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Purpose: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Method(s): We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Result(s): ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion(s): In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design.Copyright © 2020, The Author(s).

Currently there is no secured ongoing funding in Australia for next generation sequencing (NGS) such as exome sequencing (ES) for adult neurological disorders. Studies have focused on paediatric populations in research or highly specialised settings, utilised standard NGS pipelines focusing only on small insertions, deletions and single nucleotide variants, and not explored impacts on management in detail. This prospective multi-site study performed ES and an extended bioinformatics repeat expansion analysis pipeline, on patients with broad phenotypes (ataxia, dementia, dystonia, spastic paraparesis, motor neuron disease, Parkinson's disease and complex/not-otherwise-specified), with symptom onset between 2 and 60 years. Genomic data analysis was phenotype-driven, using virtual gene panels, reported according to American College of Medical Genetics and Genomics guidelines. One-hundred-and-sixty patients (51% female) were included, median age 52 years (range 14-79) and median 9 years of symptoms. 34/160 (21%) patients received a genetic diagnosis. Highest diagnostic rates were in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified (10/38, 26%) and ataxia (7/28, 25%) groups. Findings were considered 'possible/uncertain' in 21/160 patients. Repeat expansion detection identified an unexpected diagnosis of Huntington disease in an ataxic patient with negative ES. Impacts on management, such as more precise and tailored care, were seen in most diagnosed patients (23/34, 68%). ES and a novel bioinformatics analysis pipepline had a substantial diagnostic yield (21%) and management impacts for most diagnosed patients, in heterogeneous, complex, mainly adult-onset neurological disorders in real-world settings in Australia, providing evidence for NGS and complementary multiple, new technologies as valuable diagnostic tools.Copyright © 2020 Elsevier B.V.

The diagnosis of children with genetic conditions places a significant economic burden on health care services. The lack of well-defined comparative cohorts has been a limitation of health economic studies comparing first-line genomic sequencing (GS) against traditional approaches. Aim(s): To evaluate utility and cost effectiveness of early GS in pediatric patients with complex monogenic conditions compared to a matched historical cohort. Method(s): Data, including diagnosis rate and investigation costs, were collected in a prospective cohort of 92 pediatric patients who underwent singleton GS over an 18-month period (2016-2017). Inclusion required patients to have two of the following: a condition with high morbidity or mortality, a multi-system disease involving three or more organ systems, or severe limitation of daily function. For comparison, data were collected in a historical patient cohort fulfilling the inclusion criteria who underwent traditional investigations in the two years (2012-2013) prior to the availability of clinical genomic sequencing. Result(s): Genomic sequencing yielded a diagnosis in 42% while traditional investigations yielded a diagnosis in 23% (p = 0.003). 75% of diagnosed patients experienced a change in management, compared to 33% of diagnosed patients who underwent traditional investigations. In the GS cohort, four times fewer invasive investigations were observed. Compared to traditional investigations, singleton genomic sequencing at a cost of $3100 AUD resulted in a mean saving per person of $2780 AUD (95%CI $1585-$3974). Conclusion(s): Early genomic sequencing is highly costeffective while doubling the diagnostic yield of traditional approaches and improving the care of patients with complex genetic conditions.

PURPOSE: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. METHODS: We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. RESULTS: ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). CONCLUSION: In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design.

Currently there is no secured ongoing funding in Australia for next generation sequencing (NGS) such as exome sequencing (ES) for adult neurological disorders. Studies have focused on paediatric populations in research or highly specialised settings, utilised standard NGS pipelines focusing only on small insertions, deletions and single nucleotide variants, and not explored impacts on management in detail. This prospective multi-site study performed ES and an extended bioinformatics repeat expansion analysis pipeline, on patients with broad phenotypes (ataxia, dementia, dystonia, spastic paraparesis, motor neuron disease, Parkinson's disease and complex/not-otherwise-specified), with symptom onset between 2 and 60 years. Genomic data analysis was phenotype-driven, using virtual gene panels, reported according to American College of Medical Genetics and Genomics guidelines. One-hundred-and-sixty patients (51% female) were included, median age 52 years (range 14-79) and median 9 years of symptoms. 34/160 (21%) patients received a genetic diagnosis. Highest diagnostic rates were in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified (10/38, 26%) and ataxia (7/28, 25%) groups. Findings were considered 'possible/uncertain' in 21/160 patients. Repeat expansion detection identified an unexpected diagnosis of Huntington disease in an ataxic patient with negative ES. Impacts on management, such as more precise and tailored care, were seen in most diagnosed patients (23/34, 68%). ES and a novel bioinformatics analysis pipepline had a substantial diagnostic yield (21%) and management impacts for most diagnosed patients, in heterogeneous, complex, mainly adult-onset neurological disorders in real-world settings in Australia, providing evidence for NGS and complementary multiple, new technologies as valuable diagnostic tools.

