Publications by authors named "Sarah Bowdin"

40 Publications

Fifteen-minute consultation: The efficient investigation of infantile and childhood epileptic encephalopathies in the era of modern genomics.

Arch Dis Child Educ Pract Ed 2021 Jan 7. Epub 2021 Jan 7.

Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.

The investigation of children presenting with infantile and childhood epileptic encephalopathies (ICEE) is challenging due to diverse aetiologies, overlapping phenotypes and the relatively low diagnostic yield of MRI, electroencephalography (EEG) and biochemical investigations. Careful history and thorough examination remain essential as these may identify an acquired cause or indicate more targeted investigation for a genetic disorder. Whole exome sequencing (WES) with analysis of a panel of candidate epilepsy genes has increased the diagnostic yield. Whole genome sequencing (WGS), particularly as a trio with both parents' DNA, is likely to supersede WES. Modern genomic investigation impacts on the timing and necessity of other testing. We propose a structured approach for children presenting with ICEE where there is diagnostic uncertainty, emphasising the importance of WGS or, if unavailable, WES early in the investigative process. We note the importance of expert review of all investigations, including radiology, neurophysiology and biochemistry, to confirm the technique used was appropriate as well as the results. It is essential to counsel families on the risks associated with the procedures, the yield of the procedures, findings that are difficult to interpret and implication of 'negative' results. Where children remain without a diagnosis despite comprehensive investigation, we note the importance of ongoing multidisciplinary care.
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http://dx.doi.org/10.1136/archdischild-2020-320606DOI Listing
January 2021

The Cardiac Genome Clinic: implementing genome sequencing in pediatric heart disease.

Genet Med 2020 06 10;22(6):1015-1024. Epub 2020 Feb 10.

Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.

Purpose: This study investigated the diagnostic utility of nontargeted genomic testing in patients with pediatric heart disease.

Methods: We analyzed genome sequencing data of 111 families with cardiac lesions for rare, disease-associated variation.

Results: In 14 families (12.6%), we identified causative variants: seven were de novo (ANKRD11, KMT2D, NR2F2, POGZ, PTPN11, PURA, SALL1) and six were inherited from parents with no or subclinical heart phenotypes (FLT4, DNAH9, MYH11, NEXMIF, NIPBL, PTPN11). Outcome of the testing was associated with the presence of extracardiac features (p = 0.02), but not a positive family history for cardiac lesions (p = 0.67). We also report novel plausible gene-disease associations for tetralogy of Fallot/pulmonary stenosis (CDC42BPA, FGD5), hypoplastic left or right heart (SMARCC1, TLN2, TRPM4, VASP), congenitally corrected transposition of the great arteries (UBXN10), and early-onset cardiomyopathy (TPCN1). The identified candidate genes have critical functions in heart development, such as angiogenesis, mechanotransduction, regulation of heart size, chromatin remodeling, or ciliogenesis.

Conclusion: This data set demonstrates the diagnostic and scientific value of genome sequencing in pediatric heart disease, anticipating its role as a first-tier diagnostic test. The genetic heterogeneity will necessitate large-scale genomic initiatives for delineating novel gene-disease associations.
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http://dx.doi.org/10.1038/s41436-020-0757-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272322PMC
June 2020

Prolidase deficiency diagnosed by whole exome sequencing in a child with pulmonary capillaritis.

ERJ Open Res 2019 Apr 26;5(2). Epub 2019 Apr 26.

Dept of Paediatrics, University of Toronto, Toronto, ON, Canada.

http://ow.ly/rDGz30o8pcd.
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http://dx.doi.org/10.1183/23120541.00205-2018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484094PMC
April 2019

Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children.

Intensive Care Med 2019 05 7;45(5):627-636. Epub 2019 Mar 7.

School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0SP, UK.

Purpose: With growing evidence that rare single gene disorders present in the neonatal period, there is a need for rapid, systematic, and comprehensive genomic diagnoses in ICUs to assist acute and long-term clinical decisions. This study aimed to identify genetic conditions in neonatal (NICU) and paediatric (PICU) intensive care populations.

Methods: We performed trio whole genome sequence (WGS) analysis on a prospective cohort of families recruited in NICU and PICU at a single site in the UK. We developed a research pipeline in collaboration with the National Health Service to deliver validated pertinent pathogenic findings within 2-3 weeks of recruitment.

