normal. Patient 2 is a 16y-old boy measuring over 6ft with isolated hemi-hypertrophy. In both cases, hypomethylation at H19 was reported. Patient 3 is a 2y-old boy with history of IUGR, speech delay and short stature. Investigations identified a maternally inherited duplication of KCNQ1OT1: TSS – DMR. His mother inherited the same duplication from her mother, and was mildly affected, with final adult height of 4’ 11”, without growth hormone treatment, and no issues with development or feeding. The Netchine-Harbison Clinical Scoring system outlines diagnostic criteria for SRS, including pre- and post-natal growth restriction, feeding issues, and characteristic facies. None of these cases would fulfil these criteria and yet have molecular defects consistent with SRS. A low threshold for investigation of methylation abnormalities should be adopted in cases of short stature or isolated hemi-hypertrophy., SHOX deficiency is characterised by a clinical spectrum from idiopathic short stature to Leri Weill dyschondroestosis with triad of disproportionate short stature, Madelung deformity and mesomelia. Heterozygous mutations or deletions of the SHOX gene located in terminal Pseudo-Autosomal pairing region (PAR1) of either Yp11.2 or Xp22.33, cause this condition in both sexes. This disorder behaves as an autosomal dominant disorder, (rather than X linked) due to its location within the pseudo-autosomal region. Case: The proband was seen by clinical geneticist due to a co-incidental paternally inherited chromosome deletion in her son. The proband was noted to be short (143cm, 7cm below 3rd centile) and has shortened and bowed forearms. Analysis by aCGH showed an atypical Xp chromosome deletion of 881kb that included the SHOX gene. (Typical deletion involving SHOX is about 1.5Mb). In addition, she had gain of Yq11.221-q12 chromosomal material, which was inserted onto the distal region of Xp. She and her elder sister attended paediatric endocrinologist 25 years ago for their short stature. Her sister responded to growth hormone therapy, pre-treatment height (10cm below the 3rd centile) improved to above 3rd centile, height 10cm > than the proband who was not treated. Their parents heights were both, Malan syndrome, also known as Sotos 2 syndrome as it clinically resembles Sotos syndrome, is a recently described overgrowth syndrome. It is associated with deletions or mutations affecting the N terminal DNA binding site and dimerization domain (exons 2 and 3) in the Nuclear Factor I type X encoding gene (NFIX) on chromosome 19p13. Other mutations within the donor splice site of exon 6 of NFIX are known to cause the distinct clinical entity Marshall Smith syndrome. Typical clinical features are tall stature, macrocephaly, craniofacial features such as narrow and long face with high forehead, developmental delay, intellectual disability and behavioural abnormalities such as autistic traits and anxiety. Musculoskeletal abnormalities such as advanced bone age and scoliosis are also well described. Here we report a case of Malan syndrome with typical and atypical features, thus expanding the known phenotype, who was originally treated and referred as clinically suspected Marfan’s syndrome. She presented to the Department of Clinical Genetics at 13 years of age having been referred by her General Paediatrician. She was tall and slim, macrocephaly, with mild intellectual disability who showed a mildly dilated aortic root for which she was prescribed a beta-blocker. Subsequent to genetic and biochemical investigation, a pathogenic mutation was identified in the NFIX gene. This case emphasises the need to consider NFIX gene analysis in FBN1 negative Marfanoid appearing patients presenting with an atypical history and features such as intellectual disability, joints contractures, and dilated aortic root. Moreover, screening Malan syndrome patients for aortic root dilatation may help further understanding of the possible involvement in vasculature development of the NFIX gene function., Guidelines published by the Institute of cancer research (2013) and NICE (2017) recommend testing all women diagnosed with high grade serous ovarian carcinoma (HGSOC) for germline pathogenic variants in the BRCA1 and BRCA2 genes. It is predicted that using these guidelines that 10% of cases in this cohort harbour a pathogenic variant. We have carried out a retrospective study on 2years of data (April 2016-March 2018) from genetic screening of BRCA1 and BRCA2 genes on HGSOC patients. The aim of this audit was to establish the number and incidence of germline BRCA1 and BRCA2 pathogenic variants identified within this cohort in Northern Ireland and to explore the contributing factors to these results. During this period, 155 women with ovarian cancer were screened for germline mutations in the BRCA1 and BRCA2 genes by fluorescent sequence analysis of the coding sequence and associated splice sites and screening for whole exon deletion/duplication variants. The clinical details and family history of these patients were reviewed in light of existing screening guidelines and amendments to local testing protocols considered., The rapidly emerging field of Genomics promises improved diagnosis and personalised medicine at the front line of patient care. Genetic counsellors (GCs) bring essential skills and knowledge for delivering genomic information to patients and in education of healthcare professionals. In the Republic of Ireland there are 13 Genetic Counsellors (GC) working across different hospital sites with a variety of clinical roles. The majority have attained professional registration through the UK Genetic Counselling Registration Board (GCRB) or the European Board of Medical Genetics (EBMG) and/or an MSc in Genetic Counselling. The number of GCs falls significantly below recommendations for the Irish population as compared to other European countries. We are in the process of setting up a professional body called the Irish Association of Genetic Counsellors (IAGC) to represent the profession in Ireland. To achieve this two working groups have been established: Professional body: this working group has developed a constitution detailing membership, council roles and setting out the aims for the organisation - advocating for the profession, development of CPD opportunities and education of allied health professionals. Regulation: Given the significant implications associated with mishandling of genomic information this working group will aim to achieve consideration for the statutory regulation of the Genetic Counselling profession. Initial steps include direct approach to CORU - Ireland’s health and social care professional regulator. Our goal is to promote high standards of professional conduct, education, training and competency in the Genetic Counselling profession., Immunohistochemistry (IHC) performed on tumour tissue to detect loss of mis-match repair (MMR) protein expression is used to screen individuals at risk of Lynch Syndrome (HNPCC). Germline mutation analysis for HNPCC is guided by loss of expression of MMR proteins on IHC and it has been local practice to arrange MLH1 mutation analysis for isolated loss of MLH1/PMS2 protein expression for all cases without testing the tumour tissue for BRAF or promoter hypermethylation as recommended by NICE guidelines due to lack of access to BRAF/promoter hypermethylation testing locally. Presence of BRAF and/or presence of methylation of MLH1 promoter region suggest sporadic cancer and therefore molecular testing for HNPCC is not indicated in these cases. It is likely that sporadic bowel cancer is being tested for HNPCC based on IHC results alone as per existing practice. This audit would help us to quantify the issue and will help us in creating a testing pathway incorporating BRAF/ promoter hypermethylation testing for better diagnostic yield. This would avoid unnecessary genetic testing and would be a cost saving measure for the service helping us to utilize our resources efficiently, Mutations in the LMX1B gene cause nail-patella syndrome, a rare autosomal dominant disorder which is characterized by abnormalities of the nails, knees, elbows, and pelvis. The features of nail-patella syndrome vary in severity between affected individuals, even among members of the same family. Other areas of the body that can be affected in this condition are eyes (glaucoma) and kidneys where progressive disease can cause renal failure. The LMX1B gene provides instructions for producing a protein that binds to specific regions of DNA and regulates the activity of other genes. On the basis of this role, the LMX1B protein is called a transcription factor. The LMX1B protein appears to be particularly important during early embryonic development of the limbs, kidneys, and eyes. Mutations in the LMX1B gene lead to the production of an abnormally short, nonfunctional protein or affect the protein’s ability to bind to DNA. It is unclear how mutations in the LMX1B gene lead to the signs and symptoms of nail-patella syndrome. We describe a family with significant history of kidney failure and no systemic manifestations of nail-patella syndrome Molecular studies identified a pathogenic variant in one allele of LMX1B c.737G>A missense p.Arg246Gln predicted to result in an arginine to glutamine substitution at amino acid position 246. This variant has been described previously in multiple unrelated families who presented with autosomal dominant nephropathy without nail and patellar abnormalities, which suggest this variant mutation is phenotype specific. This case reports adds to a growing evidence of LMX1B-associated nephropathy without nail and skeletal manifestations seen in classical nail-patella syndrome., ICR guidelines recommended testing all women diagnosed with triple negative breast cancer (i.e. negative for the oestrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2)) under 50 years old should be offered genetic testing for BRCA 1 and 2 pathogenic mutations. It was predicted that testing in this population should identify pathogenic mutations in around 10% of this cohort. This retrospective study will analyse 2 years (April 2016 – March 2018) of BRCA 1 and 2 testing in women diagnosed with triple negative breast cancer under 50 years of age. The main aim would be to find out if BRCA 1 and 2 mutations are accurately represented for our population and to explore the contributing factors to these results. For example, establish true pathology of the triple negative referrals tested and the strength of the family history of cancer in these cases. The hope is to identify whether tighter departmental guidelines for testing and developing a testing criteria proforma for mainstreaming could be beneficial for better mutation pick up rate., Background: Polycystic kidney disease, the most common inherited renal disease, is characterized by renal cysts and progressive reduction in kidney function. Although it is well established that autosomal dominant (ADPKD) is primarily caused by mutations in PKD1 and PKD2, sequencing of PKD1 is difficult due to multiple pseudogenes. Further, there is considerable unexplained variance in the age-of-onset of PKD even within families. Aims: Firstly, to apply NGS technologies for the molecular diagnosis of ADPKD. Secondly, to identify, using genomic and clinical data, large PKD ‘super-families’ to facilitate investigation of genetic modifiers of age-of-onset. Methods: NGS sequencing was performed using a custom Roche NimbleGen SeqCap targeted panel on the Illumina