Genomic classification is rapidly becoming a routine and integral part of diagnosis in pathology. Perinatal pathology is following this trend. The aims of this study were to determine the utility of WES in perinatal autopsy for congenital anomalies and to model the outcome of WES as a prenatal test. A total of 131 probands with congenital anomalies who underwent post mortem examination were referred by pathologists to the study. 82 probands were considered suitable for sequencing. The parents of 5 declined enrolment and 10 could not be consented. 67 probands were enrolled. Autopsy identified specific diagnoses in 11 cases (17%). WES identified specific diagnoses ('pathogenic' or 'likely pathogenic' variants) in 23 cases - a diagnostic rate of 35%. The combined diagnostic rate of autopsy and sequencing was 38%. A geneticist blinded to the autopsy findings reviewed the probands' antenatal imaging reports and recommended a gene list to model the clinical utility of prenatal WES. The use of antenatal sequencing in this cohort would have identified a specific diagnosis in 18 of the 23 cases with positive sequencing findings. In conclusion, WES doubles the diagnostic rate of autopsy for congenital anomalies and our data supports the prenatal use of genomic sequencing.Copyright © 2020

Purpose: Cost-effectiveness evaluations of first-line genomic sequencing (GS) in the diagnosis of children with genetic conditions are limited by the lack of well-defined comparative cohorts. We sought to evaluate the cost-effectiveness of early GS in pediatric patients with complex monogenic conditions compared with a matched historical cohort. Method(s): Data, including investigation costs, were collected in a prospective cohort of 92 pediatric patients undergoing singleton GS over an 18-month period (2016-2017) with two of the following: a condition with high mortality, multisystem disease involving three or more organs, or severe limitation of daily function. Comparative data were collected in a matched historical cohort who underwent traditional investigations in the years 2012-2013. Result(s): GS yielded a diagnosis in 42% while traditional investigations yielded a diagnosis in 23% (p = 0.003). A change in management was experienced by 74% of patients diagnosed following GS, compared with 32% diagnosed following traditional investigations. Singleton GS at a cost of AU$3100 resulted in a mean saving per person of AU$3602 (95% confidence interval [CI] AU$2520-4685). Cost savings occurred across all investigation subtypes and were only minimally offset by clinical management costs. Conclusion(s): GS in complex pediatric patients saves significant costs and doubles the diagnostic yield of traditional approaches.Copyright © 2020, American College of Medical Genetics and Genomics.

Primary Immunodeficiency diseases (PID) are a heterogeneous group of conditions with variable clinical features that are frequently associated with significant diagnostic delay. Accurate diagnosis has significant therapeutic benefit and may lead to personalized therapies. We established the Immunology Flagship of Melbourne Genomics Health Alliance in Australia to determine the clinical utility of genomic sequencing for diagnosis and management of individuals with suspected and confirmed cases of PID. 198 adults and children with suspected or confirmed PID (n=153), autoinflammatory disease (n=33) and hereditary angioedema (HAE, n=11) were recruited to the Melbourne Genomics Immunology Flagship.Whole-exome sequencing (WES) was performed, with targeted gene analysis. Variant curation and reporting was performed according to the American Council of Medical Genetics guidelines. Overall, WES was diagnostic in 15% (30/198), confirming a preexisting diagnosis in 7% (14/198), and offering a new or more specific diagnosis in 8% (16/198). Variants of uncertain significance were identified in a further 28 patients (14%) in genes known to be associated with their clinical diagnosis, that warrant further functional validation. In the HAE group, diagnosis was confirmed in only 5 patients (45%), suggesting thatWES may not be the appropriate technique for genetic diagnosis in this condition. A higher diagnostic rate was observed for autoinflammatory disorders (20%; 8/40) compared to PID (12%; 18/146). Of those who received a diagnosis, immediate changes to patient management and treatment occurred for 17/29 patients (59%), including HSCT for 3 and specific targeted therapy for 11 (38%) individuals. We have demonstrated the utility ofWES for accurate diagnosis of complex immune diseases, with the potential to change diagnoses, guide therapeutic intervention and provide opportunities for genetic counseling. Further longitudinal analysis will determine clinical outcomes and health econ