Results: A total of 195 families had whole genome analysis performed (567 samples) and 21% received a molecular diagnosis for the underlying genetic condition in the child. The phenotypic description of the child was a poor predictor of the gene identified in 90% of cases, arguing for gene agnostic testing in NICU/PICU. The diagnosis affected clinical management in more than 65% of cases (83% in neonates) including modification of treatments and care pathways and/or informing palliative care decisions. A 2-3 week turnaround was sufficient to impact most clinical decision-making.

Conclusions: The use of WGS in intensively ill children is acceptable and trio analysis facilitates diagnoses. A gene agnostic approach was effective in identifying an underlying genetic condition, with phenotypes and symptomatology being primarily used for data interpretation rather than gene selection. WGS analysis has the potential to be a first-line diagnostic tool for a subset of intensively ill children.
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http://dx.doi.org/10.1007/s00134-019-05552-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483967PMC
May 2019

Reappraisal of Reported Genes for Sudden Arrhythmic Death: Evidence-Based Evaluation of Gene Validity for Brugada Syndrome.

Circulation 2018 09;138(12):1195-1205

Toronto General Hospital Research Institute, University of Toronto, Ontario, Canada (S.U., M.H.G.).

Background: Implicit in the genetic evaluation of patients with suspected genetic diseases is the assumption that the genes evaluated are causative for the disease based on robust scientific and statistical evidence. However, in the past 20 years, considerable variability has existed in the study design and quality of evidence supporting reported gene-disease associations, raising concerns of the validity of many published disease-causing genes. Brugada syndrome (BrS) is an arrhythmia syndrome with a risk of sudden death. More than 20 genes have been reported to cause BrS and are assessed routinely on genetic testing panels in the absence of a systematic, evidence-based evaluation of the evidence supporting the causality of these genes.

Methods: We evaluated the clinical validity of genes tested by diagnostic laboratories for BrS by assembling 3 gene curation teams. Using an evidence-based semiquantitative scoring system of genetic and experimental evidence for gene-disease associations, curation teams independently classified genes as demonstrating limited, moderate, strong, or definitive evidence for disease causation in BrS. The classification of curator teams was reviewed by a clinical domain expert panel that could modify the classifications based on their independent review and consensus.

Results: Of 21 genes curated for clinical validity, biocurators classified only 1 gene ( SCN5A) as definitive evidence, whereas all other genes were classified as limited evidence. After comprehensive review by the clinical domain Expert panel, all 20 genes classified as limited evidence were reclassified as disputed with regard to any assertions of disease causality for BrS.

Conclusions: Our results contest the clinical validity of all but 1 gene clinically tested and reported to be associated with BrS. These findings warrant a systematic, evidence-based evaluation for reported gene-disease associations before use in patient care.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.035070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6147087PMC
September 2018

Periodic reanalysis of whole-genome sequencing data enhances the diagnostic advantage over standard clinical genetic testing.

Eur J Hum Genet 2018 05 16;26(5):740-744. Epub 2018 Feb 16.

Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.

Whole-genome sequencing (WGS) as a first-tier diagnostic test could transform medical genetic assessments, but there are limited data regarding its clinical use. We previously showed that WGS could feasibly be deployed as a single molecular test capable of a higher diagnostic rate than current practices, in a prospectively recruited cohort of 100 children meeting criteria for chromosomal microarray analysis. In this study, we report on the added diagnostic yield with re-annotation and reanalysis of these WGS data ~2 years later. Explanatory variants have been discovered in seven (10.9%) of 64 previously undiagnosed cases, in emerging disease genes like HMGA2. No new genetic diagnoses were made by any other method in the interval period as part of ongoing clinical care. The results increase the cumulative diagnostic yield of WGS in the study cohort to 41%. This represents a greater than 5-fold increase over the chromosomal microarrays, and a greater than 3-fold increase over all the clinical genetic testing ordered in practice. These findings highlight periodic reanalysis as yet another advantage of genomic sequencing in heterogeneous disorders. We recommend reanalysis of an individual's genome-wide sequencing data every 1-2 years until diagnosis, or sooner if their phenotype evolves.
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http://dx.doi.org/10.1038/s41431-018-0114-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945683PMC
May 2018