platform. Bioinformatics was performed using a custom, in-house pipeline based on GATK best practices. Copy number variants were identified from NGS data. Whole exome sequencing was performed on selected families using Roche NimbleGen library preparation. Pathogenicity was assigned to variants using ACMG pathogenicity guidelines. Results: 73 ADPKD patients were sequenced and a molecular diagnosis was obtained in 63% (41/73) indicating that NGS technologies were successful for variant identification in difficult to sequence PKD1 regions. We identified five pairs of individuals recorded as unrelated who shared rare PKD1 variants and have inflated genomic relatedness (IBD) scores. Conclusions: NGS with specific capture methods is suitable for the sequencing of renal disease genes including PKD1. We identified one large ADPKD pedigree chart using genomic data for the generation of Irish ADPKD ‘super-families’. Sequencing of additional ADPKD patients (underway) will facilitate expansion of ‘super-families’ concept., Approximately 80% of breast cancers overexpress the estrogen receptor α (ERα) and depend on this key transcriptional regulator for growth. The discovery of novel mechanisms controlling ERα function represents major advances in our understanding of breast cancer progression and potentially offers new therapeutic opportunities. Here, we investigated the role of deubiquitinating enzymes (DUBs), which remove ubiquitin moieties from proteins, in regulating ERα in breast cancer. We performed an RNAi loss-of-function screen using a library of shRNA vectors targeting all 108 known or putative human DUB genes. Suppression of a number of DUBs repressed or enhanced the activity of an estrogen-response-element (ERE) luciferase reporter. Interestingly, suppression of the BRCA2-associated DUB, USP11, was found to downregulate ERα transcriptional activity. Subsequent validation using two individual siRNAs targeted to USP11 revealed a reduction in expression of endogenous ERα target genes in ZR-75-1 cells, as quantified using qRT-PCR. Estradiol (E2) stimulation enhanced USP11 expression in the cell nucleus, while proteomic analysis by mass spectrometry revealed a significant change to the proteome in USP11 knockdown cells in the presence of E2 only. Furthermore, USP11 expression was found to be upregulated in LCC1 breast cancer cells when compared to other cell lines. RNA-seq in LCC1 USP11 knockdown revealed a downregulation of several putative ERα target genes and many cell cycle-associated genes. To support the prognostic relevance of USP11, immunohistochemical staining of a breast cancer tissue microarray (103 ERα+ patients) was performed. Kaplan-Meier analysis of this cohort revealed a significant association between high USP11 expression and poor overall (p=0.030) and breast cancer-specific survival (p=0.041). These results suggest a role for USP11 in ERα transcriptional activity and identify USP11 as a potential therapeutic target in ERα+ breast cancer.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability of around 50%. DNA methylation patterns can serve as biomarkers of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study (EWAS) meta-analysis in 10,462 samples (7,344 ALS patients and 3,118 controls), representing the largest case-control study of DNA methylation for any disease to date. We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We show that DNA-methylation-based proxies for HDL-cholesterol, BMI, white blood cell (WBC) proportions and alcohol intake were independently associated with ALS. Integration of these results with our latest GWAS showed that cholesterol biosynthesis was causally related to ALS. Finally, we found that DNA methylation levels at several DMPs and blood cell proportion estimates derived from DNA methylation data, are associated with survival rate in patients, and could represent indicators of underlying disease processes.

Rupture of an intracranial aneurysm leads to subarachnoid hemorrhage, a severe type of stroke. To discover new risk loci and the genetic architecture of intracranial aneurysms, we performed a cross-ancestry, genome-wide association study in 10,754 cases and 306,882 controls of European and East Asian ancestry. We discovered 17 risk loci, 11 of which are new. We reveal a polygenic architecture and explain over half of the disease heritability. We show a high genetic correlation between ruptured and unruptured intracranial aneurysms. We also find a suggestive role for endothelial cells by using gene mapping and heritability enrichment. Drug-target enrichment shows pleiotropy between intracranial aneurysms and antiepileptic and sex hormone drugs, providing insights into intracranial aneurysm pathophysiology. Finally, genetic risks for smoking and high blood pressure, the two main clinical risk factors, play important roles in intracranial aneurysm risk, and drive most of the genetic correlation between intracranial aneurysms and other cerebrovascular traits.

Because hyper-excitability has been shown to be a shared pathophysiological mechanism, we used the latest and largest genome-wide studies in amyotrophic lateral sclerosis (n = 36,052) and epilepsy (n = 38,349) to determine genetic overlap between these conditions. First, we showed no significant genetic correlation, also when binned on minor allele frequency. Second, we confirmed the absence of polygenic overlap using genomic risk score analysis. Finally, we did not identify pleiotropic variants in meta-analyses of the 2 diseases. Our findings indicate that amyotrophic lateral sclerosis and epilepsy do not share common genetic risk, showing that hyper-excitability in both disorders has distinct origins. ispartof: NEUROBIOLOGY OF AGING vol:92 ispartof: location:United States status: published

Behcet’s disease (BD) is a complex, multifactorial rare disease, which is poorly understood. Genetic and environmental factors contribute to BD, but the process of diagnosis is challenging with inconsistent clinical manifestations. A recent survey of individuals living with rare disease(s) in Northern Ireland revealed ~50% of individuals receive ≥1 misdiagnosis with 1/20 seeing >10 doctors. Individuals with BD report a range of symptoms, which are variable in onset, severity, and frequency for this systemic vasculitis. Patients describe prolonged journeys to diagnosis with multiple healthcare professionals and medical specialties; there is no BD specialist in Northern Ireland. Using invitations via social media, voluntary groups, and direct contact we are using surveys incorporating micro-narratives, one-to-one semi-structured interviews, and focus groups to collect detailed family histories and stressor information to help characterise recurrent features in patients living with BD and their relatives in Northern Ireland. BD is most often reported in populations along the Silk Road. The highest prevalence is reported in Turkey at 20-420/100,000, compared 1.5/100,000 individuals in the UK. Mapping through general practitioners revealed a much higher than expected prevalence of 12.6/100,000 in the Northern Ireland population. Clusters were observed in Co. Down and Co. Antrim and plotted with social-demographic information. This high ‘UK’ prevalence and the identification of several families with multiple members diagnosed makes NI ideal to explore genetic and epigenetic risk factors for BD. This project involves deep phenotyping and strategies to improve recognition of Behcet’s disease, build collaborative partnerships, improve data collection, enhance training, and information sharing., The National Rare Disease Office (NRDO), initiated in June 2015, collates and disseminates Irish rare disease (RD) information. The prevalent nature of RD (1 in 16 of the population, approximately 80% of which has a genetic basis) and the burden to the health care system is under-recognised and a neglected public health issue. Awareness of rare diseases is a challenge, especially for GPs who each care for > 90 RD patients. The NRDO has made 58 presentations, lectures and publications and received numerous enquiries (58% of contacts from patients/ families, 25% from health care professionals and 4% researchers). Mapping Irish RD clinical and research expertise is developing through Orphanet Ireland. Enrolment of clinical expert centres has increased by 50%,but only, Aims To assess the tumour surveillance advice given to patients in Northern Ireland with confirmed PTEN hamartoma tumour syndrome (HTS). Methods We used the surveillance advice laid out by the Pan Thames Cancer Genetics Group in 2014 to benchmark our patients against. A coding search was carried out on our regional information management system to identify all patients with a confirmed diagnosis. The written/ electronic notes of these patients were reviewed. We adhered to the National PTEN audit inclusion criteria of including patients older than16 years, those with a pathogenic/likely pathogenic PTEN mutation or at 50% risk and those who had received advice between 01/08/10 - 01/08/2015. Results 21 patients were identified. All patients had a pathogenic PTEN mutation. 6 children were excluded. 1 adult was excluded due to lack of documented advice. 6 patients had a cancer diagnosis. 9 patients had a positive family history of cancer. Annual breast screening was recommended for 67% of patients which involved mammography in 83% and MRI in 17%. Annual thyroid USS and TFTs were recommended for 54% and 31% of patients respectively. 16% of female patients had gynaecology referrals completed. An annual dermatological review was recommended for 23% of patients. Widely variable colonoscopy and renal USS screening was recommended for 77% and 65% of patients respectively. No cases of Lhermitte-Duclos disease were identified vs 12% in the national UK audit. Conclusions There is a need for regional PTEN tumour surveillance guidelines to be produced and implemented through a regional PTEN specialist clinic., Catastrophic genomic alterations can drive unusually aggressive cancer phenotypes. We describe a diagnostically challenging rapidly fatal case of medullary thyroid carcinoma (MTC) occurring in a young, morbidly obese man presenting with diffuse bone marrow involvement and disseminated intravascular coagulation. Whole-exome sequencing and shallow whole-genome sequencing was carried out for the primary tumour and multiple metastases. We identified three germline SNP’s within the RET proto-oncogene which remained undetected using routine hospital genetic testing procedures. Indeed, one of the variants identified (L769L) has been previously reported in literature to be associated aggressive MTC presentation, yet remains untested for in the routine diagnosis of MTC. Supported by findings from shallow whole genome sequencing, we report for the first time in thyroid cancer, the occurrence of a catastrophic “chromothripsis-like pattern” (CTLP) event, which involved shattering of chromosome 4 leading to complete abrogation of normal chromosomal function, in addition to dramatic wide-spread copy number aberrations (CNA), across both primary tumour and bone marrow samples. We further describe the presence of loss-of-heterozygosity (LOH) in key genes involved in DNA repair mechanism pathways such as ATM, which possibly facilitated the CTLP event, in addition to LOH in other disease-associated genes such as ALK and NOTCH1 as key drivers of the aggressive and rapidly fatal clinical course in this patient and unresponsiveness to the standard-of-care targeted agent chosen. Given a