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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.

Neurofibromatosis (NF1) affects 1/2500 people throughout the world. Children with NF1 require a multidisciplinary service ideally, delivered on a single site. NF1 is a very variable condition with children requiring the expertise of genetics, paediatricians, ophthalmologists, dermatologists, neurologists and other specialities as required. Building such a service concentrates expertise, facilitates coordination of care and fosters ideal opportunities for research. Aims: 1) To develop a service ensuring children had access to a multidisciplinary clinic on an annual basis. 2) Hold monthly clinics offering ophthalmology, medical, developmental and dermatology follow up. 3) To create a registry of patients which captures the incidence and prevalence of NF1 in Ireland. To offer best possible care for the children attending the service by following international consensus guidelines. 4) To liaise with NF1 Association, families and research authorities. Methods: 1) Appointment of a CNS/CNM2 in Neurofibromatosis as funded by the NCH Foundation. 2) Visit to the complex NF1 Clinic in Manchester’s Children’s Hospital and learn from their service, MDT and guidelines. 3) Establish links with genetics, oncology, radiology and orthopaedic depts. in OLCHC. 4) Create a referral pathway for HCPs to ensure children with NF1 are referred to most appropriate service in a timely fashion. 5) To register the service on Orphanet and gain entry into an ERN as a multi-site service in conjunction with OLCHC. Results/Conclusion: To date, the service has been running for 9 months. The CNM2 provides telephone service and coordinates clinics. The Clinic has been registered in Orphanet and the process has begun to create a patient registry and enter the service in the ERN., Germline mutations in the succinate dehydrogenase subunit genes SDHB, SDHC and SDHD are the most frequent causes of inherited phaeochromocytomas and paragangliomas. Patients presenting with these tumours are usually offered genetic testing for these and other genes as part of standard clinical investigations. However, the information regarding penetrance and phenotype genotype correlations associated with SDHB/C/D mutations is variable, making it difficult to determine an optimum management strategy for this group. In order to address this issue we undertook a retrospective cohort study of patients who underwent genetic testing for SDHB, SDHC or SDHD. 195 patients were identified through the Irish Genetics laboratory electronic database as having had a genetic test for SDHB, SDHC or SDHD and referral source, referral reason and genetic test outcome were analysed. Analysis of penetrance and phenotype presentation was determined through a Clinical Genetics chart review of 147 patients from 40 separate families. Analysis of age-related tumour risks according to relevant gene and mutation type (for SDHB and SDHD) provided estimates of penetrance and genotype-phenotype correlations. Increased knowledge of the molecular basis of phenotypic variability commonly observed in individuals with germline SDHB/C/D mutations will facilitate the development of age-appropriate management protocols based on gene specific tumour risks., Irish Travellers are an endogamous, ethnically Irish population of ~40,000. Consanguinity is common. Knowledge of Traveller disorders exists but mainly in specialised Irish centres. Most Traveller disorders are published but ethnicity is not explicit, hampering diagnoses, particularly if the patient is overseas where knowledge about this population is poor. Aims: To catalogue inherited Irish Traveller disorders through identifying the disorders, detailing mutations, use of coding, (OMIM, Orphacodes & ICD10), publications, and help develop a database to facilitate diagnoses. Methods: A literature review was undertaken. Key national and international Clinician/scientists were contacted to identify relevant disorders and publications. Laboratory and clinical databases were searched to retrieve disorders & mutations. Annotations were updated. An Excel database was established listing each disorder, its appropriate code, associated mutation and relevant publication. Results: 86 distinct rare genetic disorders resulting in 75 phenotypes were identified; 78/86 were autosomal recessive; 4 of these were dominant disorders presenting only in the recessive state. Seven dominant disorders with no recessive phenotype were included as > one affected individual existed. One common 17q12 duplication was included, presenting in two unrelated families. Homozygous mutations were found in all recessive disorders bar one. The genetic basis of 78/86 was established. A further 2/76 have common haplotypes; the genetic basis of six disorders remains unclear. Linkage disequilibrium was observed in 4 families with co-existing McArdles disease and microcephaly & 11 individuals have co-existing Friedreich’s ataxia & galactosemia. Conclusion: Our work is the first step towards cataloguing inherited Irish Traveller disorders. Future challenges include development of an online mutation database., Primary Trimethylaminuria (TMA)(OMIM 136132), is an autosomal recessive rare disorder which results in diminished capacity to oxidise the dietary derived amine trimethylaminuria to its odourless metabolite Trimethylamine-n-oxide (TMA-n-Oxide). Severe primary TMA has been defined as the percentage of unmetabolised free TMA in urine being >40% and mild/moderate TMA range is 10-39%. More than 30 variants of the Flavin monooxygenase 3 (FMO3) have been reported to cause primary TMA. Diagnosis of primary TMA has implications for management of the patient in relation to treatment and genetic counselling. We sequenced the entire FMO3 gene coding region in 10 patients who had a biochemical diagnosis of TMA made in the past 5 years. Three of the patients had severe TMAU (% TMA range 39.4 to 45), (Group A) and 7 had mild to moderate TMAU (%TMA range 10-30), (Group B). We identified causative (loss of function) in 5/10 individuals. Homozygosity for loss of function mutations was detected for 2/3 cases with severe TMAuria (Group A). 3/7 of the patients with mild to moderate TMAuria biochemically had a genetic diagnosis. Two were homozygous for Glu158Lys/ Glu308Gly and the other was compound heterozygous for P153L and A232T. Primary TMAU is rare in Ireland and mutational analysis should not replace biochemical diagnosis.The rate of detection of pathogenic mutations was low using the recommended biochemical cut-offs. The E305X mutation the first FMO3 mutation described in OMIM (136132.0001) in an Irish Australian family may be an Irish Mutation. Two new apparent FMO3 mutations are described in this Irish population. A cut- off of free TMA levels higher than that suggested on the Gene Utility card may be more beneficial in directing genotyping., Background: As part of the Irish Kidney Gene project, 2000 people with renal disease were surveyed and >30% of participants reported a family history for their condition. This strongly suggests an underlying genetic component for the development of kidney disease. Blood and urine tests as well as kidney biopsies are frequently used to inform on aetiology of the disease. However, in around 10% of cases, aetiology is simply unknown, making it difficult for physicians to provide a clear diagnosis or prognosis to these patients. Aim: This project aims to utilise genomic sequencing to stratify patients with hereditary renal disease (HRD). In doing so we seek to aid clinical diagnosis, provide insight into pathogenesis and in some cases point to specific therapies. Methods: We developed a custom, targeted NGS panel for inherited kidney diseases which we have applied to 48 HRD patients. The panel includes 11 genes which are established causes of polycystic kidney disease, von Hippel Lindau syndrome, renal cysts and diabetes syndrome and Alport syndrome. The NimbleGen Heat-Seq kit was used for library preparation and samples were sequenced using an Illumina MiSeq platform at Beaumont Hospital. Data was analysed using