The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

CMAJ 2018 02;190(5):E126-E136

The Centre for Applied Genomics (Reuter, Walker, Thiruvahindrapuram, Whitney, Yuen, Trost, Paton, Pereira, Herbrick, Wintle, Merico, Howe, MacDonald, Lu, Nalpathamkalam, Sung, Wang, Patel, Pellecchia, J. Wei, Strug, Bell, Kellam, Mahtani, Hosseini, Fiume, Marshall, Buchanan, Scherer); Divisions of Clinical Pharmacology and Toxicology (I. Cohn), or Clinical, and Metabolic Genetics (Sondheimer, Weksberg, Shuman, Bowdin, Meyn, Monfared), The Hospital for Sick Children; Departments of Paediatrics (Sondheimer, R. Cohn) and Molecular Genetics (Yuen, Weksberg, Shuman, R. Cohn, Ellis, Meyn), University of Toronto; Deep Genomics Inc. (Merico); Department of Psychiatry (Bassett), University Health Network and Centre for Addiction and Mental Health, University of Toronto; Li Ka Shing Knowledge Institute (Bombard), St. Michael's Hospital; Institute of Health Policy, Management and Evaluation (Bombard), University of Toronto; Centre for Genetic Medicine (Stavropoulos, Bowdin, Ray, Monfared); Molecular Genetics Laboratory (Stavropoulos, Ray, Marshall), Division of Genome Diagnostics, Paediatric Laboratory Medicine; Developmental and Stem Cell Biology (Hildebrandt, W. Wei, Romm, Pasceri, Ellis); Ted Rogers Cardiac Genome Clinic (Hosseini); Cytogenetics Laboratory (Joseph-George), Division of Genome Diagnostics, Paediatric Laboratory Medicine, The Hospital for Sick Children; Departments of Biochemistry and Laboratory Medicine, and Pathobiology (Keeley), University of Toronto; DNAstack (Cook, Fiume); McLaughlin Centre (Lee, Scherer), University of Toronto; Medcan Health Management Inc. (Davies, Hazell); Dalla Lana School of Public Health (Szego), Department of Family and Community Medicine, and The Joint Centre for Bioethics, University of Toronto; Centre for Clinical Ethics (Szego), St. Joseph's Health Centre, Toronto, Ont.

Background: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers.

Methods: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant.

Results: Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set ( = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual.

Interpretation: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.
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http://dx.doi.org/10.1503/cmaj.171151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798982PMC
February 2018

Genome sequencing as a platform for pharmacogenetic genotyping: a pediatric cohort study.

NPJ Genom Med 2017 26;2:19. Epub 2017 May 26.

Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada M5G 1X8.

Whole-genome sequencing and whole-exome sequencing have proven valuable for diagnosing inherited diseases, particularly in children. However, usage of sequencing data as a pharmacogenetic screening tool to ensure medication safety and effectiveness remains to be explored. Sixty-seven variants in 19 genes with known effects on drug response were compared between genome sequencing and targeted genotyping data for coverage and concordance in 98 pediatric patients. We used targeted genotyping data as a benchmark to assess accuracy of variant calling, and to identify copy number variations of the gene. We then predicted clinical impact of these variants on drug therapy. We find genotype concordance across those panels to be > 97%. Concordance of predicted phenotype between estimates of whole-genome sequencing and targeted genotyping panel were 90%; a result from a lower coverage depth or variant calling difficulties in our whole-genome sequencing data when copy number variation and/or the haplotype were present. Importantly, 95 children had at least one clinically actionable pharmacogenetic variant. Diagnostic genomic sequencing data can be used for pre-emptive pharmacogenetic screening. However, concordance between genome-wide sequencing and target genotyping needs to be characterized for each of the pharmacologically important genes.
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http://dx.doi.org/10.1038/s41525-017-0021-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677914PMC
May 2017

Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray.

Eur J Hum Genet 2017 12 20;25(12):1303-1312. Epub 2017 Nov 20.

Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.

The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.
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http://dx.doi.org/10.1038/s41431-017-0020-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865210PMC
December 2017

Genome-wide sequencing expands the phenotypic spectrum of EP300 variants.