possible rapid generation of tumor neo-antigens as a result of the CTLP event, immunotherapy may have been more suitable as a treatment option. Moreover, the presence of disease-associated SNP’s within the RET proto-oncogene, support their inclusion as part of routine RET genetic testing for aggressive MTC cases. These results provide a rationale for application of comprehensive genomic analysis of cancers presenting with unusually aggressive behavior to facilitate more appropriate therapeutic options and diagnoses., The Target 5000 research project aims to provide genetic testing for the estimated 5,000 people in Ireland who have an inherited retinal condition. Many clinical trials are available for patients with sight loss, however, many such trials require patients to have their causative mutation identified in order to enter the trial. The objective of the study is to genetically characterise patients with inherited retinal degenerations (IRDs) in Ireland and in principle to make clinical trials more accessible to some Irish people suffering from sight loss. The study also seeks to identify previously undiscovered pathological mutations in a panel of known retinopathy genes evaluated utilizing target capture next generation sequencing (NGS). Thus far in the study, as part of Target 5000 roughly 10% of the Irish IRD population has been sequenced and the results obtained are encouraging. Target 5000 offers not only a chance to discover new causative mutations, but is vital in giving patients access to information regarding the pathogenesis of their disease. Over 50 novel mutations have been discovered, as well as some previously ambiguous phenotypes resolved. More precise matching of genotype with phenotype from this study and similar studies globally should start to enable clinicians to better formulate accurate future diagnoses and at times prognoses., MicroRNAs are understood to play a functional role within the establishment of epigenetic marks and are in turn under epigenetic control. Emerging evidence suggests microRNAs are vital for both kidney development and renal function. This study aimed to identify differential methylation affecting microRNAs in patients with end-stage renal disease (ESRD). Methylation status was determined for 485,577 unique CpG sites in 105 individuals with ESRD and 52 donor controls with no evidence of renal disease using the HumanMethylation450K BeadChip array (Illumina). Statistically significant associations (P, Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease characterized by rapid-onset loss of upper and lower motor neurones, resulting in progressive paralysis and death from respiratory failure. Schizophrenia is a neuropsychiatric disease with positive symptoms, negative symptoms and impairment over a range of cognitive abilities. We have recently shown that schizophrenia occurs more frequently than expected in the pedigrees of ALS patients, suggesting an aetiological relationship between both diseases. Using linkage disequilibrium score regression with summary statistics for GWAS of ALS and schizophrenia comprising over 100,000 unique individuals, we estimated the genetic correlation between ALS and schizophrenia to be 14.3% (95% CI 7.05-21.6; p = 1×10-4). Up to 0.12% of the variance in ALS was explained by schizophrenia polygenic risk scores (p = 8.4×10). We leveraged the apparent pleiotropic relationship between ALS and schizophrenia to identify five potential novel ALS-associated genomic loci at conditional false discovery rate < 0.01. Diagnostic misclassification in the schizophrenia cohort did not contribute significantly to our observations (BUHMBOX p = 0.94) and we estimated that 4.86% (2.47-7.13%) of ALS cases would need to be misdiagnosed as schizophrenia to observe our genetic correlation estimate under a true genetic correlation of 0%. Our results indicate that the lifetime risk for comorbid ALS and schizophrenia increases from 1 in 40,000 to 1 in 34,336, which would require an incident cohort of 16,488 ALS patients to observe epidemiologically. Our findings suggest shared underlying biology between ALS and schizophrenia which will direct novel approaches in research and therapeutic development., Background Imprinted genes are autosomal, but only expressed from one parental allele and are often clustered in small groups. They play an important role in the regulation of normal mammalian development. Differentially methylated regions (DMR) on each allele are important in regulating the genes, with marks being characterised as primary or secondary DMRs, depending on whether they are inherited from the germ cells or arise later, respectively. Imprinting disorders such as Prader-Willi Syndome (PWS) and Beckwith-Weidemann Syndrome (BWS) arise either from uniparental disomy or faulty DNA methylation. We wished to determine 1) which of the loci are most sensitive to loss of methylation 2) to more precisely define the sensitive regions and 3) determine what happens at primary versus secondary imprints. Methods Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in hTERT-immortalised adult fibroblasts using shRNA. Genome wide methylation levels were assayed using the Illumina 450k BeadChip array and analysed using bioinformatic approaches. Results We found that 1) the imprinted loci varied extensively in their sensitivity to loss of methylation 2) the extended locus involved in PWS was particularly sensitive 3) that loss of methylation at primary DMR appears to drive gains in methylation at secondary DMR. Conclusion Our results point to a mechanistic link between primary and secondary DMR which may explain why imprints are difficult to reprogram in somatic tissues., Osteoarthritis (OA) is a degenerative joint disease that affects millions of people globally with no disease-modifying strategies yet available. Our understanding of the pathology of OA is inadequate and this impedes investigation of efficient diagnosis and treatment. To expand our understanding of the underlying cellular pathology of OA, we studied a monogenic condition, familial osteochondritis dissecans (FOCD), associated with a known mutation in the ACAN gene. Patients with FOCD develop early onset OA with multiple joint involvement. The objectives of the project were to investigate the cellular pathogenesis of FOCD by studying (a) chondrogenesis of patient-derived bone marrow-mesenchymal stem cells (BM-MSCs) and (b) induced pluripotent stem cells (iPSCs) generated from patient fibroblasts. Our findings revealed that the mutation resulted in a misfolded or unfolded aggrecan protein, which accumulated in the rough endoplasmic reticulum (rER) during protein production. The consistent accumulation resulted in ER stress throughout chondrogenesis. Moreover, the rER stress caused abnormal or disregulated global extracellular matrix (ECM) production and assembly. Importantly, ECM composition analysis indicated that the patient chondrocytes produced abundant amounts of OA-associated markers. Using patient-specific stem cell models, we have discovered a cellular pathogenesis of FOCD involving abnormal cell function and defective tissue formation, contributing to the OA phenotype., Aims The Irish Travellers are a nomadic population primarily found within Ireland and the UK. Consanguineous unions are common, and as a population they are socially and genetically isolated from the surrounding, “settled” Irish population. Previous low-resolution genetic analyses suggested a common Irish origin between the settled and the Traveller populations. It is not known, however, what is the extent of population structure within the Irish Traveller population, the time of divergence from the general Irish population, and the extent of autozygosity. Methods We recruited Irish Travellers from across Ireland and the UK. For inclusion, a participant had to have had at least three grandparents with a surname associated with the Irish Travellers. DNA was extracted from saliva samples, and genotypes were generated using the Illumina OmniExpress SNP genotyping platform. With this data, we investigated population structure using fineStructure, quantified the levels of autozygosity with PLINK, and estimated a time of divergence using a method based on Identity by Descent (IBD) segment sharing. Results We merged, cleaned, and analysed data from 42 Irish Travellers, 2232 settled Irish, 2039 British, 143 Roma Gypsies, and 931 individuals from 57 world-wide populations. We confirm an Irish origin for the Irish Travellers, demonstrate evidence for population substructure within the population, confirm high levels of autozygosity consistent with a consanguineous population, and for the first time provide estimates for a date of divergence between the Irish Travellers and settled Irish. Conclusion Our findings have implications for disease mapping within Ireland, and they additionally inform on the social history of the Irish Traveller population., Copy number variants at 16p13.11 have been described in association with a variety of neurodevelopmental disorders. While deletions of this region are perhaps better described, the clinical significance of the reciprocal duplication is less clearly defined. Phenotypes reported in association with the duplication include developmental delay, speech delay, behavioural difficulties and neurodevelopmental phenotype such as autism, schizophrenia and ADHD. However, the region appears to be subject to variable expressivity and incomplete penetrance. To date we have detected duplications of 16p13.11 in 5 probands using oligonucleotide array CGH. Of these patients 3 showed duplications within the typical ~1.5Mb duplication region while 2 patients had a larger ~2.8Mb duplication, encompassing all of the above region. The clinical phenotype of these patients will be described. Two of these patients have inherited the duplication from their mothers, one was a de novo finding and the inheritance of the others is currently unknown. One of the maternal duplication carriers are also known to have a phenotype. Our data provides further clinical information on the phenotypic features of patients with this syndrome and provides more evidence for the pathogenic nature of this duplication., Introduction Patients referred to the NI Regional Cancer Genetics Service for genetic counselling were sent a questionnaire to evaluate patient satisfaction. The questionnaire focused on satisfaction surrounding the referral process, waiting times and communication during and after the appointment. Method One hundred patients, whose episode of care was completed between November 2015 and June 2016, were sent an anonymised structured questionnaire by post. Patients were seen by a genetic counsellor for assessment of their family history of cancer, predictive testing and genetic mutation screening Results To date (23/06/2016) the questionnaire response rate is 34%. So far 91% have expressed satisfaction with the service that they received. Useful comments and observations have been feedback in the questionnaire to aid service improvement. Data collection will be completed imminently to allow for complete analysis. Discussion Useful data has been collected which reinforces the service currently being delivered by genetic counsellors whilst also highlighting areas of service development., Leber’s Hereditary Optic Neuropathy (LHON) is one of the most commonly inherited optic neuropathies and results in significant visual morbidity among young adults. 