a custom bioinformatics pipeline and variants were classified according to the ACMG guidelines. Results/Conclusions: To date, this panel has identified candidate pathogenic variation in a third of samples studied. Future work in this project will include the development of a larger targeted panel including >100 known renal disease genes., Breast cancer is the most common female malignancy worldwide. Up to 10% of cases are the result of an inherited monogenic mutation, while a further 25% appear in familial clusters. Only 30% of hereditary breast cancers are attributed to mutations in BRCA1 and BRCA2, identified as high-risk genes through linkage analysis. While BRCA mutational status is highly informative, and allows clinicians to modify surveillance, prevention and therapeutic strategies, the risk conferred by mutations in other genes is more difficult to define in light of variable penetrance. Next-generation sequencing has been rapidly evolving to advance testing sensitivity and throughput in a cost-effective manner. This progression has made multi-gene testing a practical option when looking to identify inherited mutation(s) in a clinical setting. However, current clinically available multi-gene panels generate many variants of unknown significance in genes that are presently not considered clinically useful. The aim of our study was to design a multi-gene panel to enable the detection of rare, probably pathogenic variants contributing to the susceptibility of breast cancer in an Irish population. An extensive literature review was conducted in order to generate a list of 282 genes with potential association to breast cancer. Targeted DNA enrichment and multiplexed next-generation sequencing was performed on a cohort of 167 samples from the west of Ireland. 90 breast cancer patients and 77 geographically-matched controls were included in this study. Bioinformatic analysis was performed following GATK best practices workflow. Variant data for our 282 selected genes will be presented and discussed., Increasingly accurate surveys of human health throughout the life course has led experts to propose that stresses on the developing child whilst in the mother’s womb can affect the individual’s health later in life. Such long-term effects on health are thought to be mediated by a semi-permanent trace on the genes called an epigenetic mark, mediated by processes such as DNA methylation. DNA methylation patterns may be altered by the mother’s diet, particularly folate – a key component in the DNA methylation cycle. Currently, mothers are recommended to supplement their diet with 400μg folic acid/day as a preventative measure against neural tube defects prior to/during the first trimester. However, there remains no clinical recommendation as to whether mothers should continue supplementation during the latter two trimesters and the potentially heritable effects. Thus, we analysed cord blood samples (n=93) from the Folic Acid Supplementation in the Second and Third Trimesters (FASSTT) randomised control trial for genome-wide DNA methylation. Offspring exposed to folic acid in later pregnancy had fewer highly methylated genomic regions and more intermediately methylated sites. Upon further interrogation, gene ontology analysis revealed these sites are enriched for genes associated with cognition and neurological system processes, and tissue analysis revealed enrichment of affected genes associated with the brain. Cognitive and psychosocial testing of the children at age 7 years, using standardised tests (WPPSI, TEIQue-CSF, RASP), showed that the children supplemented during pregnancy scored significantly higher for emotional intelligence, resilience and verbal IQ. Thus, this study offers a potential biological mechanism linking maternal folate levels with childhood cognition., Introduction: We previously identified the mitochondrial 10-formyltetrahydrofolate synthase enzyme, MTHFD1L, as a risk factor for human Neural Tube Defects (NTD). This association was further supported by a mouse model of mutant mthfd1l, that exhibited an NTD and was rescued with maternal formate supplementation. The abundance of MTHFD1L is also increased in a range of cancers. MTHFD1L performs the last step in mitochondrial one carbon metabolism to produce formate for transport into the cytoplasm. Aim: Given the pivotal role of MTHFD1L in human disease, we sought to decipher the cellular response to the expression level of MTHFD1L in HEK293 cells. Methods: Human MTHFD1L was overexpressed in a stably transfected line using a pcDNA3.2 vector and knocked down using two inducible shRNA constructs that were clonally selected. Cells were grown and sampled over a five-day period. Expression level was confirmed by RT-qPCR. Intracellular and media formate levels were measured using GC-MS. Proteomics analysis was performed on whole cell lysates using LC-MS/MS on an Ultimate 3000 nano LC system coupled to a LTQ Orbitrap XL. Results: Intracellular and media formate levels directly correlated with expression level of MTHFD1L compared to controls within an approximately 1.5 to 3 fold range. Our proteomics analysis showed that MTHFD1L expression level had an effect on proteins involved in DNA synthesis, replication and repair. Discussion: We have demonstrated that MTHFD1L expression level has a direct impact on both intra- and extra-cellular levels of formate and may act as a signal for uncontrolled cell proliferation., Ireland has remained relatively isolated from mainland Europe, notwithstanding historical migrations including the Norse-Vikings, Anglo-Normans, and the British Plantations. Although previous studies have shown the Irish to have elevated levels of homozygosity compared to mainland Europe, the extent of genetic structure within Ireland, and the genomic impact of historical migrations, is largely unknown. Here we illustrate fine-scale genetic structure across Ireland that follows sociological boundaries and present evidence of admixture events into Ireland. Utilising the ‘Irish DNA Atlas’, a DNA cohort (n = 194) of genealogically described Irish individuals with four generations of ancestry linked to specific regions in Ireland, we analysed in combination with 2,039 individuals of regional British ancestry (the PoBI dataset) and show that the Irish population subdivides into 10 distinct geographically-stratified genetic clusters; three of shared British/Irish ancestry, and seven of predominantly ‘Gaelic’ Irish ancestry. This structure is remarkably homogenous, and is associated with very little gene flow barriers within Ireland. Additionally, using a reference of 6,760 European individuals and two ancient Irish genomes, we quantified the ancestry of these Irish clusters within the context of Europe as well as ancient Ireland. We show high levels of north-west French-like and Norwegian-like ancestry within Ireland, and homogenous levels of ancient Irish ancestry in our ‘Gaelic’ Irish clusters. Finally we detect admixture events into Ireland, coinciding with the Plantations of Ulster, as well as Norse-Viking activity within Ireland. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry., Schizophrenia affects 1% of adults and is a major global health problem. I am interested in the potential role of the centrosome in schizophrenia. The centrosome, an organelle within cells, plays a crucial role in brain development where it directs cell shape, polarity and motility. The centrosome also seeds the growth of antenna-like signalling structures called primary cilia. Rare mutations in centrosome genes cause disorders that present with severe cognitive deficits and variable neuropsychiatric phenotypes. GWAS data has implicated many genes in schizophrenia. We have shown that seven schizophrenia risk genes encode proteins with centrosomal functions. Of these, SDCCAG8 is also associated with educational attainment in GWAS and the genome-wide significant SNPs for the two phenotypes are in high linkage disequilibrium indicating a pleiotropic effect. We have found that a schizophrenia risk SNP in SDCCAG8 is significantly associated with poorer performance in a social cognition task, in a large Irish dataset of schizophrenia patients and controls (p=0.001). To analyse the molecular function of SDCCAG8 we have used genome editing to knock it out in neuronal and retinal cells. Preliminary data shows that loss of SDCCAG8 impairs cells’ ability to make primary cilia and that their capacity to repair genome damage is reduced. Current work is addressing whether SDCCAG8 affects activities that may contribute to schizophrenia, including cell migration and cell signalling. This could identify molecular mechanisms by which SDCCAG8 mutations contribute to schizophrenia risk and cognition, and help uncover the processes that implicate centrosome genes in neurodevelopmental phenotypes., Multiple genetic loci have been identified for non-melanoma skin cancer (NMSC) in the general population. Polygenic risk score (PRS) was defined as the sum of all alleles associated with a trait weighted by the effect size of that allele as determined by a previous genome-wide association study (GWAS). We tested whether PRS, calculated using a GWAS of NMSC in a non-transplant population, can be used to determine risk of developing and time to NMSC post-transplant. Post-kidney transplant NMSC cases (n=155) and controls (n=442) were collected from Tennessee, Ireland and Scotland. Genetic variants that reached pre-defined levels of significance were chosen from a squamous cell carcinoma (SCC), and basal cell carcinoma (BCC) GWAS, both conducted in non-transplant populations. Using these GWAS results, BCC and SCC PRSs were calculated at each p-value threshold (pT) for each sample. PRSs were tested as a predictor of case:control status using logistic regression and time to NMSC post-transplant in a survival model. SCC PRS calculated at pT 1x10-6 was the most significant predictor of case: control status of NMSC post-transplant (OR per 1 stdev increase in PRS=2.3; corrected P (Pc)=0.04). When NMSC was subdivided into SCC and BCC, SCC PRS pT 1x10-6 significantly predicted case:control SCC (OR=2.5, Pc=0.02) and BCC status (OR=7.6, Pc=0.02). SCC PRS pT 1x10-5 also significantly predicted time to BCC (Pc=0.007, HR=1.8) and SCC (Pc=0.05, HR=1.4). PRS of non-transplant NMSC can be used to predict case:control status of post-transplant NMSC, SCC and BCC as well as time to developing BCC and SCC post-transplant., Introduction: Rare diseases are diseases, which affect a small number of people compared to the general population. In Europe, a disease is considered rare when it affects no more than 5 per 10,000 individuals. A disease can be rare in one region but common in another. The objective of this study was to derive a proxy estimate the number of childhood onset rare diseases through referrals to the country’s only Genetics center, as the Republic of Ireland does not have a centralized rare disease registry. Methods: A retrospective review of referrals to cytogenetics and clinical genetics for the years 2000-2016 for patients born in the year 2000 was undertaken. Anonymized data was catalogued into rare, common, normal, likely rare & unclassifiable by review of records, and assigned Orphacodes based on diagnosis. Census live birth data was used as the denominator. Results: 54,7891 live births were recorded by the census in 2000. 1872 referrals to Genetics (representing 1749 individuals born in 2000) were retrieved for review. 1007 had cytogenetic testing only, of which 51 had rare chromosomal anomalies. Review of 742 referrals to clinical genetics yielded 581 with a rare disease (78%), 7 with a likely rare disease, 56 with a common disorder, 83 who were normal (at risk relative) & 15 unclassified (hadn’t yet been seen). Of the 53/1749 who had died (3%), 51 had a rare disease with congenital malformations (24) the most common cause., Neurofibromatosis type 1 (NF1) is a relatively common autosomal dominant genetic condition, with an incidence of around 1 in 3000. All NF1 patients attend our regional NF1 clinic intermittently and our departmental database records clinical details. Currently, we have 468 living patients affected with NF1 in Northern Ireland. NF1 is caused by mutations, or occasionally deletions, of the neurofibromin tumour suppressor gene, which leads to over-activation of the RAS-MAPK pathway, and tumour formation. These vary from benign lesions, such as neurofibromas, through to malignant peripheral nerve sheath tumours (MPNSTs) and tumours in other sites, particularly the central nervous system, that can be associated with significant morbidity and mortality. MEK inhibitors have recently been shown to be an effective treatment modality in the tumours associated with NF1. We have studied our population to determine the number of patients with plexiform neurofibromas, who are at risk of MPNSTs, and the proportions of patients with tumours elsewhere. This will allow us to identify which patients could benefit from MEK inhibitors in the future., Tuberous Sclerosis complex (TSC) is an autosomal dominant genetic condition which results, in the majority of patients, from a mutation in the TSC1 or TSC2 genes. Many of the patients are affected by angiomyolipomas and sub-ependymal giant cell astrocytomas. There is evidence that mTOR inhibitors, particularly Everolimus, shrink such tumours. In addition, the recent EXIST-3 study showed that Everolimus led to a significant reduction in seizure frequency in TSC patients whose seizures had previously proved resistant to anti-epileptic drug treatment. Consequently, a European licence has been granted to prescribe Everolimus for this indication. In order to determine the potential number of patients who may be eligible for consideration of this treatment, we undertook a complete population survey of epilepsy in our TSC patients. Information was extracted from our database and descriptive statistics were carried out. We were particularly interested in obtaining numbers of those whose seizures were poorly-controlled, defined as requiring 3 or more anti-epileptic drugs to manage their seizures, or requiring neurosurgical intervention. Many of the TSC patients with a diagnosis of epilepsy were also diagnosed with learning difficulties. The possibility of an association between degree of seizure control and severity of learning difficulties was explored. Finally, the annual cost of prescribing Everolimus to Northern Ireland’s TSC patients with poorly-controlled seizures was estimated., Charcot neuroarthropathy is associated with neurological deficit and is often seen in patients with a history of diabetes. Zygodactyly is a common congenital malformation with cutaneous webbing of the second and third toes. To determine the frequency of Zygodactyly in midfoot (tarso-metatarsal) Charcot neuropathy due to diabetes, we analysed a prospective series of twenty-five patients with Charcot neuropathy referred to podiatry clinics from diabetes and vascular departments. Twenty-nine patients with diabetes (but no Charcot neuropathy) were used as controls. Nineteen of the twenty-five patients with type 2 diabetes, peripheral neuropathy, and midfoot Charcot neuroarthropathy, exhibited Zygodactyly as did one of the twenty-nine controls. There was a significant difference between the two groups (Chi squared test p< 0.001). None of the cases or controls had any dysmorphic features or other limb malformations. Zygodactyly occurred in association with midfoot Charcot neuroarthropathy (diabetic neuropathy) in 76% of cases. No association between Zygodactyly, diabetes and Charcot neuropathy has previously been recognised. Genes such as OPG and RANKL affect foot and bone development and MSX1 and PLA2G6 affect spinal and distal nerve development. The possibility of a genetic contribution in patients who develop type 2 diabetes, peripheral neuropathy and Charcot neuroarthropathy must be considered. Zygodactyly may act as a predictive marker for Charcot neuropathy and further identification of regulatory genes may be possible. Until then, recognition of Zygodactyly may allow early intervention and a reduction of complications in patients with Charcot neuropathy., Development of an unusual clinical phenotype across both common and rare cancer types presents a significant