Eur J Med Genet 2018 Mar 10;61(3):125-129. Epub 2017 Nov 10.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada. Electronic address:

Many disease genes are defined by their role in causing specific clinically recognizable syndromes. Heterozygous loss of function of the gene EP300 is responsible for a minority of cases of Rubinstein-Taybi syndrome (RSTS). With the application of whole-exome sequencing and whole-genome sequencing, there is the potential to discover new genotype-phenotype correlations. The purpose of this case series is to describe three unrelated females without classic manifestations of RSTS who were unexpectedly found on genome-wide sequencing to have likely pathogenic variants in EP300. These individuals expand our knowledge of the disease spectrum by virtue of their very rare or novel clinical features. Results are placed within the context of all prior published EP300 cases not ascertained by targeted testing, which are disproportionately female compared with a cohort identified because of a clinical suspicion of RSTS (p = 0.01). There are implications for diagnosis, management, and genetic counselling of individuals with EP300-related disease.
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http://dx.doi.org/10.1016/j.ejmg.2017.11.002DOI Listing
March 2018

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test.

Genet Med 2018 04 3;20(4):435-443. Epub 2017 Aug 3.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.

PurposeGenetic testing is an integral diagnostic component of pediatric medicine. Standard of care is often a time-consuming stepwise approach involving chromosomal microarray analysis and targeted gene sequencing panels, which can be costly and inconclusive. Whole-genome sequencing (WGS) provides a comprehensive testing platform that has the potential to streamline genetic assessments, but there are limited comparative data to guide its clinical use.MethodsWe prospectively recruited 103 patients from pediatric non-genetic subspecialty clinics, each with a clinical phenotype suggestive of an underlying genetic disorder, and compared the diagnostic yield and coverage of WGS with those of conventional genetic testing.ResultsWGS identified diagnostic variants in 41% of individuals, representing a significant increase over conventional testing results (24%; P = 0.01). Genes clinically sequenced in the cohort (n = 1,226) were well covered by WGS, with a median exonic coverage of 40 × ±8 × (mean ±SD). All the molecular diagnoses made by conventional methods were captured by WGS. The 18 new diagnoses made with WGS included structural and non-exonic sequence variants not detectable with whole-exome sequencing, and confirmed recent disease associations with the genes PIGG, RNU4ATAC, TRIO, and UNC13A.ConclusionWGS as a primary clinical test provided a higher diagnostic yield than conventional genetic testing in a clinically heterogeneous cohort.
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http://dx.doi.org/10.1038/gim.2017.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895460PMC
April 2018

Use of Clinical Exome Sequencing in Isolated Congenital Heart Disease.

Circ Cardiovasc Genet 2017 06;10(3)

From the Division of Cardiology, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1161/CIRCGENETICS.116.001581DOI Listing
June 2017

Recommendations for the integration of genomics into clinical practice.

Genet Med 2016 11 12;18(11):1075-1084. Epub 2016 May 12.

Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Ontario, Canada.

The introduction of diagnostic clinical genome and exome sequencing (CGES) is changing the scope of practice for clinical geneticists. Many large institutions are making a significant investment in infrastructure and technology, allowing clinicians to access CGES, especially as health-care coverage begins to extend to clinically indicated genomic sequencing-based tests. Translating and realizing the comprehensive clinical benefits of genomic medicine remain a key challenge for the current and future care of patients. With the increasing application of CGES, it is necessary for geneticists and other health-care providers to understand its benefits and limitations in order to interpret the clinical relevance of genomic variants identified in the context of health and disease. New, collaborative working relationships with specialists across diverse disciplines (e.g., clinicians, laboratorians, bioinformaticians) will undoubtedly be key attributes of the future practice of clinical genetics and may serve as an example for other specialties in medicine. These new skills and relationships will also inform the development of the future model of clinical genetics training curricula. To address the evolving role of the clinical geneticist in the rapidly changing climate of genomic medicine, two Clinical Genetics Think Tank meetings were held that brought together physicians, laboratorians, scientists, genetic counselors, trainees, and patients with experience in clinical genetics, genetic diagnostics, and genetics education. This article provides recommendations that will guide the integration of genomics into clinical practice.Genet Med 18 11, 1075-1084.
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http://dx.doi.org/10.1038/gim.2016.17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557020PMC
November 2016

FGFR-associated craniosynostosis syndromes and gastrointestinal defects.

Am J Med Genet A 2016 12 2;170(12):3215-3221. Epub 2016 Aug 2.

Faculty of Dentistry, University of Toronto, Toronto, Canada.