95% of LHON patients will present with one of three primary mitochondrial mutations; G3460A, G11778A and T14484C. We describe a novel real time diagnostic test to detect the three common mutations leading to LHON. The test uses a combination of multiplex allele specific PCR (ARMS PCR) in combination with high resolution melt curve analysis to detect the presence of the G3460A, G11778A and T14484C mutations. PCR primer sets were designed to produce a control PCR product and PCR products only in the presence of the 3460A, 11778A and 14484C mutations in a multiplex single tube format. Products produce discrete well separated melt curves allowing clear detection of the mutations. The test has proved to be robust, cost and time effective with the real time closed tube system taking approximately 1 hour to complete. This test provides a simple, robust, easy to read output that is both cost and time effective, thus providing an alternative method to individual endpoint PCR – RFLP, PCR followed by Sanger / pyrosequencing and next generation sequencing. It will also allow diagnostic laboratories to detect 95% of LHON causing mutations in a single tube assay allowing diagnostic laboratories to avoid costly NGS assays for the vast majority of LHON patients, thus allowing resources to be focussed on patients with unknown mutations requiring further analysis., Atherosclerotic coronary artery disease (CAD) is a progressive chronic inflammatory condition that can lead to Major Adverse Cardiac Events (MACE) such as heart attacks. Currently there is no definitive test to predict MACE risk. Tumour necrosis factor alpha converting enzyme (TACE), also known as A Disintegrin And Metalloproteinase 17 (ADAM17) is a membrane-anchored protein responsible for the ectodomain shedding of a variety of transmembrane proteins such as cytokines, chemokines, growth factors and their receptors. TACE has been linked to several major acute and chronic inflammatory diseases including atherosclerosis. The aim of this study was to investigate if TACE may be a valuable predictive biomarker for CAD and MACE risk. TACE levels were measured in the plasma of CAD patients including those with acute coronary syndrome (ACS) and elective patients attending the catheterisation laboratory for coronary angiogram. TACE levels were measured using ELISA and quantitative real time PCR. Levels were compared with control samples collected from apparently healthy individuals and a subset of patients with no CAD as evidenced by coronary angiogram. Other factors that might affect TACE detection were also measured including sample type and storage time. To date 207 consecutive CAD patients and 40 controls have been recruited to the study. Results demonstrate that CAD patients have higher levels of plasma TACE in comparison to controls. TACE protein levels were especially highest in those ACS and elective patients with a previous history of MACE. Results to date indicate that TACE may be a useful marker to predict disease progression and recurrent MACE in CAD patients., Introduction NRG1 (neuregulin1) is a candidate tumour suppressor gene. NRG1 encodes ligands for members of the ERBB family, and has been shown to be silenced by methylation in breast cancer1. Breast and thyroid cancers share some genetic loci (e.g. PTEN, STK11), and an increased risk of thyroid cancer has been noted in survivors of breast cancer2. A single nucleotide variant (C>G) in NRG1 (rs2439302), has been associated with increased risk of non-medullary thyroid cancer3. Aim Our aim was to investigate the association between rs2439302 in NRG1 and predisposition to thyroid and breast cancers in an Irish population. Methods A two-arm case-control study was undertaken. Patients with mutations in high-risk cancer susceptibility genes were excluded. Controls included adults with no personal or familial history of breast or thyroid cancers. Male controls were included in thyroid case- control analysis only. DNA was extracted from whole blood/buccal swabs by ethanol precipitation. Genotyping was performed using Taqman-based PCR. Results 257 patients with thyroid cancer, 518 with breast cancer and 367 unaffected controls were genotyped. Homozygous carriers of the variant were found to have an increased risk of thyroid cancer (OR1.89 (1.21-2.95), p=0.005), but risk for mono-allelic carriers was not significantly increased (OR1.27 (0.87-1.84), p=0.21). The presence of the variant was not associated significantly with breast malignancy for mono-allelic (OR1.31 (0.95-1.8), p=0.095) or biallelic mutation carriers (OR1.15 (0.76-1.73), p=0.51). Conclusion Homozygous carriers of the G allele were found to be at increased risk of thyroid cancer, but no association was observed between the variant and breast cancer., The UGT1A gene family encode (UGT) activity that facilitate the transfer of glucuronic acid to a range of xenogenous and endogenous substrates, the polar end products of which are better suited for elimination through urine and bile. UGT1A genes exhibit an inducible pattern of expression regulated through the activities of such nuclear receptors (NRs) as pregnane X receptor (PXR) farensoid X receptor (FXR) and liver X receptor (LXR) that form a complex interactive network of ‘sensors’ to facilitate the elimination of potentially harmful metabolites and exogenous toxins. We have previously reported that activation of vitamin D receptor (VDR) through both synthetic agonists and nutritionally derived ligands, can induce the expression of both phase I metabolic (CYP3A) and phase III transporter (ABCA1) genes. Little is known however, as to how activated VDR may impact upon the regulation of phase II genes such as UGT1A1. In this study we demonstrate that ligand-activated VDR can significantly enhance the expression of several members of the UGT1A gene family. With particular respect to UGT1A1, we identify within the proximal promoter region of this gene a functional vitamin D response element (VDRE) also recognized by PXR but distinct from previously established regulatory elements that mediate FXR and LXR signalling. Based upon our data, we propose a model for VDR and circulating levels of vitamin D as maintaining stable expression of phase II and functionally related genes as a means to provide baseline protection against the effects of toxic xeno and endobiotic metabolites., Depression is a complex disorder with multiple symptoms, including a persistent low mood, anhedonia and cognitive impairments, and is currently the third leading cause of global disability. The underlying pathophysiology of depression is poorly understood but a growing body of evidence supports an important role for the microbiome in the aetiology of depression and other psychiatric disorders. While much interest is currently focused on the role of the microbiome-gut-brain axis in brain physiology and neurochemistry, the importance of the oral microbiome has received little attention. The aim of this study is to characterise the oral microbiome in adults with severe depression versus matched controls with no history of the disease. To achieve this, participants were asked to complete an online validated mental health survey and to provide a saliva sample. We identified 46 individuals who met the DSM-V criteria for severe depression and 46 age and sex-matched controls with no history of depression. Bacterial DNA was extracted from the saliva samples and 16S rRNA surveys were conducted using next generation sequencing. Differences in the bacterial community composition of the oral microbiota between patients and controls were determined. Metagenomic analyses were conducted using machine learning and computational intelligence algorithms using the 16S RNA data to generate inferred metagenome feature sets. Charting the oral microbiome in depressed patients could therefore provide new insights into the development of the condition, and lead to the identification of novel diagnostic and therapeutic response biomarkers., The nuclear receptors (NRs) pregnane X receptor (PXR) and constitutive androstane receptor (CAR) modulate transcriptional networks that dictate the bioavailability of many endogenous and exogenous compounds such as steroid hormones and therapeutic drug compounds. Elucidating those factors that invoke PXR/ CAR activity has been important for understanding the genetic basis for both metabolic disease and inter-individual variations in drug response. PXR is most closely related to Vitamin D receptor (VDR) for which there is relatively little is known for how this NR may impact upon these same physiological processes. In this study, we employed enteric cell models and ex-vivo based human colon explants to examine how activated VDR may impact upon the expression of genes of a metabolism and transporter function. We find that in relation to PXR and other evaluated NRs, VDR is the most efficient and dominant receptor for induced expression of CYP2B6, CYP3A4/5 and ABCA1. We note that upon activation with the synthetic agonist EB1089, VDR will achieve striking and sustained elevated expression of CYP3A4 at mRNA, protein and enzymatic level suggesting the potential for selective metabolic gene targeting through ligand design. In addition, we report members of the UGT1A gene family to be novel VDR regulated genes, thus extending the known metabolic effects of vitamin D to also encompass expression of phase II (conjugating) genes. This study intimates that systemic vitamin D status and/or activating VDR ligands may have pharmacokinetic relevance to co-administered drug regimes., Ancient genomes are often typically analysed with regard to ancestry and physical phenotype. Less common is examination and identification of genetic diseases, primarily due to the very low numbers of samples sequenced and poor level of sequencing related to the difficulties in sequencing from ancient DNA. Here we present the results of analysing 21 ancient Irish genomes. The data were screened for a wide range of pathogenic genotypes and markers. Giving information for the potential effects and prevalence of certain conditions as well as the earliest known confirmation of their presence. Using records of the remains, we also examined if any displayed phenotypes correlated to identified diseases., Coronary Artery Disease is the largest contributor of CVD, the leading cause of death worldwide. It is caused by atherosclerosis, a build-up of cholesterol in the blood vessels and chronic inflammation. The NLRP3 inflammasome plays a critical role in the secretion of IL-1β, and there is significant evidence that it is involved in the pathogenesis of a number of inflammatory diseases including atherosclerosis. Recent studies demonstrate that particular cell surface receptors namely the scavenger receptor CD36 and the endocannabinoid receptor CB1 are involved in the activation and regulation of the NLRP3 inflammasome and they have also been implicated in the pathogenesis of atherosclerosis. The present study aimed to investigate expression and activation levels of the NLRP3 inflammasome, the CD36 and CB1 receptors in blood samples obtained from patients with atherosclerosis at very high risk of a Major Adverse Cardiac Event (MACE) such as a heart attack. The cell signalling processes involved in NLRP3 inflammasome activation were also investigated in a THP1 in vitro model of atherosclerosis. Results to date indicate increased expression of NLRP3 in patients at very high risk of MACE and also demonstrate that THP1 macrophages require both the CD36 and CB1 receptors for optimal NLRP3 expression in response to oxidized