challenge from a diagnostic and therapeutic perspective. We describe two distinct cases involving an Ovarian adenocarcinoma and a Medullary Thyroid cancer (MTC) patient and wherein both patients presented with metastases at highly unusual locations, followed by development of an aggressive disease. In first case involving a patient diagnosed with ovarian adenocarcinoma presented with a rare solitary extracranial brain metastases with no other associated metastases after 2 years post-hysterectomy and chemotherapy. Despite surgical removal of the metastatic lesion and stereotactic radiotherapy, the patient showed a further relapse at the initial as well as two additional extracranial regions. Our current analysis of whole-genome sequencing of primary tumour and extracranial lesion, reveal a remarkable difference in the genomic aberration landscape between the primary tumour and the metastases. In addition, we also identify several structural variants including novel gene fusions as well as gross chromosomal abnormalities, which could be potentially utilized as targets for treating this patient further. In the second case, whole-exome sequencing of primary tumour and bone-marrow metastases in the MTC patient identified three germline single nucleotide polymorphisms (SNPs) within the RET proto-oncogene that remained undetected using routine hospital genetic testing procedures. More importantly, we report for the first time in thyroid cancer on the occurrence of a “chromothripsis-like pattern”, which involved shattering of chromosome 4 leading to complete abrogation of normal chromosomal function, along with dramatic widespread copy number aberrations across both primary tumour and bone marrow samples. These results provide a rationale for the application of comprehensive genomic analysis of cancers presenting with unusual and aggressive phenotypes to facilitate more appropriate therapeutic options and diagnoses., Transient Neonatal Diabetes (TNDM) is characterised by diabetes that develops in the first 6 weeks of life and resolves by 18 months. Approximately 70% of cases are classified as TNDM Type-1 (TNDM1), caused by methylation defects on chromosome 6q24. It is associated with some congenital anomalies, however associated hepatobiliary abnormalities are not described. Choledochal cysts are congenital dilations of part or all of the bile duct, occurring in 100,000-150,000 live births. The 5 major types are classified according to the extent of hepatobiliary involvement. Surgical excision of the cyst is indicated to prevent complications such as stone formation, malignancy, cyst rupture and pancreatitis. We describe a case of TNDM1 due to whole chromosome paternal uniparental disomy 6, with co-existence of a type 1a choledochal cyst in a female born following intrauterine growth retardation. Hyperglycaemia soon after birth led to insulin treatment and a diagnosis of TNDM1, with resolution of the diabetes by 4 months of life. Follow up of antenatal findings of a cystic anomaly demonstrated the presence of a type 1a choledochal cyst on ultrasound and magnetic resonance cholangiopancreatography. Sucessful surgical excision of the cyst and a roux-en-Y hepaticojejunostomy was undertaken at 6 months of age. To our knowledge the co-existence of these disorders has not previously been reported. Further genetic analysis by whole exome sequencing is now in progress to determine if a mutation in the PKHD1 gene, unmasked by the paternal UPD of the entire chromosome 6, explains the associated choledochal cyst in this case., Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted as constitutional variants to future generations. Marfan syndrome (MFS) is a clinically variable systemic connective tissue disorder involving ocular, skeletal, and cardiovascular systems. The risk to siblings of an identified de novo variant in a proband remains above population risk but less than the 50% risk attributed probands (~75%) who have an affected parent. This is due to somatic and germline mutations reported in rare cases. We describe the phenotypic variability in three siblings with a confirmed heterozygous pathogenic exon 52 fibrillin1 (FBN1) gene variant with clinically unaffected parents Parental leucocyte DNA was tested and did not identify the FBN1 gene variant. Paternity has been unequivocally confirmed and subsequent testing of parental buccal samples failed to detect the variant. One brother had aortic valve replacement and aortic aneurysm repair at 35 while another brother had surgery of aortic dilatation at the sinuses of Valsalva at 32. The brothers had variable joint hypermobility, patellar dislocations and ophthalmic presentations involving subluxed lenses, myopia and ambylopia. Early onset of varicose veins as a teenager in one and thoracolumbar scolosis in another brother were present. Their 42 year old sister has apparently normal aortic and cardiac imaging and ophthalmology but has mild Marfanoid facial features. To our knowledge this is the first reported family in the literature of 3 siblings as a result of parental mosaicism for a FBN1 gene variant and highlights the impact for genetic counselling., The inherited retinal degeneration (IRD) patient cohort used in the study has been obtained via a collaborative network of opthamoloogists whereby if an IRD is suspected given consent, a DNA sample is taken and provided to a central laboratory for genetic analysis. The study seeks to detect previously identified, together with as yet undiscovered, pathological mutations in a panel of known retinal degeneration genes utilizing target capture next generation sequencing (NGS) for 264 IRD genes. The study to date includes over 700 IRD patients from more than 500 pedigrees. While clinical trials are in progress for patients with IRDs, many such trials require patients to have a known causative mutation to participate in these trials. The Target 5000 research project aims to genetically characterise the estimated 5,000 people in Ireland with IRDs. To date, as part of Target 5000, over 10% of the Irish IRD population has been sequenced providing real insights into the genetic architecture of IRDs in Ireland. Target 5000 offers not only a chance to discover new relevant and pathogenic mutations, but is vital to providing patients with information regarding the underlying genetic pathogenesis of their disease. Thus far, during the course of the study, genetic analysis of IRD patients has helped to resolve ambiguous phenotypes and to identify causative mutations in approximately 60% of IRD cases. The growing body of data from NGS studies of IRDs globally should facilitate better correlations between genotype and phenotype and refine methods for diagnoses and prognoses., Overgrowth syndromes are characterized by tall stature, macrocephaly and other congenital features. These disorders typically arise sporadically through de novo dominant mutations in a growing list of genes. Although whole-exome sequencing (WES) allows us to examine all genes at once in a cost effective manner, we are left with a very large number of possible disease-causing variants to sift through. In addition, we must identify at least two patients with mutations in the same novel gene for the finding to be significant. To address this, we utilized detailed phenotyping of patients with undiagnosed overgrowth to group patients with significant phenotypic overlap and to help us interpret and prioritize the variants identified via WES. We performed WES for 12 undiagnosed patients from our overgrowth cohort. For most patients, there were no obvious causative variants in genes that were previously associated with human overgrowth. Therefore we analysed the participants’ clinical records to look for phenotypic traits that may lead us to new candidate genes. After further mining of the WES data, we prioritized possible disease causing variants based on a number of factors including biological function of the gene, predicted effect on protein function and a minor allele frequency, Living the ‘high life’ presents challenging conditions of extreme cold, hypobaric hypoxia and a restrictive diet that forces populations