Craniosynostosis is a relatively common birth defect characterized by the premature fusion of one or more cranial sutures. Examples of craniosynostosis syndromes include Crouzon (CS), Pfeiffer (PS), and Apert (AS) syndrome, with clinical characteristics such as midface hypoplasia, hypertelorism, and in some cases, limb defects. Mutations in Fibroblast Growth Factor Receptor-2 comprise the majority of known mutations in syndromic forms of craniosynostosis. A number of clinical reports of FGFR-associated craniosynostosis patients and mouse mutants have been linked to gastrointestinal tract (GIT) disorders, leading to the hypothesis of a direct link between FGFR-associated craniosynostosis syndromes and GIT malformations. We conducted an investigation to determine GIT symptoms in a sample of FGFR-associated craniosynostosis syndrome patients and a mouse model of CS containing a mutation (W290R) in Fgfr2. We found that, compared to the general population, the incidence of intestinal/bowel malrotation (IM) was present at a higher level in our sample population of patients with FGFR-associated craniosynostosis syndromes. We also showed that the mouse model of CS had an increased incidence of cecal displacement, suggestive of IM. These findings suggest a direct relationship between FGFR-related craniosynostosis syndromes and GIT malformations. Our study may shed further light on the potential widespread impact FGFR mutations on different developmental systems. Based on reports of GIT malformations in children with craniosynostosis syndromes and substantiation with our animal model, GIT malformations should be considered in any child with an FGFR2-associated craniosynostosis syndrome. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajmg.a.37862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503117PMC
December 2016

The clinical utility of next-generation sequencing in the neonatal intensive care unit.

Authors:
Sarah C Bowdin

CMAJ 2016 08 30;188(11):786-787. Epub 2016 May 30.

Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ont.

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http://dx.doi.org/10.1503/cmaj.160490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978569PMC
August 2016

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

NPJ Genom Med 2016 Jan;1

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.

The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.
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http://dx.doi.org/10.1038/npjgenmed.2015.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447450PMC
January 2016

The Expanding Clinical Spectrum of Extracardiovascular and Cardiovascular Manifestations of Heritable Thoracic Aortic Aneurysm and Dissection.

Can J Cardiol 2016 Jan 14;32(1):86-99. Epub 2015 Nov 14.

Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

More than 30 heritable conditions are associated with thoracic aortic aneurysm and dissection (TAAD). Heritable syndromic conditions, such as Marfan syndrome, Loeys-Dietz syndrome, and vascular Ehlers-Danlos syndrome, have somewhat overlapping systemic features, but careful clinical assessment usually enables a diagnosis that can be validated with genetic testing. Nonsyndromic FTAAD can also occur and in 20%-25% of these probands mutations exist in genes that encode elements of the extracellular matrix, signalling pathways (especially involving transforming growth factor-β), and vascular smooth muscle cytoskeletal and contractile processes. Affected individuals with either a syndromic presentation or isolated TAAD can have mutations in the same gene. In this review we focus on the genes currently known to have causal mutations for syndromic and isolated FTAAD and outline the range of associated extracardiovascular and cardiovascular manifestations with each.
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http://dx.doi.org/10.1016/j.cjca.2015.11.007DOI Listing
January 2016

Multidisciplinary Aortopathy Clinics Should Now Be the Standard of Care in Canada.

Can J Cardiol 2016 Jan 22;32(1):8-12. Epub 2015 Oct 22.

Division of Cardiology, Department of Paediatrics, The Labatt Family Heart Centre, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

Thoracic aortic aneurysm is often undiagnosed and has a very poor prognosis when presented with acute aortic dissection. Early diagnosis, expert medical management, and elective aortic surgery are the cornerstones of improvement of long-term survival in thoracic aortic disease (TAD). International guidelines now recommend the acute and long-term management of patients with TAD to occur within multidisciplinary aortopathy clinics under the care of professionals with specific training and experience. Multidisciplinary "heart teams" are recognized to be more focused on patient-centric care, to facilitate faster clinical decision times with increased adherence to guideline-directed therapy, and to improve knowledge translation and physician and patient satisfaction. The range of differential diagnoses for TAD has expanded rapidly over the past decade. Diagnosis of an index case with a syndromic or nonsyndromic familial TAD allows for preventative care. Effective family screening can save lives by allowing for elective management of thoracic aortic aneurysm rather than emergent care of acute aortic complications. Expert cardiac imaging with access to the full range of required imaging modalities is central to all clinical management decisions. Medical and surgical management of TAD is now provided as personalized care according to patient- and disease-specific factors. Special considerations apply to pregnancy management for women with TAD. Multidisciplinary aortopathy clinics should now be the standard of care for the management of TAD in Canada and we should implement best practice guidelines. With the already established and emerging clinics, the stage is now set to build a Canadian Aortopathy Clinics Trials network.
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http://dx.doi.org/10.1016/j.cjca.2015.10.003DOI Listing
January 2016

Genetic Testing in Thoracic Aortic Disease--When, Why, and How?