LDL. These preliminary findings provide an insight into the mechanism of action of the NLRP3 inflammasome in atherosclerosis and prompt further exploration of this protein complex and its regulatory receptors as potential targets for prognostic and or therapeutic development in the strive towards a more personalised approach to the management of coronary artery disease., Approximately 30% of patients with epilepsy are refractory to anti-epileptic drug (AED) treatment and continue to have debilitating seizures that severely impact upon their quality of life. Exome sequencing in encephs etc has illustrated the importance of de-novo variants in the pathogenesis of rare neurological disorders. However, the contribution of de-novo mutations to pharmacoresistance in adult epilepsy is uncertain. In this study we investigated whether a trio whole exome sequencing paradigm could be applied to identify genetic causes of chronic, refractory epilepsy. We selected adult patients (n=5) with onset of seizures after 5 years of age, had failed ≥6 AEDs and were still experiencing >4 disabling seizures per month. Patients were excluded if they had a potentially ‘explanatory’ lesion on MRI. Parents were exome sequenced to identify de-novo mutations and these were assessed bioinformatically for pathogenicity. We confirmed the presence of coding de-novo mutations that were bioinformatically predicted to be functional and damaging in 3/5 patients. One of these occurred in the gene DNM1L, which was recently implicated in pharmacoresistant epilepsy (Vanstone et al. EJHG, 2015;Nov 25). This represents a potential diagnostic yield of 20% however more data is required and more trios are currently being sequenced. We have demonstrated the potential diagnostic yield of whole exome sequencing in a small number of adult patients with chronic refractory epilepsy. Identifying genetic mutations underpinning this disorder may provide new insight into the underlying biology and offers the potential for therapeutic intervention in the form of precision medicine., IgA nephropathy (IgAN) is the most common form of glomerular nephritis worldwide1. Difference in incidences between ethnicities and familial inheritance patterns indicate this is a genetic disorder. An IgAN locus on chromosome 6q22-23 was identified via linkage analysis; however the causal gene remains elusive2. We set out to identify mutations underlying familial IgAN using whole exome sequencing. DNA was collected on 25 (unaffected and affected) individuals across 6 families with IgAN. Families were chosen on the basis of having at least 2 affected members with IgAN. We carried out full exome sequencing on 12 of the affected members from these families. Depending on the pattern of inheritance in a given family, mutations that fitted a dominant, recessive or compound heterozygote model of inheritance were screened for. These variants were then filtered based on being shared between affected individuals within a family, their minor allele frequency, region, function and predicted deleterious nature. We identified a number of potential candidate mutations in these families and including a mutation in the gene COL4A5 which was previously described as pathogenic3. Mutations in COL4A5 have previously been found in individuals with Alport syndrome, a disease which is often mistaken for IgAN. We are currently working to confirm these candidate mutations via Sanger sequencing and will be screening for segregation., Atherosclerosis is a chronic inflammatory disorder that is responsible for approximately 71% of incidents of cardiovascular disease. A mathematical model of atherosclerosis has been developed, capturing the cell types and proteins involved in atheroma formation and describing the dynamics of disease progression. This is the first model of this type to be developed using open systems biology standards. We have predicted tertiary protein structures for all the proteins involved in this atherosclerosis model and all of their recorded mutations, using phase 3 sequence data obtained from the 1000 Genomes Project. By comparing the electrostatic potentials of these tertiary structures, we predict how the dynamics of atherosclerosis stratifies across population subgroups., The aim of this pilot study was to test the feasibility of carrying out a large scale study using this design to investigate whether methylation of the oxytocin receptor (OXTR) can serve as a potential biomarker for response to oxytocin administration in women during and after labour. Background Oxytocin is a nine-amino acid peptide with hormonal and neurotransmitter functions during labour and lactation. We hypothesised that a difference in methylation levels of the oxytocin receptor (OXTR) gene may impact the woman’s ability to become established in labour and her response to oxytocin administration. Method Blood samples were taken pre-birth and postnatally from 21 women and subjected to DNA methylation analysis of the OXTR gene by pyrosequencing. Methylation status of CpG sites -924 and -934 upstream from the initiation transcription site (ITS) of the OXTR gene was determined. Expression of the OXTR gene before and after birth was measured using qPCR. Global methylation levels were examined using Luminometric Methylation Assay (LUMA). Results We found both hypo and hypermethylation of OXTR promoter at CpG sites -924 and -934 in individual samples, however we observed no profound changes in overall OXTR methylation levels within the patient cohort at these CpG sites. We found a strong correlation between OXTR promoter methylation levels found in whole blood and those found in matched PMBC samples. Global methylation analysis using Luminometric Methylation Assay (LUMA) revealed no significant differences between whole blood and PMBC. Conclusions A larger sample is required to determine whether OXTR methylation status is predictive of response to oxytocin administration. Whole blood sampling is a suitable alternative for OXTR methylation analysis in a larger cohort of women undergoing labour., Background Cardiovascular disease (CVD) is the leading cause globally of morbidity and mortality. microRNAs (miRNAs) are small, non-coding RNAs which have a fundamental role in the pathology of various diseases including CVD. Circulating serum levels of miRNAs have been proposed as potentially valuable markers of heart failure, stroke, myocardial infarction and arterial hypertension, but the specific miRNAs involved and their function remains unclear. Therefore, this pilot study aims to profile miRNA expression in premature CVD patients to identify which miRNAs correlate best with hypertension. Methods The Multiplex Circulating miRNA Assay with Firefly™ Particle Technologies was used to profile 68 miRNAs on a cardiology focus panel in serum samples from 170 premature CVD patients recruited from Altnagelvin Area Hospital and screened for the C677T polymorphism in methylenetetrahydrofolate reductase, a risk factor for hypertension. Samples were collected at baseline and following intervention with riboflavin, a co-factor for MTHFR, which significantly lowers blood pressure specifically in adults with this polymorphism. Statistical analysis was used to correlate miRNA expression with blood pressure, MTHFR genotype and other relevant clinical data. Results The assay successfully measured miRNA expression in the sample set. miRNAs which expressed differentially between MTHFR genotype groups were highlighted and the functional significance of these miRNAs was assessed using bioinformatics to identify target genes involved in CVD. Conclusions The data provides further evidence that using specific miRNAs as serum markers could aid early prediction of CVD and may lead to better diagnostic modalities and therapeutic regimes., Gene-environment interactions, particularly in genes related to regulation of serotonin and neuronal function, have been implicated in the aetiology of depression. Allelic variations in the 5’ flanking transcriptional region of the serotonin transporter gene (5-HTTLPR) and higher levels of promoter DNA methylation are associated with depression. Brain derived neurotrophic factor (BDNF) plays an important role in neuronal differentiation and survival, and is also involved in regulation of serotonin. A single nucleotide polymorphism in the BDNF gene, leading to a valine to methionine substitution at codon 66 (Val66Met), and increased methylation of the BDNF promoter have also been associated with depression. The goal of this study is to determine whether length of the 5-HTTLPR, prevalence of the Val66Met polymorphism of the BDNF gene and DNA methylation in both 5-HTT and BDNF promoter regions are associated with depression in the student population. First year students provided a saliva sample for genetic analysis and completed an online mental health survey. Presence and severity of depression was determined from survey responses based on DSM-IV criteria. Length of the 5-HTTLPR was determined by PCR and gel electrophoresis and presence of the SNP at BDNF rs6265 and examined using restriction fragment length polymorphism analysis. Bisulphite-treated DNA was amplified by PCR and pyrosequencing assays used to determine methylation patterns of BDNF and SERT. Our preliminary findings suggest that genetic and epigenetic variation in the 5HTT and BDNF genes are associated with depression in the student population and may be candidate biological markers to assist in diagnosis., BACKGROUND Prostate cancer is the most common male cancer in the UK, where it kills approximately 11,000 men annually. There has been growing interest in the role played by the anaerobic bacterium Propionibacterium acnes, an important component if the skin microflora, in the aetiology of the condition via a chronic, asymptomatic infection of the prostate leading to oncogenesis. METHODS A quantitative real-time PCR (qRT-PRC) assay for retrospective detection of P. acnes in formalin-fixed paraffin embedded sections from archived prostate samples was developed. An in vitro infection model of prostate infection with P. acnes is being optimised, which should allow us to get insight into the dysregulation P. acnes infection causes in prostate epithelial cells. RESULTS A total of 81 biopsy samples, representing one or both prostate lobes, were examined from 53 patients with prostate carcinoma, versus 111 samples from 60 patients whose biopsies were histologically normal, and the assay revealed that 35% of cancerous prostate samples were positive for the presence of P. acnes, compared with only 8% of the disease-free samples (p, Oral squamous cell carcinoma (OSCC) is one of the top ten most prevalent cancers in the world. Prognosis is poor and quality of life is commonly reduced for patients who survive. OSCC is thought to progress via a premalignant stage called dysplasia. Effective treatment of dysplasia prior to malignant transformation, or the ability to more accurately predict the 10-20% of dysplasias that will progress to OSCC, is an unmet clinical need. With the aim to better understand the biology of OSCC development, and attempt to identify potential markers of early disease and therapeutic targets, we performed parallel whole exome sequencing and total RNA sequencing on 16 micro-dissected formalin-fixed paraffin embedded dysplasia and their associated OSCC. These are the largest omic analyses on matched patient samples from the oral cavity in non-HPV infected patients where all dysplasias are associated with progression to OSCC, that has been