Objectives: To determine the utility of exome sequencing as an adjunct to perinatal post mortem for congenital anomalies. To model the likely outcome of exome sequencing as a prenatal test in the same setting. Method(s): Probands with congenital anomalies were referred by perinatal pathologists. They were enrolled for sequencing if their microarray analysis was negative and their anomalies were considered to have a monogenic cause. Singleton or trio exome sequencing was performed as an adjunct to routine perinatal autopsy and the diagnostic outcomes were compared. A geneticist independently reviewed the probands' antenatal imaging findings and recommended a phenotype specific gene list to model the clinical utility of prenatal exome sequencing. Result(s): A prospective cohort of 131 probands was referred. Fortynine (37%) were unsuitable for inclusion. The parents of five (4%) declined enrolment and 10 (8%) could not be consented. Sixty-seven probands (52%) were enrolled. One proband could not be sequenced due to a degraded DNA sample. Results are available for 65 probands (32 singletons and 33 trios). Specific diagnoses were identified at autopsy in 11 cases (17%) including two cases with negative sequencing. Sequencing identified specific diagnoses ("pathogenic" or "likely pathogenic" variants) in 23 cases giving a diagnostic rate of 35%. The combined diagnostic rate of autopsy and exome was 38%. The individual autopsy and genomic diagnostic rates were highest in probands with significant skeletal findings (39% and 61% respectively, n = 18). Genomic diagnoses were obtained from 34% of singleton exomes, with segregation when required, and 36% of trio exomes. Variants of uncertain significance (VUS) were reported in 13 cases (20%). In four, a strong phenotype-genotype match together with plausible candidate variants indicated a need for additional studies. The combined rate of diagnostic or suspicious variants was 42%. The use of antenatal sequencing in this cohort u

Background/Aim: Implementation of rapid genomic testing in neonatal and pediatric intensive care units (NICUs/PICUs) is gathering momentum, and requires the development of systems capable of consistent delivery across multiple sites. Method(s): We developed a rapid genomic diagnosis program involving 10 Australian hospitals and two laboratories with the aim of providing test results in <5 days for acutely unwell pediatric patients with suspected monogenic disorders. Rapid exome sequencing (rES) was performed as trios when possible, and analysis utilized multidisciplinary expertise. Experience was shared between clinical sites, laboratories, and professional groups to enable collective learning. Result(s): The program considered 123 patients for rES over 10 months, and approved 114 (93%). Five families declined testing (4.4%), and nine (7.9%) were withdrawn due to change in clinical circumstances. Of 100 patients tested, 53 received a diagnosis. Twelve of the diagnoses (23%) were made using approaches augmenting standard ES analysis: mitochondrial genome sequencing, ES-based copy number analysis, matchmaking of emerging genes, reverse phenotyping and RNA analysis. Median time from hospital admission to consent was 6 days (range 0-64 days); median time from sample receipt to clinical ES report was 3 days (range 2-7 days). The total cost of testing was AU $1,123,000 (AU$11,230 per case). Changesin management following a result occurred in 77% of diagnosed patients and 10% of undiag-nosed patients. Conclusion(s): We demonstrate the feasibility of a national, highly integrated clinical-laboratory approach to rapid genomic diagnosis, which delivers results within a timeframe relevant to acute pediatrics, while optimizing clinical utility and resource allocation.