Can J Cardiol 2016 Jan 30;32(1):131-4. Epub 2015 Sep 30.

Centre for Medical Genetics, University Hospital of Antwerp/University of Antwerp, Antwerp, Belgium; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.

Advances in genetic technology over the past 10 years have revealed the polygenic basis of thoracic aortic aneurysm and thoracic aortic acute dissection (TAAD) in a subset of patients. There is mounting evidence to show that clinical risk stratification for aneurysmal dilatation and acute dissection can be based on genotype for some of the known genes, allowing individualized medical and surgical management with the aim of reducing morbidity and mortality. This evidence has led to a recommendation by the American College of Cardiology Foundation and the American Heart Association that the underlying genetic mutation should dictate the timing of aortic repair. Other benefits of identifying a specific genetic cause include prediction of multisystem involvement in syndromic forms of TAAD and cascade screening for other at-risk family members. Mutation analysis for genes associated with TAAD in a clinical setting is typically ordered by geneticists or cardiologists with an interest or expertise in cardiac genetics. We present an approach to assist cardiologists and vascular surgeons in recognizing which patients would benefit from genetic testing, provide justification for such testing, and outline a practical approach to ordering the tests.
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http://dx.doi.org/10.1016/j.cjca.2015.09.018DOI Listing
January 2016

MKS1 regulates ciliary INPP5E levels in Joubert syndrome.

J Med Genet 2016 Jan 21;53(1):62-72. Epub 2015 Oct 21.

Department of Pediatrics, University of Washington, Seattle, Washington, USA Seattle Children's Research Institute, Seattle, Washington, USA.

Background: Joubert syndrome (JS) is a recessive ciliopathy characterised by a distinctive brain malformation 'the molar tooth sign'. Mutations in >27 genes cause JS, and mutations in 12 of these genes also cause Meckel-Gruber syndrome (MKS). The goals of this work are to describe the clinical features of MKS1-related JS and determine whether disease causing MKS1 mutations affect cellular phenotypes such as cilium number, length and protein content as potential mechanisms underlying JS.

Methods: We measured cilium number, length and protein content (ARL13B and INPP5E) by immunofluorescence in fibroblasts from individuals with MKS1-related JS and in a three-dimensional (3D) spheroid rescue assay to test the effects of disease-related MKS1 mutations.

Results: We report MKS1 mutations (eight of them previously unreported) in nine individuals with JS. A minority of the individuals with MKS1-related JS have MKS features. In contrast to the truncating mutations associated with MKS, all of the individuals with MKS1-related JS carry ≥ 1 non-truncating mutation. Fibroblasts from individuals with MKS1-related JS make normal or fewer cilia than control fibroblasts, their cilia are more variable in length than controls, and show decreased ciliary ARL13B and INPP5E. Additionally, MKS1 mutant alleles have similar effects in 3D spheroids.

Conclusions: MKS1 functions in the transition zone at the base of the cilium to regulate ciliary INPP5E content, through an ARL13B-dependent mechanism. Mutations in INPP5E also cause JS, so our findings in patient fibroblasts support the notion that loss of INPP5E function, due to either mutation or mislocalisation, is a key mechanism underlying JS, downstream of MKS1 and ARL13B.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5060087PMC
http://dx.doi.org/10.1136/jmedgenet-2015-103250DOI Listing
January 2016

Novel MASP1 mutations are associated with an expanded phenotype in 3MC1 syndrome.

Orphanet J Rare Dis 2015 Sep 30;10:128. Epub 2015 Sep 30.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, 1501 NW 10th Avenue, BRB-610 M-860, Miami, FL, 33136, USA.

Background: 3MC1 syndrome is a rare autosomal recessive disorder characterized by intellectual disability, short stature and distinct craniofacial, umbilical, and sacral anomalies. Five mutations in MASP1, encoding lectin complement pathway enzymes MASP-1 and MASP-3, have thus far been reported to cause 3MC1 syndrome. Only one previously reported mutation affects both MASP-1 and MASP-3, while the other mutations affect only MASP-3.