performed to date. Whole exome analysis revealed that every OSCC and adjacent associated dysplasia sample did have a common clonal ancestor, with many shared potential drivers of progression, but that there is also considerable genomic heterogeneity between associated pre-invasive and invasive disease, as seen in a previous study1. RNAseq analysis revealed differences in the immune cell signatures present at different disease stages, distinguished early events in pathogenesis from later events and identified several novel coding and non-coding candidates with potential involvement in oral dysplasia development and malignant transformation. These findings merit further investigation in a larger retrospective longitudinal study of patients with oral dysplasia., Many disorders involving tissues, which have significant energy requirements, involve mitochondrial dysfunction often due to mutations affecting the mitochondrial genome. Some such mutations can involve genes coding for subunits of complex I of the electron transport chain leading to a complex I deficiency in disorders such as Leber Hereditary Optic Neuropathy (LHON) amongst others. Mitochondrial dysfunction leads to a lack of energy production and ultimately the death of the cell. In disorders such as LHON, retinal ganglion cells (RGCs) are affected, leading to retinal dysfunction. These observations have prompted interest in exploring innovative therapeutics to modulate mitochondrial disorders involving complex I deficiency. The Farrar laboratory has explored candidate gene therapies for complex I deficiency using Ndi1, a yeast gene which is a complex I homologue. In order to test the efficacy of candidate therapies, we have developed a robust, empirical assay of mitochondrial function. Previous assays measured the level of NADH oxidation in a sample, both before and after rotenone as a measure of complex I activity. To optimally distinguish between the activity of complex I and the potential therapeutic, the assay was modified with the addition of a second inhibitor which allowed specific measurement of the therapeutic, such as Ndi1. Given that this is an in vitro assay, it enables large-scale screening of potential therapeutics and ensures only those that show strong evidence of efficacy are then tested in vivo. In combination with other quantitative assays such as Reactive Oxygen Species (ROS) generation this allows detailed evaluation of the health of mitochondria within a sample., Schizophrenia is an adult-onset mental illness with that impacts cognitive function. The largest GWAS has revealed 108 loci associated with schizophrenia risk but how variation affects genes and impacts brain function to increase risk is largely unknown. The centrosome is the microtubule organising centre of the cell and seeds the growth of the primary cilium. The disproportionate number of brain disorders associated with centrosomal genes suggests the organelle underlies normal brain and cognitive development. Schizophrenia is neurodevelopmental and cognitive deficits are a core element of the disorder. We hypothesise that some of the newly identified risk genes for schizophrenia will function in the centrosome and variants in these genes will be associated with cognitive deficits. Cross-referencing genes with centrosomal functions with genes from schizophrenia GWAS, identified six candidate genes; SDCCAG8, MAD1L1, GIGYF2, MPHOSPH9, PRKD1 and MAPK3. The effect of risk SNPs on cognition was examined using an Irish dataset of psychosis cases and controls (n=1,236) using linear regression. Among the associations identified, the SDCCAG8 risk SNP was shown to affect attribution style, a measure of social cognition (P=0.001). The MAD1L1 risk SNP was associated with poorer performance on episodic memory tasks (P=0.003). A suitable replication dataset was not available for social cognition measures. We attempted replication for episodic memory results in UK and German samples but results were non-significant. Overall, we have identified a number of schizophrenia risk genes that function in the centrosome but further larger datasets are required to establish a role for these genes in cognition., Epigenetic mechanisms are an important heritable and dynamic means of regulating various genomic functions, including gene expression to orchestrate brain development. These processes when perturbed are thought to contribute to schizophrenia (SZ). A core feature of SZ is cognitive dysfunction. GWAS have identified 108 genomic loci associated with SZ risk, containing 350 genes. My aim was to identify genes that have epigenetic functions which map to loci associated with SZ, and to test the associated SNPs for association with cognitive deficits. Risk SNPs in 8 genes: BCL11B, CHD7, EP300, EPC2, GATAD2A, KDM3B, RERE and SATB2 were analysed using an Irish dataset of psychosis cases and controls (n=1235) who had completed tests across 5 cognitive domains. Five of the eight variants had significant associations with at least one cognitive task. Strongest associations were for CHD7 (rs6984242) for IQ (p=0.001) and episodic memory (p=0.007). These results did not replicate in independent samples. We link rs6984242 to CHD7 via a long range expression quantitative trait loci (eQTL) and CHD7 has not been previously reported as a candidate risk gene for SZ. To further explore its novel association with SZ, we identified a set of 45 interacting genes and used SNPs across these genes to develop a polygenic risk score for SZ, independent of CHD7 itself. This score was tested for association with cognitive function. Significant associations(p, The relevance of nutrition and other environmental influences on epigenetic modifications including DNA methylation is a topic of considerable interest. Folate One Carbon Metabolism (FOCM) is the principal supplier of the methyl groups required for DNA methylation, giving folate status a strong biological plausibility of having an impact on an individual’s and an offspring’s DNA methylation profile at both the mitotic and meiotic level. We sought to identify DNA methylation sites in the human genome that are sensitive to folate status i.e., Folate-sensitive Differentially Methylated Regions (FS-DMR) using a folic acid intervention trial in pregnant women known as FASSTT (Folic Acid Supplementation in the Second and Third Trimesters). To minimize the amount of DNA methylation ‘noise’ due to non-folate related factors such as other environmental stimuli and individual genetic variation, we compared the DNA methylation profile of the same individual pre- and post- intervention to identify putative FS-DMR. We selected six healthy pregnant women, three from the folic acid intervention arm and three from the placebo arm of the trial. We performed MeDIP (Methylated DNA Immunoprecipitation) on all 12 samples and hybridized to a Roche Nimblegen Delux 2.1M promoter array. While we observed DNA methylation changes pre- and post- folic acid intervention in each individual, the actual DNA methylation sites were not consistent across all three individuals. Of course, it is possible that a more in-depth Next Generation Sequencing approach might yield our elusive FS-DMRs. However, the published literature to date does not appear to support such a promise., The loss of retinal ganglion cells (RGCs) is a hallmark of a number of retinopathies. There are a number of gene therapies being developed that have shown efficacy in preserving RGCs when administered using an AAV vector. Localising expression of any therapeutic to the target cell type (ganglion cell layer, GCL) would represent a significant optimisation of the approach. The packaging capacity of AAV (4.7kb) imposes a limit on the size of promoters and genes relevant for AAV-mediated gene delivery. Few GCL-specific promoter sequences have been defined of a size suitable for use in AAV-guided gene expression. Exploring this, a panel of genes was chosen with GCL-limited expression profiles. A pipeline program was developed that analysed regions upstream of these genes for sequence conservation across placental mammals (as a proxy for putative promoter function), weighted by enriched GCL expression levels. Adopting this strategy, ganglion cell promoter 1 (GCP1), demonstrating the key features outlined above, was identified. To test its function, GCP1 (2.2kb in size) was engineered into an AAV2 virus expressing EGFP. Here we demonstrate the effectiveness of GCP1 in localising EGFP expression to the GCL when administered via intravitreal injection. Furthermore, absence of EGFP expression was demonstrated when targeted towards photoreceptors via subretinal injection, verifying GCP1 tissue-specificity. Expression of AAV2.GCP1-EGFP was compared to expression from a non-specific promoter construct, AAV2.CMV-EGFP. GCP1-EGFP was shown to provide equivalent expression to CMV-EGFP in the GCL. GCP1 thus offers a tissue-specific promoter option, suitable for deployment within AAV vectors without compromising functionality., Purpose Hypoxia is a common hallmark of the tumour microenvironment. Recently we have shown the anti-androgen bicalutamide induces profound hypoxia in prostate tumours in vivo. This resulted in the promotion of epithelial to mesenchymal transition. Here we target tumour hypoxia using a novel unidirectional hypoxia-activated prodrug OCT1002 to enhance the anti-tumour effect of bicalutamide. Experimental Design The effect of OCT1002 treatment on LNCaP-luc cells was measured in normoxia and hypoxia in vitro. In vivo, tumour growth and lung metastases were measured in mice treated with bicalutamide, OCT1002 or a combination. Dorsal skin fold chambers were used to image tumour vasculature in vivo. Longitudinal genetic changes in tumours were analysed using PCR. Results Reduction of OCT1002 to its active form (OCT1001) decreased LNCaP-luc cell viability. In LNCaP-luc spheroids, OCT1002 caused increased apoptosis and decreased clonogenicity. In vivo, treatment with OCT1002 alone or with bicalutamide, showed significantly greater tumour growth control and reduced lung metastases compared to controls. Re-establishment of the tumour vasculature following bicalutamide-induced vascular collapse is inhibited by OCT1002. Significantly, the up-regulation of RUNX2 and its targets caused by bicalutamide alone were also blocked by OCT1002. Conclusions OCT1002 selectively targets hypoxic tumour cells and enhances the anti-tumour efficacy of bicalutamide. Furthermore, bicalutamide causes changing genetic profiles during treatment, with development of a more malignant genotype; OCT1002 can block this effect. This study indicates that more attention should be attached to understanding genetic changes that may occur during treatment. Early targeting of hypoxic cells with OCT1002 can provide a means of inhibiting prostate tumour growth and malignant progression., Background In prostate cancer (PCa), abnormal expression of several microRNAs (miRNAs) has been previously reported. Increasing evidence shows that aberrant epigenetic regulation is a contributing factor to their altered expression in cancer. In this study we investigate whether expression of miR-200c and miR-141 in PCa is related to the DNA methylation status of their promoter. Methods PCR analysis of miR-200c and miR-141, and CpG methylation analysis of their common promoter, was performed in PCa cell-lines and in FFPE prostate biopsy specimens. The functionality of miR-200c and miR-141 expression in prostate cancer cells was assessed by a series of in vitro