Children with intellectual disability and multiple congenital anomalies can be a difficult group to diagnose with vast clinical and genetic heterogeneity. Until the advent of whole exome sequencing (WES), a genetic basis usually went unknown. WES has been successful in expanding the list of ID-associated genes and is rapidly becoming the standard of care for this clinical group. We present a 5-year-old boy with marked global developmental delay, bilateral optic colobomas, pre-axial polydactyly, congenital heart disease and dental anomalies. Karyotype and chromosomemicroarray were normal. EEG was non-specifically abnormal. WES was performed using Nextera Rapid Capture Exome kit (Illumina) with >100x mean coverage. Data was processed using Cpipe and a phenotype-driven gene list for variant prioritization and assessed as per the ACMG variant classification guidelines. A novel heterozygous mutation in PUF60 (c.1154-1166del) was found resulting in a frameshift mutation. Subsequent segregation studies found this variant was a de novo variant in the proband and it was classified as pathogenic. Verheij syndrome is a neurodevelopmental syndrome due to interstitial deletions of 8q24.3, which includes the PUF60 gene. Recent reports implicate variants in PUF60 as causing a similar phenotype to Verheij syndrome. A literature review revealed 18 such cases now documented with markedly heterogenous phenotypes. The PUF60 syndrome phenotypic spectrum has been established to include: developmental delay/intellectual disability, unilateral ocular coloboma, microcephaly, short stature, craniofacial, cardiac and renal defects. We describe a case with the unique constellation of bilateral ocular coloboma, pre-axial polydactyly, proximal insertion of the right hallux and dental anomalies.

Background: As genomic sequencing becomes more widely available in clinical settings for diagnostic purposes, a number of genetic counseling issues are gaining precedence. The ability to manage these issues will be paramount as genetic and non-genetic healthcare professionals navigate the complexities of using genomic technologies to facilitate diagnosis and inform patient management. Method(s): Counseling issues arising when counseling for diagnostic genomic sequencing were identified by four genetic counselors with ten years of collective experience providing genetic counseling in this setting. These issues were discussed and refined at a meeting of genetic counselors working in clinical genomics settings in Melbourne, Australia. Illustrative cases were selected where pre- and post-test genetic counseling was provided in clinical settings to individuals who received singleton or trio whole exome sequencing with targeted analysis. Case summaries were compiled by the author providing counseling to the individual or family, using detailed consult notes recorded in a research database, which included reflections regarding psychosocial issues. Counseling issues raised and challenges for the counselor were extracted to ascertain the applicability of existing genetic counseling competencies to managing counseling issues arising. Outcome(s): Counseling issues discussed include a reappraisal of how genetic counselors manage hope in the genomic era, informed consent for secondary use of genomic data, unexpected or unsolicited secondary findings, and trio sequencing. The authors seek to contribute to the evolving understanding of genetic counseling for diagnostic genomic sequencing through considering the applicability of existing genetic counseling competencies to managing emerging counseling issues, and discussing genetic counseling practice implications.

As genomic sequencing becomes more widely available in clinical settings for diagnostic purposes, a number of genetic counseling issues are gaining precedence. The ability to manage these issues will be paramount as genetic and non-genetic healthcare professionals navigate the complexities of using genomic technologies to facilitate diagnosis and inform patient management. Counseling issues arising when counseling for diagnostic genomic sequencing were identified by four genetic counselors with 10 years of collective experience providing genetic counseling in this setting. These issues were discussed and refined at a meeting of genetic counselors working in clinical genomics settings in Melbourne, Australia. Emerging counseling issues, or variations of established counseling issues, were identified from the issues raised. Illustrative cases were selected where pre- and post-test genetic counseling was provided in clinical settings to individuals who received singleton or trio WES with targeted analysis. Counseling issues discussed in this paper include a reappraisal of how genetic counselors manage hope in the genomic era, informed consent for secondary use of genomic data, clinical reanalysis of genomic data, unexpected or unsolicited secondary findings, and trio sequencing. The authors seek to contribute to the evolving understanding of genetic counseling for diagnostic genomic sequencing through considering the applicability of existing genetic counseling competencies to managing emerging counseling issues and discussing genetic counseling practice implications.