Methods: We evaluated six unrelated individuals with 3MC1 syndrome and performed Sanger sequencing for all coding exons of MASP1. We also measured complement lectin and alternative pathway activities in an affected individual's serum.

Results: We found two novel splice site mutations, c.1012-2A > G in one and c.891 + 1G > T in two probands, and three novel missense mutations, c.1451G > A (p.G484E), c.1657G > A (p.D553N), and c.1987G > T (p.D663Y). Missense mutations affect only MASP-3, while splice site mutations affect both MASP-1 and MASP-3. In a proband who is homozygous for c.891 + 1G > T, we detected a total lack of lectin complement pathway activity and a 2.5-fold lower alternative pathway activity. The phenotype observed in patients whose both MASP-1 and MASP-3 are affected and in those whose only MASP-3 is affected does not appear to be different. We observed structural brain abnormalities, neonatal tooth, a vascular anomaly and a solid lesion in liver as novel phenotypic features of 3MC1 syndrome.

Conclusion: Novel mutations and additional phenotypic features expand the genotypic and phenotypic spectrum of 3MC1 syndrome. Although patients with MASP-1 dysfunction in addition to disrupted MASP-3 have an altered complement system, their disease phenotype is not different from those having only MASP-3 dysfunction.
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http://dx.doi.org/10.1186/s13023-015-0345-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589207PMC
September 2015

Heterozygous mutations in ERF cause syndromic craniosynostosis with multiple suture involvement.

Am J Med Genet A 2015 Nov 22;167A(11):2544-7. Epub 2015 Jun 22.

Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.

Craniosynostosis is a clinically and genetically heterogeneous condition. Knowledge of the specific genetic diagnosis in patients presenting with this condition is important for surgical and medical management. The most common single gene causes of syndromic craniosynostosis are mutations in FGFR1, FGFR2, FGFR3, TWIST1, and EFNB1. Recently, a new single gene cause of craniosynostosis was published, together with phenotype data that highlight the clinical importance of making this specific molecular diagnosis. Phenotypic features of "ERF-related craniosynostosis" include sagittal or multiple-suture synostosis, Chiari malformation, and language delay. In order to determine the contribution of ERF mutations to genetically undiagnosed patients with craniosynostosis, we sequenced the coding regions of ERF in 40 patients with multi-suture or sagittal suture synostosis. We identified heterozygous ERF mutations in two individuals (5%). One mutation positive individual had pansynostosis, while the second had bilateral coronal and metopic synostosis. Both presented in infancy or childhood (age 3 months, and 6 years 9 months, respectively). One had CNS abnormalities including Chiari I malformation. Dysmorphic features included hypertelorism, proptosis, depressed nasal bridge, and retrognathia, in keeping with previously reported cases. The individuals did not require repeated cranial surgeries. ERF-related craniosynostosis should be suspected in patients presenting with multiple suture or sagittal synostosis.
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http://dx.doi.org/10.1002/ajmg.a.37218DOI Listing
November 2015

Exome sequencing identifies rare variants in multiple genes in atrioventricular septal defect.

Genet Med 2016 Feb 21;18(2):189-98. Epub 2015 May 21.

Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

Purpose: The genetic etiology of atrioventricular septal defect (AVSD) is unknown in 40% cases. Conventional sequencing and arrays have identified the etiology in only a minority of nonsyndromic individuals with AVSD.

Methods: Whole-exome sequencing was performed in 81 unrelated probands with AVSD to identify potentially causal variants in a comprehensive set of 112 genes with strong biological relevance to AVSD.

Results: A significant enrichment of rare and rare damaging variants was identified in the gene set, compared with controls (odds ratio (OR): 1.52; 95% confidence interval (CI): 1.35-1.71; P = 4.8 × 10(-11)). The enrichment was specific to AVSD probands, compared with a cohort without AVSD with tetralogy of Fallot (OR: 2.25; 95% CI: 1.84-2.76; P = 2.2 × 10(-16)). Six genes (NIPBL, CHD7, CEP152, BMPR1a, ZFPM2, and MDM4) were enriched for rare variants in AVSD compared with controls, including three syndrome-associated genes (NIPBL, CHD7, and CEP152). The findings were confirmed in a replication cohort of 81 AVSD probands.