to adapt to survive. The Quechua are an indigenous high altitude population of Peru and Bolivia. They have resided at altitudes greater than 2500 meters above sea level (m.a.s.l) for the past 10,000 years, following their arrival in South America. Previous studies have characterised their adaptive physiology and identified genes under natural selection (ref). However our understanding of their genetic adaptation to hypoxia is incomplete, as previous studies focused on common genetic variation and applied a limited number of selection tests. To shed further light on genetic adaptation in the Quechua, we established a cohort of 43 Quechua individuals from Cerro de Pasco, Peru (4330 m.a.s.l). We performed whole genome sequencing to a mean depth of 34X. We detailed the demographic history of Quechua using principal components analysis, Admixture and Treemix. We performed five tests of selection, (iHS, XP-EHH, ΔiHH, FST and ΔDAF) on real, and simulated Quechua data incorporating details of the demographic history of the population. We performed a composite of multiple signals (CMS), which aggregates information from the five tests of selection, and identified robust signals of positive selection in high altitude Quechua individuals. The Quechua appear as a relatively homogenous population, with 10% European ancestry. We report the top 1% of genes under selection identified by CMS. We identify putative hypoxia associated genes under selection as well as the previously reported well-characterised hypoxia gene EGLN1., DNA methylation is an important epigenetic mechanism of regulating gene expression that is affected in certain human diseases including imprinting disorders and cancer. In mouse, UHRF1 is an essential cofactor of DNMT1, the enzyme responsible for maintaining methylation patterns. To investigate the effects of loss of UHRF1 on methylation patterns in human cells, UHRF1 levels were decreased in immortalized hTERT fibroblast cell lines using short hairpin RNA. Genome-wide effects on methylation were investigated by the Illumina Infinium HumanMethylation450 BeadChip array. Online bioinformatics software tools were used to identify FDR-significant hypomethylated gene classes, which were then verified by pyrosequencing. Transcriptional effects on these gene classes were investigated by the genome-wide Illumina HumanHT-12 v4 Expression BeadChip array, and verified by RT-qPCR. While UHRF1 depletion caused widespread demethylation, the replication-dependent histone gene cluster and the cancer testis antigen genes were identified as most significantly hypomethylated in UHRF1 knockdown cells. Pyrosequencing confirmed hypomethylation in promoter regions of cancer testis antigen genes TSPY2, MAGEC1, MAGEC2 and MAGEA12, and histone gene HIST2H2AA4 in knockdown cell lines. Hypomethylation in these gene classes correlated with an increase in expression in the knockdown cell line. In addition, cells were rescued using UHRF1 cDNA and showed a return to wild type transcription levels in the rescue cell line. We have shown that these genes are regulated by promoter DNA methylation, confirming the sensitivity of cancer-testis genes to demethylation, supporting possible use of methyltransferase inhibitors to boost antigen presentation in cancers, and the crucial role of UHRF1 in cell cycle regulation., X-linked Retinitis Pigmentosa (XLRP) is a severe, early-onset form of inherited retinal degeneration (IRD). It is estimated that approximately 15% of XLRP cases are due to mutations in RP2 (Retinitis Pigmentosa 2). The ubiquitously expressed RP2 protein is involved in ciliary trafficking of lipid-modified proteins – a process vital for photoreceptor function and survival. Most pathogenic RP2 mutations are suggested to result in truncation or complete loss of the protein. The most common stop mutation, R120X, appears to trigger nonsense-mediated decay of the transcript. RP2 is therefore an excellent candidate for gene augmentation therapy. In recent years, personalised cell models have emerged as invaluable tools for the elucidation of disease pathogeneses and have greatly enhanced pre-clinical proof of concept studies. Through the Target 5000 programme, a project focused on genetic characterisation of the 5,000 IRD patients in Ireland, a male patient harbouring the R120X RP2 mutation was identified. A patient-derived dermal fibroblast cell model of the disease was thus generated and characterised. The transduction efficiencies of AAV vectors of various serotypes in fibroblasts were tested and compared, after which it was decided to proceed with an AAV2/2.CAG.RP2 vector to explore RP2 delivery in this patient-derived cell model. In addition, the effects of RP2 overexpression in vivo in murine photoreceptors and retinal pigment epithelium cells were analysed., Mitochondrial dysfunction leads to a lack of energy production and ultimately the death of the cell. Recently a number of disorders have been shown to have mitochondrial dysfunction including but not limited to; Multiple Sclerosis, Parkinson’s and Leber’s Hereditary Optic Neuropathy (LHON). In LHON, Complex I of the Electron Transport Chain (ETC) is affected which leads to a severe shortage of energy in the cell and eventually cell death. In particular retinal ganglion cells (RGCs) are affected, leading to retinal dysfunction and blindness. These observations have prompted interest in exploring innovative therapeutics to modulate mitochondrial disorders involving complex I deficiency. The team has explored candidate gene therapies for complex I deficiency, which could classically be delivered via Adeno Associated Viruses (AAV) such as AAV serotype 2 (AAV2), among other vectors. As such the team has developed novel in vitro methods for the analysis of complex I deficiency and the evaluation of novel candidate therapies, allowing us to monitor the efficacy of these therapeutics. Assays include a suite of methods to enable evaluation of Complex I activity and oxidative phosphorylation efficiency among other mitochondrial biomarkers. Such assays in principle would be of value for future in vitro and or in vivo studies involving therapies directed towards targeting complex I deficiencies., Background: Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However new putative gDMR have recently been described, along with an improved delineation of the existing gDMR locations. We therefore aimed to re-examine the dependence of methylation at gDMRs on the activities of the methyltransferases in mouse embryonic stem cells (ESCs). Method: We examined the most complete current set of imprinted gDMRs that could be assessed using quantitative pyrosequencing assays in two types of ESCs: those lacking DNMT1 (1KO) and cells lacking a combination of DNMT3A and DNMT3B (3abKO). Results: Loss of methylation was approximately equivalent in both cell types. 1KO cells rescued with a cDNA-expressing DNMT1 could not restore methylation at the imprinted gDMRs, confirming previous observations. However, nearly all gDMRs were remethylated in 3abKO cells rescued with a DNMT3A2 expression construct (3abKO + 3a2). Transcriptional activity at the H19/ Igf2 locus also tracked with the methylation pattern, confirming functional reprogramming in the latter. Conclusions: DNMT3A/B plays a vital role in methylation maintenance at imprints as the rescue with DNMT3A2 can restore imprints in these cells. This provides a useful system to explore factors influencing imprint reprogramming., SATB2, BCL11B and GATAD2A map to regions containing genomewide significant SNPs for schizophrenia and regulate key stages of neurodevelopment via epigenetic mechanisms. SATB2 mediates the projection of neurons across the cerebral hemispheres by regulating the activity of BCL11B via the NuRD nucleosome remodelling complex, which contains. GATAD2A. We hypothesized that genes within the NuRD complex and genes regulated by SATB2 in the pre- and post-natal brain may contribute to schizophrenia etiology. To test, we developed three gene-sets. 1.)Genes reported in mouse knockout studies of SATB2 during cortical development (SATB2_ Cortical). 