Background: Exome sequencing has the potential to be used in newborn screening and international research is investigating the feasibility of this approach. It is not yet clear how parents will respond to the genomic newborn screening in their children. Aim(s): To explore parents' interest in genomic testing and what factors influence decision making about the scope of results received. Method(s): Families that consented for WES to identify the cause of hearing loss in their child were eligible. They could choose additional analysis of selected childhood onset genetic conditions unrelated to hearing loss. Families were provided with a decision aid and a genetic counseling session over two sites. Participants could choose to receive results for childhood onset genetic conditions with a known treatment or intervention pathway (Choice B), or all conditions, some of which do not have a known treatment or intervention pathway (Choice C). The families' completed evaluation surveys regarding their decision making post recruitment and at return of results. Result(s): Of the 107 patients who consented for WES, 64% opted to receive additional findings. Of those, 42% selected Choice B and 58% Choice C. Decisional conflict was lower among those who chose additional findings. The rate of uptake is significantly different between the two recruitment sites. Discussion(s): A majority of parents are requesting additional information. Analysis of genetic counseling notes and patient demographics will provide insight into parents' decision making. Conclusion(s): The results of this project illustrate the importance of providing choice around additional findings in genomic testing.

Purpose: The purpose of the study was to implement and prospectively evaluate the outcomes of a rapid genomic diagnosis program at two pediatric tertiary centers. Method(s): Rapid singleton whole-exome sequencing (rWES) was performed in acutely unwell pediatric patients with suspected monogenic disorders. Laboratory and clinical barriers to implementation were addressed through continuous multidisciplinary review of process parameters. Diagnostic and clinical utility and cost-effectiveness of rWES were assessed. Result(s): Of 40 enrolled patients, 21 (52.5%) received a diagnosis, with median time to report of 16 days (range 9-109 days). A result was provided during the first hospital admission in 28 of 36 inpatients (78%). Clinical management changed in 12 of the 21 diagnosed patients (57%), including the provision of lifesaving treatment, avoidance of invasive biopsies, and palliative care guidance. The cost per diagnosis was AU$13,388 (US$10,453). Additional cost savings from avoidance of planned tests and procedures and reduced length of stay are estimated to be around AU$543,178 (US$424,101). The clear relative advantage of rWES, joint clinical and laboratory leadership, and the creation of a multidisciplinary "rapid team" were key to successful implementation. Conclusion(s): Rapid genomic testing in acute pediatrics is not only feasible but also cost-effective, and has high diagnostic and clinical utility. It requires a whole-of-system approach for successful implementation.Copyright © 2018, American College of Medical Genetics and Genomics.

As genomic sequencing (GS) technologies are increasingly utilized, consideration is needed to determine how best to integrate the technology into different medical disciplines. This includes consideration of how GS should be provided outside clinical genetics services, in particular how non-genetic health professionals can integrate GS into their clinical practice. There exists a gap in the literature regarding the clinical implementation of genomics at a service delivery level, particularly an exploration of the experiences of genetic counselors delivering GS within various healthcare models and in collaboration with non-genetic health professionals. Genetic counselors reflected on their diverse experiences of counseling for whole exome sequencing for a diverse range of medical conditions as part of a state-wide implementation project in Melbourne, Australia. Illustrative examples outline four different models of service provision; genetics outpatient, non-genetic specialist outpatient, multi-disciplinary outpatient, and inpatient. The successes and challenges of implementing genomics through these healthcare models were identified from the perspective of genetic counselors directly involved. Genetic counselors and other health care professionals will need to develop an awareness of the benefits and limitations of different healthcare models for the implementation of GS, and the need for flexibility in determining method of approach.