Conclusion: Mutations in genes with strong biological relevance to AVSD, including syndrome-associated genes, can contribute to AVSD, even in those with isolated heart disease. The identification of a gene set associated with AVSD will facilitate targeted genetic screening in this cohort.
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http://dx.doi.org/10.1038/gim.2015.60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988035PMC
February 2016

Absent CNKSR2 causes seizures and intellectual, attention, and language deficits.

Ann Neurol 2014 Nov 4;76(5):758-64. Epub 2014 Oct 4.

Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada; Cytogenetics Laboratory, Alberta Children's Hospital, Calgary, Alberta, Canada; Department of Anatomical Pathology and Cytopathology, Calgary Laboratory Services, Calgary, Alberta, Canada.

Synaptic function is central to brain function. Understanding the synapse is aided by studies of patients lacking individual synaptic proteins. Common neurological diseases are genetically complex. Their understanding is likewise simplified by studies of less common monogenic forms. We detail the disease caused by absence of the synaptic protein CNKSR2 in 8 patients ranging from 6 to 62 years old. The disease is characterized by intellectual disability, attention problems, and abrupt lifelong language loss following a brief early childhood epilepsy with continuous spike-waves in sleep. This study describes the phenotype of CNKSR2 deficiency and its involvement in systems underlying common neurological disorders.
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http://dx.doi.org/10.1002/ana.24274DOI Listing
November 2014

The genome clinic: a multidisciplinary approach to assessing the opportunities and challenges of integrating genomic analysis into clinical care.

Hum Mutat 2014 May 7;35(5):513-9. Epub 2014 Apr 7.

Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada; The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.

Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genetic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to guide health care decisions throughout life, to anticipate, diagnose, and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific, and clinical paradigms. The potential benefits of presymptomatic identification of at risk individuals, improved diagnostics, individualized therapy, accurate prognosis, and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models, and increased health care costs. Here, we review the challenges of integrating genomic analysis into clinical practice and describe a prototype for implementing genetic medicine. Our multidisciplinary team of bioinformaticians, health economists, ethicists, geneticists, genetic counselors, and clinicians has designed a "Genome Clinic" research project that addresses multiple challenges in genomic medicine-ranging from the development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference, and the ethics of consent.
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http://dx.doi.org/10.1002/humu.22536DOI Listing
May 2014

Predictive genomic testing of children for adult onset disorders: a Canadian perspective.

Am J Bioeth 2014 ;14(3):19-21

a St. Joseph's Health Centre , The Hospital for Sick Children, and University of Toronto.

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http://dx.doi.org/10.1080/15265161.2013.879960DOI Listing
October 2014

Loeys-Dietz syndrome: a primer for diagnosis and management.

Genet Med 2014 Aug 27;16(8):576-87. Epub 2014 Feb 27.

1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA [2] Howard Hughes Institute, Chevy Chase, Maryland, USA.

Loeys-Dietz syndrome is a connective tissue disorder predisposing individuals to aortic and arterial aneurysms. Presenting with a wide spectrum of multisystem involvement, medical management for some individuals is complex. This review of literature and expert opinion aims to provide medical guidelines for care of individuals with Loeys-Dietz syndrome.
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http://dx.doi.org/10.1038/gim.2014.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131122PMC
August 2014

Metachronous neuroblastoma in an infant with germline translocation resulting in partial trisomy 2p: a role for ALK?

J Pediatr Hematol Oncol 2014 Apr;36(3):e193-6

*Department of Paediatrics, Division of Haematology/Oncology ‡Division of Molecular Genetics §Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada †Haematology/Oncology Service, KK Women's and Children's Hospital, Singapore, Singapore.

A male infant with dysmorphic features, intestinal malrotation, and developmental delay was found to have a germline translocation resulting in partial trisomy 2p and monosomy 16p. At 3 and 9 months of age, he developed localized neuroblastoma in each adrenal, which was managed with surgical resection. Tumors were MYCN non-amplified, with 2p copy gain consistent with the germline translocation. The potential increased risk of neuroblastoma associated with partial trisomy 2p is discussed in the context of this and previously published cases, and may be due to increased constitutional expression of MYCN and ALK genes, both located within the duplicated 2p region.
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http://dx.doi.org/10.1097/MPH.0b013e3182a8f25dDOI Listing
April 2014