2.)Genes mapping to SATB2 ChIP-seq peaks generated from mouse cortices at E15.5 (SATB2_Pre-natal). 3.)Genes mapping to SATB2 ChIP-seq peaks generated from mouse P0 hippocampal neurons (SATB2_Post-natal). We performed competitive gene set analysis (GSA) using MAGMA to test if genes within a gene-set were more strongly associated with schizophrenia than other genes in the genome. We applied GSA to schizophrenia GWAS (n=150,064). We also investigated these gene-sets for a genetic contribution to educational attainment (EA; proxy for cognition) using GWAS (n=405,072). After multiple test correction, we observed significant associations for (1)SATB2_Cortical with schizophrenia (P=8.65x10-05) and EA (P=0.00049), (2)SATB2_Pre-natal with EA (P=0.0068) and (3)SATB2_Post-natal with schizophrenia (P=0.0069) and EA (P=2.03x10-06). Further GSA established that effect sizes are stronger for these gene-sets when analysis is limited to genes that are highly expressed in neurons or at different key timepoints during neurodevelopment of the cortex or hippocampus. These data support a role for the NuRD complex and genes regulated by SATB2 in schizophrenia and EA, Background: Dacogen (5-aza-2’deoxycitidine) is currently used to treat Acute Myeloid Leukaemia (AML) and is in trials for myeloid dysplastic syndrome and some solid cancers. As a hypomethylating agent it is thought to act by inhibiting the enzymes which add methyl groups to DNA, chief among them DNMT1. Improved targeting has been hindered by a lack of understanding with respect to the exact mechanism of action on DNMT1 and of the gene targets affected by altered methylation following treatment. Methods: We performed a comparative treatment of the same normosomic, non-transformed fibroblast cell line hTERT1604 over three days with either pharmacological 5-aza-2’deoxycitidine (Dacogen) or with SMARTpool siRNA directly targeting DNMT1. DNA was collected for analysis of methylation levels using Illumina 450k BeadChip methylation arrays. Data was analysed in R using the tailored RnBeads pipeline and in-house scripts. Results: Both Dacogen and DNMT1 siRNA caused overall hypomethylation in the treated cells, with the latter proving more efficient at demethylation at genes in particular. Amongst the targets experiencing demethylation, some hypomethylated promoters were unique to Dacogen treatment and therefore off-target with respect to the reduction in DNMT1. However an unexpected phenomenon almost exclusively caused by 5-Aza-2’-deoxycytidine treatment was gain in methylation. Therefore we also compared our findings to an independent published 450k dataset of Dacogen treated AML cells (KG1a). Our results suggest Dacogen is also having an important effect on methylation unrelated to the inhibition of DNMT1 thus suggesting further avenues for therapeutic improvements., Disruptive, damaging ultra-rare variants (dURVs) are more abundant in schizophrenia (SZ) patients than controls and are more concentrated in neuronally-expressed genes with synaptic functions. dURVs in highly constrained genes influence educational attainment (EA; a proxy for cognition) in the general population. We used MAGMA to perform gene set analysis of the largest available GWAS datasets to investigate if association signals for SZ and EA similarly mapped to highly constrained genes and to neuronally-expressed genes with synaptic functions. We investigated if SZ and EA associations were enriched in brain regions at different timepoints from early development through to adulthood. Highly constrained genes (probability of being loss-of-function intolerant; pLI>0.9; n=3,230) are strongly enriched for association with SZ(p=3.14E-08) and EA(p=1.27E-09) in comparison to genes under less constraint (0.1, Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease affecting 45,000 people in Ireland. Prolonged joint inflammation results in tissue damage with consequent reduced functional capacity and quality of life. Damage to the joints of hands and feet, assessed by x-ray, is an important outcome measure that has genetic input of around 60%. Recent studies have identified single nucleotide polymorphisms (SNPs) in immune-related genes that are associated with severity of tissue damage in RA. One of our studies identified an association with C5orf30, a previously uncharacterized regulator of tissue damage and inflammation (1, 2). However a more comprehensive genome wide analysis is required to more fully characterize the genetic basis of RA severity. This project will identify genetic variants, and their synergistic combinations, that are associated with severity of RA. We will analyse genomewide SNP data in 1,007 RA patients using state-of-the-art genetic epidemiology and computational techniques, including negative binomial modelling, to identify variants linked with joint damage severity. The study population is uniquely large and detailed clinical and genetic datasets will be used for validation studies using five European early RA cohorts. Simulations for statistical power indicate excellent power will be achieved for moderately frequent alleles, for effect sizes (IRR) over 1.4. The aim is to develop both a genetic prognostic score for RA, and to identify novel mediators of tissue destruction. The earlier identification of RA patients at risk of poorer outcome would facilitate patient stratification and inform therapeutic targeting with more aggressive regimes whilst avoiding such treatment in patients likely to have a better outcome, Bloodstream infection and sepsis are often instigated by the bacterium Staphylococcus aureus. Upon accessing the bloodstream, S. aureus binds to the endothelium triggering vascular leakage, inflammation and oedema. These characteristics are difficult to treat pharmacologically as the nature of signalling guiding this host response remains unclear. microRNAs (miRNAs) regulate ~60% of the human genome through post-transcriptional silencing/ degradation of target genes. Previously, bacteria were shown to profoundly affect miRNA expression via up-regulation of dendritic miR-99b elicited by M. tuberculosis infection. This study investigates contributions of S. aureus induced endothelial miRNA dysregulation to sustained and excessive host responses in sepsis. Sheared (10dynes/cm2) human endothelial cells were treated with plasma and TNFα to mimic sepsis conditions. Infection induced miRNA alterations were uncovered using Taqman cards to generate miRNA profiles of uninfected and infected cells (RQ = 2-ΔΔCt). Potential mRNA targets were established bioinformatically and confirmed by RNAseq, western blots and qPCR. Following infection, 58 endothelial miRNA were significantly downand 35 significantly up-regulated, including miR-330 (p, DNA methylation is a critical mechanism for regulating gene expression and ensuring genomic stability. However, loss of function mutations of methyltransferase enzymes such as DNMT1 in normal differentiated cells result in a lethal phenotype. Consequently, existing investigations have only assessed DNMT1 knockdowns in embryonic stem cells or cancer cell lines. Here, isogenic lines of hypomorphic, normal, immortalised fibroblasts have instead been generated via stable integration with short hairpin RNA. Enrichment analysis of epigenome-wide methylation arrays indicated widespread demethylation within promoter and gene body regions. In addition, four specific gene categories were highlighted as most affected; protocadherins, genes regulating body mass, olfactory receptors and cancer/testis antigens. Comparison of short-term siRNA and long-term shRNA-mediated depletion of DNMT1 indicated that many regions recover methylation as shRNA-containing cell lines adapt to lowered levels of DNMT1. Interestingly, polycomb-regulated genes are refractory to de novo DNA methylation in these cells following recovery, reinforcing the concept of mutually-exclusive domains that are regulated by these two major epigenetic mechanisms., Background: The MTHFR C677T is a common polymorphism of the folate metabolising enzyme methylene tetrahydrofolate reductase (MTHFR) associated with hypertension. Riboflavin is a cofactor to MTHFR in the one-carbon cycle for generating