Background: The Melbourne Genomics Health Alliance is establishing systems and producing evidence to guide incorporation of genomics into the Victorian healthcare system. Through one of its clinical flagship projects, the Alliance is offering WES to families who have an infant with moderate to profound bilateral hearing loss born in 2016 or 2017. Aim(s): The aim of this project is to define the genetic etiology of congenital hearing loss, streamline the care of affected children and explore parents' interest in genomic testing. Method(s): Families who have an eligible child are identified by the statewide Victorian Infant Hearing Screening Program (VIHSP). Participants are offered pediatrician-run hearing clinic appointment and genetics appointment. WES with targeted gene analysis is performed in conjunctionwith microarray. Result(s): 70% of eligible participants consented to WES. Of the 107 patients recruited, 52 results have been issued to date. The rate of diagnosis is 67%; 33% have connexin mutations, 17% have another non-syndromic deafness gene identified, 17% have a syndromic diagnosis. Microarray has contributed to 10% of diagnoses when combined with WES results. An additional 34% of participants have received a diagnosis using WES over our centre's usual investigation methods of connexin testing and microarray. Discussion(s): Understanding the genetic etiology for infants with congenital hearing loss provides important information for families regarding prognosis, reproductive risk and screening for associated health problems in their child. Conclusion(s): This study provides a comprehensive understanding of the genetic etiology of congenital hearing loss over this two year period.

Background: Genetic counseling in the era of genomics has undergone significant changes to deal with additional variants, more potential outcomes and implications of data storage and reanalysis. With the advent of ultra-rapid genomic testing via the Acute Care Genomics AGHA flagship, we reflect on how counseling must adapt with new challenges. Case Report: A term neonate born to consanguineous parents was transferred to a tertiary perinatal centre with respiratory insufficiency requiring positive pressure support and profound hypotonia and weakness. Initial investigations for common causes of hypotonia and weakness were normal. Result(s): In the clinical setting of minimal improvement, ultra-rapid genomic testing identified a rare homozygous pathogenic variant in RYR1. Discussion(s): In the neonatal intensive care setting, families often have limited time to adjust to critical illness before the concept of whole exome sequencing is introduced, which may reduce their ability to process complex information and make informed decisions about genetic investigations. Preliminary information giving and consent is time-pressured, with less opportunity to reflect on the implications of testing prior to making a final decision. A focus on potentially positive benefits of genomic testing, such as identifying a treatable disease or diagnosing a condition with a favourable prognosis, combined with rapid receipt of results, may limit families' ability to prepare for potentially devastating genetic diagnoses. Professionals involved in facilitating ultra-rapid genomic testing should be mindful of the potential to preferentially focus on these positive outcomes and adapt counseling to promote families' psychological adjustment to results and minimise the impact of diagnoses.

Background: The diagnosis of children with complex genetic conditions places a significant economic burden on healthcare services. Studies measuring the cost of first-line exome sequencing (ES) against that of traditional diagnostic approaches are limited by the lack of well-defined comparative cohorts. Aim(s): To evaluate utility and cost-effectiveness of early ES in pediatric patients with severe, likely mono-genic medical conditions. Method(s): Data, including diagnosis rate and investigation costs, was collected from a prospective cohort of 92 pediatric patients who underwent singleton ES over a 2-year period (2016-2017). Inclusion required patients to have two of the following: a condition with high morbidity or mortality, multisystem disease involving three or more organ systems, or severe limitation on daily function. For comparison, data was collected from a historical cohort of patients fulfilling the inclusion criteria who underwent standard investigations in the 2 years (2012-2013) prior to the availability of clinical exome sequencing. Result(s): Exome sequencing yielded a diagnosis in 40/92 (43%) compared with 21/91 (23%) inthe historical cohort. ES directed management changes in 33% of patients compared to 14% receiving standard care, while producing a 4-fold reduction in invasive investigations. The average cost per diagnosis following ES was AUD$10,659 compared to the AUD$37,810 cost per diagnosis of traditional diagnostic investigations. Conclusion(s): Early exome sequencing reduces the cost per diagnosis by 2.5-fold while almost doubling the diagnostic yield of traditional approaches. It improves the care of patients with severe genetic conditions by directing management, resolving uncertainty, and mitigating the need for invasive investigations.