bioassays. Results miR-200c and miR-141 expression correlates inversely with the methylation status of the miR-200c/miR-141 promoter in PCa cells. In PC3 cells, miR-200c and miR-141 expression is elevated by treatment with the demethylating agents suggesting their expression is linked to methylation. Expression of miR-200c and miR-141 in prostate biopsy tissue was inversely correlated with methylation in CpG sites closest to the miR-200c/miR-141 loci. Over-expression of miR-200c in PC3 cells inhibited growth and clonogenic potential, as well as inducing apoptosis. Expression of the genes DNMT3A and TET1/TET3 were down-regulated by miR-200c and miR-141 respectively. Finally, treatment with the soy isoflavone genistein caused demethylation of the promoter CpG sites closest to the miR-200c/miR-141 loci resulting in increased miR-200c expression. Conclusions Our findings provide evidence that miR-200c and miR-141 are under epigenetic regulation in PCa cells. Profiling their expression and methylation status may have potential in the improved diagnosis and prognosis of PCa., Increasingly accurate surveys of human health throughout the life course has led experts to propose that stresses on the child while still in the mother’s womb can affect the individual’s health much later in life. Such long-term effects on health are thought to be mediated by a semi-permanent trace on the genes of the affected person called an epigenetic mark. Epigenetic mechanisms, such as DNA methylation, are dynamic during pregnancy whereby epigenetic marks are seeded which persist throughout the lifetime of the developing child. It has been suggested that these patterns may be altered by the mother’s diet, particularly folate – a key component in the DNA methylation cycle. Currently, mothers are universally recommended to supplement their diet with 400μg folic acid/day as a preventative measure against neural tube defects in the offspring prior to and during the first trimester. However, there remains no clinical recommendation as to whether mothers should continue supplementation during the final two trimesters and the potentially heritable effects on DNA methylation. Observational studies have suggested that folate-rich maternal diets are associated with changes in DNA methylation of the child during this period of gestation. We present here the results of a randomised control trial (FASSTT study) examining the effects of folic acid supplementation in late gestation (week 12 onwards) on DNA methylation of several gene classes in offspring cord blood samples. We report small but significant sex-specific differences between the two intervention groups. These preliminary results indicate that folic acid supplementation throughout pregnancy may exert significant effects on cord blood DNA methylation., Introduction New-onset diabetes after transplantation (NODAT) is a common complication of kidney transplantation which increases risk of subsequent graft failure, cardiovascular complications and death. NODAT is defined as the new requirement for oral hypoglycaemic agents or insulin as a result of hyperglycaemia after renal transplant. The first genome wide association study (GWAS) for NODAT was published by our group in 2014; seven of the eight top-ranked, common SNPs are implicated in β-cell apoptosis. Methods To further understand the genetic architecture of the NODAT phenotype we used whole exome sequencing for 134renal transplant recipients from a Northern Ireland renal transplant cohort. We sequenced 53 individuals with NODAT (cases)and 81 transplant recipients without NODAT (controls). Library preparation was performed using the Ion TargetSeq™ Exome Kit with samples sequenced on an Ion Torrent Proton sequencer. TheIon OneTouch 2 for emulsion PCR and Ion Enrichment System were used. Association analysis was performed using PLINK Version 1.9 to identify variants associated with NODAT (with age and weight at transplant included in the regression model). Results Following appropriate quality control, initial analysis identified 6 variants nominally associated with NODAT (Ptrend, The Irish Traveller community has a high incidence of autosomal recessive (AR) disorders due to consanguinity. The Division of Molecular Genetics at the DCG offers genetic testing, primarily to members of this community, for five specific pathogenic mutations found in five AR disorders. The pathogenic mutations are detected by bi-directional Sanger sequencing and the service includes: Gene Disorder/ Disease Phenotype LARS (leucyl-tRNA synthetase) Infantile Liver Failure Syndrome 1 (ILFS1) Infantile hepatopathy with failure to thrive (FTT) and developmental delay. MCM4 (minichromosome maintenance 4) Natural Killer Cell & Glucocorticoid Deficiency with DNA Repair Defect (NKGCD) FTT, adrenocorticotropin hormone (ACTH) resistance, familial glucocorticoid deficiency (FGD), mosaic Fanconi anaemia and recurrent infections due to NK cell deficiency. STRA6 (stimulated by retinoic acid 6 gene) Autosomal recessive isolated colobomatous microanopthalmia (MCOPS9) Microphthalmia, anophthalmia, coloboma.Specific STRA6 mutation can also cause the Matthew-Wood syndrome [anophthalmia/ severe microphthalmia, with pulmonary hypoplasia/ aplasia] LEPRE1 (Leucine-and proline-enriched proteoglycan 1)syn. PH31(prolyl-3-hydroxylase-1) Type VIII Osteogenesis Imperfecta, Variable phenoptype of bone fragility, susceptibility to fracture, short stature, bowing of the long bones and can be perinatally lethal. ATP8B1 (ATPase, Class I, Type 8B, Member1) Progressive Familial Intrahepatic Cholestasis type 1 (PFIC1) syn. Byler disease Hepatic and systemic accumulation of bile acids, hepatic fibrosis, end-stage liver disease and growth retardation. This study will detail (1) the service offered to users, (2) an audit of the test requests received over the last two years, (3) the challenges encountered in offering this unique service and (4) some interesting family pedigrees., Background Hypoxia in prostate tumours has been linked with promotion of disease progression and metastasis. miR-210 is a microRNA which is apparently affected by hypoxia, but this relationship has not been extensively studied in a prostate cancer setting. Therefore, in this study, we investigate the link between hypoxia and miR-210 in prostate cancer cells. Methods We have used 2D and 3D cell prostate cell models of hypoxia to investigate the functionality of miR-210. Expression levels of miR-210 have been measured by qPCR and functional bioassays used to examine its effect on prostate cell behaviour. Target genes have been identified and bioinformatic analysis has been employed to investigate a clinical significance for miR-210 in prostate cancer. Results miR-210 is induced by hypoxia in prostate cancer cell-lines. Over-expression of miR-210 impacts upon target genes, including SP1 and TPD52, which in turns affects cell proliferation. Data-mining of online repositories of clinical data and bioinformatic analysis of miR-210 cellular networks reveal that miR-210 plays a key role in a number of important cell processes, the dysregulation of which can lead to development of prostate cancer. Conclusions We propose that miR-210 could be an important microRNA in the pathogenesis of prostate cancer and has potential as a biomarker in this disease.

To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology. ispartof: Nature Genetics vol:48 issue:9 pages:1037-+ ispartof: location:United States status: published

The most recent genome-wide association study in amyotrophic lateral sclerosis (ALS) demonstrates a disproportionate contribution from low-frequency variants to genetic susceptibility to disease. We have therefore begun Project MinE, an international collaboration that seeks to analyze whole-genome sequence data of at least 15 000 ALS patients and 7500 controls. Here, we report on the design of Project MinE and pilot analyses of successfully sequenced 1169 ALS patients and 608 controls drawn from the Netherlands. As has become characteristic of sequencing studies, we find an abundance of rare genetic variation (minor allele frequency < 0.1%), the vast majority of which is absent in public datasets. Principal component analysis reveals local geographical clustering of these variants within The Netherlands. We use the whole-genome sequence data to explore the implications of poor geographical matching of cases and controls in a sequence-based disease study and to investigate how ancestry-matched, externally sequenced controls can induce false positive associations. Also, we have publicly released genome-wide minor allele counts in cases and controls, as well as results from genic burden tests.

NIPA1 (nonimprinted in Prader-Willi/Angelman syndrome 1) mutations are known to cause hereditary spastic paraplegia type 6, a neurodegenerative disease that phenotypically overlaps to some extent with amyotrophic lateral sclerosis (ALS). Previously, a genomewide screen for copy number variants found an association with rare deletions in NIPA1 and ALS, and subsequent genetic analyses revealed that long (or expanded) polyalanine repeats in NIPA1 convey increased ALS susceptibility. We set out to perform a large-scale replication study to further investigate the role of NIPA1 polyalanine expansions with ALS, in which we characterized NIPA1 repeat size in an independent international cohort of 3955 patients with ALS and 2276 unaffected controls and combined our results with previous reports. Meta-analysis on a total of 6245 patients with ALS and 5051 controls showed an overall increased risk of ALS in those with expanded (>8) GCG repeat length (odds ratio = 1.50, p = 3.8×10-5). Together with previous reports, these findings provide evidence for an association of an expanded polyalanine repeat in NIPA1 and ALS.

Objective: After the initial report of a CHCHD10 mutation in mitochondrial disease with features resembling amyotrophic lateral sclerosis (ALS), CHCHD10 mutations have been considered to be a frequent cause for ALS. However, the exact pathogenicity and clinical significance of these mutations remain unclear. Here, we aimed to determine the role of CHCHD10 mutations in ALS.\ud Methods: We analyzed 4,365 whole genome sequenced ALS patients and 1,832 controls from 7 different countries and examined all nonsynonymous single nucleotide variants in CHCHD10. These were tested for association with ALS, independently and in aggregate using several genetic burden tests (including sequence kernel association test [SKAT], optimal unified test \ud [SKAT-O], and Firth logistic regression).\ud Results: We identified 3 new variants in cases, but only 1 was ALS-specific. lso, 1 control-specific mutation was identified. There was no increased burden of rare coding mutations among ALS patients compared to controls \ud (p=0.86, p=0.86, and p=0.88 for SKAT, SKAT-O, and Firth, respectively). The few carriers with potential pathogenic CHCHD10 mutations exhibited a slowly progressive ALS-like phenotype with atypical features such as myopathy and\ud deafness. \ud Interpretation: CHCHD10 mutations seem to be a far less prevalent cause of pure ALS than previously suggested, and instead appear related to more complex phenotypes. There appears to be insufficient evidence for the pathogenicity of most previously reported variants in pure ALS. This study shows that routine testing for CHCHD10 mutations in pure ALS is not recommended and illustrates the importance of sufficient genetic and functional evidence in establishing pathogenicity of genetic variants.