methyl groups important for biological reactions such as DNA methylation. Supplementation with riboflavin has previously been shown to reduce blood pressure specifically in individuals with the homozygous MTHFR 677TT genotype. The mechanisms underlying the blood pressure lowering effect of riboflavin are currently unknown however aberrant DNA methylation has been implicated in the development of hypertension. The aims of this study were to examine global DNA methylation on hypertension in adults stratified by MTHFR genotype and in response to intervention with 1.6mg/ day of riboflavin in individuals with the MTHFR 677TT genotype. Methods: Stored peripheral blood leukocyte samples from participants who had consented and participated in targeted RCTs at Ulster University’s Nutrition Innovation Centre for food and HEalth (NICHE) and previously screened for the MTHFR C677T polymorphism were accessed for this study. Bisulphite conversion and pyrosequencing was used to analyse global and gene-specific DNA methylation. Results: Preliminary results show that methylation at the repeat element, LINE-1, and imprinted gene, IGF2 was not significantly different between the MTHFR C677T genotypes at baseline. However, subsequent supplementation with riboflavin resulted in a decrease in global methylation and an increase in IGF2 methylation in MTHFR 677TT participants. Conclusion: This is the largest study to date examining the interaction between the MTHFR C677T genotypes, riboflavin supplementation and DNA methylation. Riboflavin supplementation influenced repeat element and imprinted gene methylation in MTHFR 677TT genotype individuals. Further work will provide insights into the mechanism of riboflavin action in lowering blood pressure in these genetically at risk adults., Background: microRNAs are small, non-coding RNAs which are potentially valuable markers of cardiovascular disease (CVD) risk, including hypertension. This novel investigation aims to profile circulating serum concentrations of microRNAs in premature CVD patients to identify microRNAs that correlate best with hypertension. Methods: Serum samples from an existing cohort of 75 premature CVD patients were analysed for expression of 68 CVD-related microRNAs. Patients had been screened for the methylenetetrahydrofolate reductase (MTHFR) gene polymorphism C677T, a risk factor for hypertension. Samples had been collected at baseline and following intervention with riboflavin, co-factor for the MTHFR enzyme, as part of a placebo-controlled double-blind, randomized trial. The associations between miRNA expression and blood pressure at baseline and post-intervention were investigated. Comparisons of data between CC and TT MTHFR genotype groups, and in response to intervention, were assessed using ANOVA, Pearson’s correlation and corrected t-test statistical analyses. Results: microRNA expression was successfully detected and quantified in all samples. At baseline miR-199a-5p expression was inversely correlated (r=-0.51;p, Background: Hypoxia in prostate tumours has been associated with disease progression and metastasis. MicroRNAs are short non-coding RNA molecules which are important in several cell processes, but their role in hypoxic signalling is still poorly understood. miR-210 has been linked with hypoxic mechanisms, 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: In this study we have used prostate cancer models of hypoxia to investigate the functionality of miR-210. Expression levels of miR-210 have been measured by qPCR in in vitro and in vivo samples. Functional bioassays were used to examine its effect on prostate cancer 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 cells. Over-expression of miR-210 impacts upon target genes which in turn may affect cell proliferation. Data-mining of online repositories of clinical prostate sample data shows that miR-210 is significantly correlated with Gleason grade and other clinical markers of prostate cancer progression. Further in silico 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 promote the development of prostate cancer. Conclusions: We propose that miR-210 is an important regulator of cell response to hypoxic stress and may play an important role in the pathogenesis of prostate cancer. Further study will focus on determining its function in prostate cancer and its potential as a biomarker in this disease.

Aims The Irish DNA Atlas is a DNA collection being assembled with the aim of describing the fine-scale population structure in Ireland. Understanding such structure can inform on optimal design of clinical genetic studies as well as the history of the Irish population. We will present an overview of and the preliminary findings from the study. Methods We are recruiting individuals with all eight greatgrandparents born in Ireland, within 30 kilometres of each other. Participants are asked to complete a detailed birth-brief, which records place and date of birth of three generations of ancestors. We also collect some basic health-related details. DNA is extracted from a saliva sample. We have genotyped using an Illumina OmniExpressdense SNP genotyping platform. We present a number of analyses designed to visualise genetic structure, including; Principle Component, ADMIXTURE, and Runs of Homozygosity analysis. Results To date we have recruited 162 participants. The mean great-grandparental area is 32 kilometres, with an average greatgrandparental date of birth of 1850. Therefore the individuals in the Atlas provide insight to the genetic landscape of Ireland before significant movement of people from the 20th century onwards. An analysis of dense genotyping data from 142participants shows that the Atlas participants cluster closely with British individuals in a Europe wide PCA, but present different ancestral population components when compared with British, and other European populations. Irish individuals also present slightly higher levels of homozygosity relative to mainland European levels. PCA targeted at specific areas of interest within Ireland also hint at fine-scale substructure. Conclusion Ireland shows typical features of a homogenous population, well suited to the study of rare variation in disease risk., Background Progress in diagnostic and therapeutic strategies in medicine is dependent upon high-quality biomedical research. Translation of research findings into the clinic relies on patient participation in innovative clinical trials. We investigated attitudes to genetic research in Ireland, in particular with respect to commercial and financial implications. Methods A multi-centre cross-sectional survey study was performed. Consecutive patients attending four out-patient clinics were asked to complete paper-based questionnaires. An electronic version of the same questionnaire was created on Survey Monkey with a link made public on a social media website for a period of 24 hours. Data was analysed using SPSS. Results 351 questionnaires were completed (99 paper, 252 electronic). The majority of respondents were female (n = 288, 82%), and highly educated, with 244 (70%) attending college/university. Most participants supported genetic research (267, 76%), more frequently for common diseases (274, 78%) than rare disorders (204, 58%, p < 0.001, x2). 