Background: Hereditary kidney conditions are rare but account for a significant burden on hospitals in both adults and children. Aim(s): Monash Health is a KidGen/ Australian Genomics Health Alliance/ Melbourne Genomics Health Alliance flagship recruitment site, aiming to assess the impact of multidisciplinary renal-genetic clinics on patient care while providing access to whole exome sequencing (WES). Method(s): A three-year audit (2015-2017) of renal patients referred to the Monash Health genetics service provides a picture of the renal genetics landscape at the outset of renal flagship WES testing. The electronicmedical record was searched using renal keywords; each file was manually assessed for inclusion and exclusion criteria. Data collection included referrer specialty, condition, family history, inheritance pattern, type and cost of genetics testing and impact of genetic testing on management and reproductive options. Result(s): Through keywordmatching, 676 patients were identified and 86 met inclusion criteria; 59 (69%) were probands with a primary renal condition and 35 (40.1%) were referred by a nephrologist. Cystic renal disease was the commonest reason for referral. Genetic testing was arranged for 50 patients of whom 21 (42%) had informative results. Diagnosis rate improved from 2015 to 2017; cost per informative patient diagnosis was $2,499. Conclusion(s): This audit provides a snapshot of the utility of clinical genetics input in a renal genetics context at the outset of improved WES access. Fourteen referred patients were unaffected, providing them with reproductive reassurance. Diagnosis rate improved from 2015 to 2017 as more molecular diagnoses were obtained, thus improving patient management.

Fragile X syndrome (FXS) is usually associated with a CGG repeat expansion >200 repeats within the FMR1 gene, known as a full mutation (FM). FM alleles produce abnormal methylation of the FMR1 promoter with reduction or silencing of FMR1 gene expression. Furthermore, premutation (PM: 55-199 CGGs) and full mutation alleles usually expand in size when maternally transmitted to progeny. This study describes a PM allele carried by the mother decreasing to a normal sized allele in a male from a dichorionic diamniotic (DCDA) twin pregnancy, with the female twin inheriting FM (200-790 CGGs), PM (130 CGGs) and normal-sized (39 CGGs) alleles. Further evidence of instability of the maternal PM allele was shown by a male proband (older brother) mosaic for PM (CGG 78 and 150 CGGs) and FM (200-813 CGGs), and a high level of FMR1 promoter methylation, between 50 and 70%, in multiple tissues. The fully-retracted, normal-sized allele was identified by PCR CGG sizing in the male twin, with no evidence of a FM allele identified using Southern blot analysis in multiple tissues collected postnatally and prenatally. Consistent with this, prenatal PCR sizing (35 CGGs) showed inconsistent inheritance of the maternal normal allele (30 CGGs), with single-nucleotide polymorphism (SNP) linkage analysis confirming that the abnormal FMR1 chromosome had been inherited from the mother's PM chromosome. Importantly, the male twin showed no significant hypermethylation of the FMR1 promoter in all pre and postnatal tissues tested, as well as normal levels of FMR1 mRNA in blood. In summary, this report demonstrates the first postnatal follow up of a prenatal case in which FMR1 mRNA levels were approaching normal, with normal levels of FMR1 promoter methylation and normal CGG size in multiple pre and postnatally collected tissues.Copyright © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Background and aims: Immune diseases are a heterogeneous group of conditions with variable clinical features, therefore frequently associated with significant diagnostic delay. Accurate genetic diagnosis has significant therapeutic benefit and may lead to personalized therapies. Access to genetic testing has previously been limited by cost and a limited number of Australian laboratories offering testing. We established the Immunology Flagship of Melbourne Genomics Health Alliance to determine the clinical utility of genomic sequencing for diagnosis and management of 3 groups of immune diseases. Method(s): 197 adults and children with suspected or confirmed Primary Immunodeficiency (PID; n = 153), systemic auto-inflammatory disease (SAID; n = 33) and hereditary angioedema (HAE; n = 11) were recruited to the Melbourne Genomics Immunology Flagship. Whole-exome sequencing (WES) was performed at the Australian Genomic Research Facility (AGRF), with targeted gene analysis. Variant curation and reporting was performed according to the American Council of Medical Genetics guidelines. Result(s): Overall, WES was diagnostic in 30 patients (15%), confirming a preexisting diagnosis in 14 (7%), and offering a more specific diagnosis in 16 (8%). A further 29 patients (14%) had variants of uncertain significance (VUS) identified in genes known to be associated with their clinical diagnosis, that warrant further functional validation. In the HAE group, diagnosis was confirmed in only 5 patients (45%), suggesting that WES may not be the appropriate technique for genetic diagnosis in this condition. SAIDs had a higher diagnostic rate than PIDs, at 20% and 12% respectively. Conclusion(s): WES is a useful tool for accurate diagnosis of complex immune diseases, and has the potential to change diagnoses, guide therapeutic intervention and provide opportunities for genetic counseling. Further longitudinal analysis, and continuing progress of the Australian Genomics Health Alliance, Geneti