© 2018 American Neurological Association Objective: After the initial report of a CHCHD10 mutation in mitochondrial disease with features resembling amyotrophic lateral sclerosis (ALS), CHCHD10 mutations have been considered to be a frequent cause for ALS. However, the exact pathogenicity and clinical significance of these mutations remain unclear. Here, we aimed to determine the role of CHCHD10 mutations in ALS. Methods: We analyzed 4,365 whole genome sequenced ALS patients and 1,832 controls from 7 different countries and examined all nonsynonymous single nucleotide variants in CHCHD10. These were tested for association with ALS, independently and in aggregate using several genetic burden tests (including sequence kernel association test [SKAT], optimal unified test [SKAT-O], and Firth logistic regression). Results: We identified 3 new variants in cases, but only 1 was ALS-specific. Also, 1 control-specific mutation was identified. There was no increased burden of rare coding mutations among ALS patients compared to controls (p = 0.86, p = 0.86, and p = 0.88 for SKAT, SKAT-O, and Firth, respectively). The few carriers with potential pathogenic CHCHD10 mutations exhibited a slowly progressive ALS-like phenotype with atypical features such as myopathy and deafness. Interpretation: CHCHD10 mutations seem to be a far less prevalent cause of pure ALS than previously suggested, and instead appear related to more complex phenotypes. There appears to be insufficient evidence for the pathogenicity of most previously reported variants in pure ALS. This study shows that routine testing for CHCHD10 mutations in pure ALS is not recommended and illustrates the importance of sufficient genetic and functional evidence in establishing pathogenicity of genetic variants. Ann Neurol 2018;83:110–116. ispartof: Annals of Neurology vol:84 issue:1 pages:110-116 ispartof: location:United States status: published

Background: Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive, fatal motor neuron disease with a variable natural history. There are no accurate models that predict the disease course and outcomes, which complicates risk assessment and counselling for individual patients, stratification of patients for trials, and timing of interventions. We therefore aimed to develop and validate a model for predicting a composite survival endpoint for individual patients with ALS. Methods: We obtained data for patients from 14 specialised ALS centres (each one designated as a cohort) in Belgium, France, the Netherlands, Germany, Ireland, Italy, Portugal, Switzerland, and the UK. All patients were diagnosed in the centres after excluding other diagnoses and classified according to revised El Escorial criteria. We assessed 16 patient characteristics as potential predictors of a composite survival outcome (time between onset of symptoms and noninvasive ventilation for more than 23 h per day, tracheostomy, or death) and applied backward elimination with bootstrapping in the largest population-based dataset for predictor selection. Data were gathered on the day of diagnosis or as soon as possible thereafter. Predictors that were selected in more than 70% of the bootstrap resamples were used to develop a multivariable Royston-Parmar model for predicting the composite survival outcome in individual patients. We assessed the generalisability of the model by estimating heterogeneity of predictive accuracy across external populations (ie, populations not used to develop the model) using internal–external cross-validation, and quantified the discrimination using the concordance (c) statistic (area under the receiver operator characteristic curve) and calibration using a calibration slope. Findings: Data were collected between Jan 1, 1992, and Sept 22, 2016 (the largest data-set included data from 1936 patients). The median follow-up time was 97·5 months (IQR 52·9–168·5). Eight candidate predictors entered the prediction model: bulbar versus non-bulbar onset (univariable hazard ratio [HR] 1·71, 95% CI 1·63–1·79), age at onset (1·03, 1·03–1·03), definite versus probable or possible ALS (1·47, 1·39–1·55), diagnostic delay (0·52, 0·51–0·53), forced vital capacity (HR 0·99, 0·99–0·99), progression rate (6·33, 5·92–6·76), frontotemporal dementia (1·34, 1·20–1·50), and presence of a C9orf72 repeat expansion (1·45, 1·31–1·61), all p

The aim of this thesis was to identify new genetic susceptibility factors, describe the genetic architecture of ALS and explore the utility of gene expression profiles as a biomarker for ALS. Following the technical advances over time, this thesis includes single gene studies, genome-wide associations studies (GWAS), transcriptome analyses and whole genome sequencing studies. Leveraged together, they have led to several conclusions and perspectives.

© 2017 The Author(s). We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05-21.6; P=1 × 10-4) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10-7). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08-1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies.

Copyright © 2014, BMJ Publishing Group Ltd. All rights reserved. This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/3.0/, Background: The GGGGCC-repeat expansion in C9orf72 is the most frequent mutation found in patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Most of the studies on C9orf72 have relied on repeat-primed PCR (RP-PCR) methods for detection of the expansions. To investigate the inherent limitations of this technique, we compared methods and results of 14 laboratories. Methods: The 14 laboratories genotyped DNA from 78 individuals (diagnosed with ALS or FTD) in a blinded fashion. Eleven laboratories used a combination of amplicon-length analysis and RP-PCR, whereas three laboratories used RP-PCR alone; Southern blotting techniques were used as a reference. Results: Using PCR-based techniques, 5 of the 14 laboratories got results in full accordance with the Southern blotting results. Only 50 of the 78 DNA samples got the same genotype result in all 14 laboratories. There was a high degree of false positive and false negative results, and at least one sample could not be genotyped at all in 9 of the 14 laboratories. The mean sensitivity of a combination of amplicon-length analysis and RP-PCR was 95.0% (73.9-100%), and the mean specificity was 98.0% (87.5-100%). Overall, a sensitivity and specificity of more than 95% was observed in only seven laboratories. Conclusions: Because of the wide range seen in genotyping results, we recommend using a combination of amplicon-length analysis and RP-PCR as a minimum in a research setting. We propose that Southern blotting techniques should be the gold standard, and be made obligatory in a clinical diagnostic setting., This project was funded by the Swedish Science Council, the Brain Research Foundation, Mr B Hållsten's Brain Research Foundation, The Ulla-Carin Lindquist's Fundation for ALS Research, the Knut and Alice Wallenberg Foundation, Swedish Brain Power, the European Community's Health Seventh Framework Programme (FP7/2007–2013) (grant agreement no. 259867), The Belgian Science Policy Office Interuniversity Attraction Poles (IAP) programme, the Flemish Government supported Europe Initiative on Centers of Excellence in Neurodegeneration (CoEN), the Flemish Government initiated Methusalem excellence research programme, Alzheimer Research Foundation, the Medical Foundation Queen Elisabeth, the Research Foundation Flanders (FWO) and the FWO provided a postdoctoral scientist fellowship to JvdZ, University of Antwerp Research Fund, the Swiss ALS Foundation, the Italian Ministry of Health (RF-2009-1473856), Grant-in-Aid for the Research Committee of CNS Degenerative Diseases and Comprehensive Research on Disability Health and Welfare from the Ministry of Health, Labour and Welfare in Japan and Dr Van Blitterswijk is supported by the Milton Safenowitz Post-Doctoral Fellowship for ALS research from the ALS Association.

Item does not contain fulltext Previously, we have reported amyotrophic lateral sclerosis (ALS) families with multiple mutations in major ALS-associated genes. These findings provided evidence for an oligogenic basis of ALS. In our present study, we screened a cohort of 755 sporadic ALS patients, 111 familial ALS patients (97 families), and 765 control subjects of Dutch descent for mutations in vesicle-associated membrane protein B (VAPB). We have identified 1 novel VAPB mutation (p.V234I) in a familial ALS patient known to have a chromosome 9 open reading frame 72 (C9orf72) repeat expansion. This p.V234I mutation was absent in control subjects, located in a region with high evolutionary conservation, and predicted to have damaging effects. Taken together, these findings provide additional evidence for an oligogenic basis of ALS.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons., Dutch Research Council (NWO); VENI Scheme Grant; VIDI Grant; Prinses Beatrix Spierfonds; Neuromuscular Fellowship Grant; Medical Research Council (MRC); Clinical Infrastructure Award; Epidemiology Unit; Integrative Epidemiology Unit; Canadian Institutes of Health Research; IWT; National Institute on Aging; National Health and Medical Research Council (NHMRC); Enabling Grant; NHMRC/Australian Research Council Strategic Award; NHMRC; NHMRC Centre of Research Excellence Grant; National Health and Medical Research Council of Australia (NHMRC) Research Fellowship; United Kingdom, Medical Research Council; Economic and Social Research Council; European Union (EU); Horizon 2020; European Community's Health Seventh Framework Programme; EuroMOTOR; European Research Council (ERC); Research and Innovation Programme; EScORIAL; ALS Foundation Netherlands; Alzheimer’s Society PhD Studentship; ARSla Funding; Biogen; University of Bristol; Motor Neurone Disease Association (MNDA); NIHR Maudsley Biomedical Research Centre; Dutch Ministry of Education, Culture, and Science; Netherlands Organization for Scientific Research (NWO; BRAINSCAPES); Gravitation Program; ALS Liga België; National Lottery of Belgium; KU Leuven Opening the Future Fund; KU Leuven Funds, “Een Hart voor ALS”, “Laeversfonds voor ALS Onderzoek” and the “Valéry Perrier Race against ALS Fund”; E. von Behring Chair for Neuromuscular and Neurodegenerative Disorders; ALS Liga België; “Live now” Charity Foundation; Moscow ALS palliative Care Service; Canadian Institutes of Health; Research Australia; Ice Bucket Challenge Grant; NIH Intramural Research Programs; FightMND Mid-Career Fellowship; NIHR Senior Investigator; Sheffield NIHR Biomedical Research Centre; Motor Neurone Disease Association; National Institute for Health Research (NIHR) Biomedical Research Centre; Maudsley NHS Foundation Trust; King’s College London; NIHR Senior Investigator Award; Netherlands Organization for Health Research and Development; Vici Scheme; Netherlands Organization for Health Research and Development STRENGTH Project; PPP Allowance