103 (29%) had participated in scientific research, and 57(16%) had donated material to a bio-bank. The majority (n = 213, 61%) would not support research with potential financial/commercial gain. 106(30%) would decline to participate in research if researchers would benefit financially, compared to 49(14%) if the research was supported by a pharmaceutical company, (p < 0.001, x2). Respondents would provide buccal samples (258, 74%) more readily than tissue (225, 64%) or blood (222, 63%). Conclusion A high level of support for genetic research exists among the Irish population, but active participation is dependent upon a number of factors, notably, type of biological material required, frequency of the disease in question, and commercial interest of the researchers., Introduction Although the etiology of schizophrenia (SZ) is largely unknown, it is increasingly clear that genetic and environmental interactions contribute to cognitive deficits associated with this disorder. Recent Genome wide association studies (GWAS) have indicated a link between SZ and immune dysregulation, especially genetic mutations related to the major histocompatibility complex (MHC). Cognitive deficits are core features of Schizophrenia and related disorders, which relate to genetic risk. This study aims to explore the relationship between MHC risk variants for SZ and cognitive deficits, while also relating findings to brain activity. Methods To test if MHC risk variants impair cognition, ANCOVA analysis is performed on genetics data previously collected in a GWAS. Cognition measures are compared in groups with and without MHC genetic risk, in a population of SZ sufferers and healthy controls. Functional MRI imaging will also be performed to test if genetic risk relates to altered neural activity. Results Preliminary analyses suggest that MHC risk variants contribute to impairments in cognition in domains of social cognition, IQ and attention. Further analysis will be performed to test for environmental mediators of this relationship, looking at cannabis use and urbanicity. BOLD fMRI will also be used to test for a relationship between MHC risk and altered neural activity, using MATLAB SPM. Conclusions The MHC genetic variant may serve as a significant risk marker for schizophrenia, and further elucidate etiology of this neurodevelopmental disorder. Future studies on neurobiology of social cognition, and greater knowledge of genetic risk may establish targets for interventions., Aim To create a bioluminescence mouse model which expresses firefly luciferase in the corneal epithelium to assess gene editing and gene silencing for the cornea. Methods A gene targeting vector was generated where the Krt12 coding sequence in and the splice donor site of exon 1 were replaced with a transgene cassette containing a luc2-Multiple Targeting Cassette (MTC) gene fusion. The vector was transfected by electroporation into the Taconic Artemis C57BL/6N Tac ES cell line. Homologous recombinant clones were isolated and validated, and the mice bred with luc2-positive/ PuroR-negative offspring used for colony establishment. To visualise the expression of luc2 within the corneal epithelium, luciferin substrate diluted in viscotears was applied to the front of the eye and then luciferase expression was imaged and assessed using a Xenogen IVIS Lumina Imager and LivingImage 3.2 software. Intrastromal injection of siGlo siRNA was used to determine the localisation of siRNA within the corneal epithelium and then the established mouse model was treated with either native or Accell “self-delivery” siRNA. Results The Accell “self-delivery” siRNA induced potent sustained allele specific silencing for 7 days, while native versions of siRNA resulted in significant knock-down for 1 day only (p < 0.05). We have created and validated a bioluminescence mouse model and have utilised it to assess siRNA in vivo. This mouse model coupled with the Lumina imager will allow us to assess topical delivery of gene therapies to the ocular surface allowing validation for future translation to clinical use., Background Methylation of DNA sequences at promoters, CpG islands and other elements plays a vital role in regulating gene activity. In human, loss of methylation is known to play a causative role in imprinting disorders and in inappropriate germline gene expression in cancers. While in mouse, loss of function mutants have given great insight into the targets of methylation, functional studies in human have been largely limited to cancer cells and more recently stem cells, not normal adult cells. Methods Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in normosomic hTERT-immortalised adult fibroblasts. Genome-wide methylation levels were assayed using the Illumina 450K bead array. Results were analysed using RnBeads and Galaxy. Locusspecific methylation was verified using pyrosequencing and clonal analysis. Validation was achieved using transient siRNA. Results Loss of function was poorly tolerated and all clonally-expanded cell lines had spontaneously restored DNMT1 levels by silencing of the shRNA. Evidence for a genome-wide methylation erasure event followed by a wave of remethylation could be clearly traced. Gene bodies and the shores of CpG islands showed the clearest loss of methylation overall. While most CpG islands are normally unmethylated and so unaffected, both imprints and germline genes fall into the rarer category of normally methylated islands: of these two, lasting loss of methylation was much more common among imprints than germline genes. Conclusions 1: transient loss of methylation is poorly tolerated; 2: a robust mechanism for remethylation exists even in adult cells; 3: aberrant remethylation is frequent on recovery and 4: Imprints are particularly sensitive., Background Dihydrofolate reductase (DHFR) is essential for the conversion of folic acid to active folate needed for one-carbon metabolism. Common genetic variation within DHFR is restricted to the noncoding regions and previous studies have focused on a 19 bp deletion/insertion polymorphism (rs70991108) within intron 1. Reports of an association between this polymorphism and blood folate biomarker concentrations are conflicting. Objective We aimed to evaluate whether the DHFR 19bp deletion/ insertion polymorphism affects circulating folate biomarkers in the largest cohort to address this question to date. Methods Young healthy Irish individuals (n= 2,507) between 19 to 36 years old were recruited between February 2003 and 2004. Folic acid intake from supplements and fortified foods was assessed using a customized food intake questionnaire. Concentrations of serum folate and vitamin B-12, red blood cell (RBC) folate and plasma total homocysteine (tHcy) concentration were measured. Data were analysed using linear regression models. Results Folic acid intake was positively associated with serum (P 326μg folic acid/day; P = 0.96). A non-significant trend towards lower RBC folate by genotype (P = 0.09) was observed in the lowest folic acid intake quintile (0 – 51 μg/day). Conclusion In this cohort of young healthy individuals the DHFR 19bp deletion allele does not significantly affect circulating folate status, irrespective of folic acid intake. Our data rule out a strong functional effect of this polymorphism on blood folate concentrations.

BACKGROUND: Cornelia de Lange syndrome (CdLS) is a multisystem disorder with distinctive facial appearance, intellectual disability and growth failure as prominent features. Most individuals with typical CdLS have de novo heterozygous loss-of-function mutations in NIPBL with mosaic individuals representing a significant proportion. Mutations in other cohesin components, SMC1A, SMC3, HDAC8 and RAD21 cause less typical CdLS.METHODS: We screened 163 affected individuals for coding region mutations in the known genes, 90 for genomic rearrangements, 19 for deep intronic variants in NIPBL and 5 had whole-exome sequencing.RESULTS: Pathogenic mutations [including mosaic changes] were identified in: NIPBL 46 [3] (28.2%); SMC1A 5 [1] (3.1%); SMC3 5 [1] (3.1%); HDAC8 6 [0] (3.6%) and RAD21 1 [0] (0.6%). One individual had a de novo 1.3 Mb deletion of 1p36.3. Another had a 520 kb duplication of 12q13.13 encompassing ESPL1, encoding separase, an enzyme that cleaves the cohesin ring. Three de novo mutations were identified in ANKRD11 demonstrating a phenotypic overlap with KBG syndrome. To estimate the number of undetected mosaic cases we used recursive partitioning to identify discriminating features in the NIPBL-positive subgroup. Filtering of the mutation-negative group on these features classified at least 18% as ‘NIPBL-like’. A computer composition of the average face of this NIPBL-like subgroup was also more typical in appearance than that of all others in the mutation-negative group supporting the existence of undetected mosaic cases.CONCLUSIONS: Future diagnostic testing in ‘mutation-negative’ CdLS thus merits deeper sequencing of multiple DNA samples derived from different tissues.