Background: Accurate and timely diagnosis is critical in providing prognostic information and guiding treatment in acutely unwell patients with suspected monogenic disorders. Aim(s): We describe the development and implementation of a rapid genomic diagnosis program in a routine clinical setting. Method(s): Rapid singleton wholeexome sequencing was performed in acutely unwell patients with suspected monogenic disorders from two pediatric tertiary centers. Technical, organizational, and clinician barriers to implementation were addressed through a cycle of continuous audit and improvement. Service performance parameters and the diagnostic and clinical utility of providing rapid WES were assessed. Result(s): During the study period, time to result reduced from 109 days to 13 days (median 18 days), and this was accompanied by changes in referral and test initiation patterns. Of 26 enrolled patients, 14 (54%) received a molecular genetic diagnosis. Clinical management changed in nine diagnosed patients (64%), including the provision of lifesaving treatment, avoidance of invasive biopsies, and palliative care guidance. A result was provided prior to death or discharge from hospital in 16 of 26 cases (62%). The rapid diagnosis of a riboflavin transporter defect in one patient is estimated to have saved 113 days in intensive care (AUD$508,500) compared to providing the result with a standard turnaround time. Discussion(s): The provision of rapid genomic results in acutely unwell patients with suspected monogenic disorders is feasible in the routine clinical setting and has high diagnostic and clinical utility. It challenges traditional clinical and laboratory genetics service models, and requires a whole-of-system approach for successful implementation.

Fragile X syndrome (FXS) is usually associated with a CGG repeat expansion >200 repeats within the FMR1 gene, known as a full mutation (FM). FM alleles produce abnormal methylation of the FMR1 promoter with reduction or silencing of FMR1 gene expression. Furthermore, premutation (PM: 55⁻199 CGGs) and full mutation alleles usually expand in size when maternally transmitted to progeny. This study describes a PM allele carried by the mother decreasing to a normal sized allele in a male from a dichorionic diamniotic (DCDA) twin pregnancy, with the female twin inheriting FM (200⁻790 CGGs), PM (130 CGGs) and normal-sized (39 CGGs) alleles. Further evidence of instability of the maternal PM allele was shown by a male proband (older brother) mosaic for PM (CGG 78 and 150 CGGs) and FM (200⁻813 CGGs), and a high level of FMR1 promoter methylation, between 50 and 70%, in multiple tissues. The fully-retracted, normal-sized allele was identified by PCR CGG sizing in the male twin, with no evidence of a FM allele identified using Southern blot analysis in multiple tissues collected postnatally and prenatally. Consistent with this, prenatal PCR sizing (35 CGGs) showed inconsistent inheritance of the maternal normal allele (30 CGGs), with single-nucleotide polymorphism (SNP) linkage analysis confirming that the abnormal FMR1 chromosome had been inherited from the mother's PM chromosome. Importantly, the male twin showed no significant hypermethylation of the FMR1 promoter in all pre and postnatal tissues tested, as well as normal levels of FMR1 mRNA in blood. In summary, this report demonstrates the first postnatal follow up of a prenatal case in which FMR1 mRNA levels were approaching normal, with normal levels of FMR1 promoter methylation and normal CGG size in multiple pre and postnatally collected tissues.