Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases

Abstract Background Whole-exome sequencing (WES) has become an efficient diagnostic test for patients with likely monogenic conditions such as rare idiopathic diseases or sudden unexplained death. Yet, many cases remain undiagnosed. Here, we report the added diagnostic yield achieved for 101 WES cases re-analyzed 1 to 7 years after initial analysis. Methods Of the 101 WES cases, 51 were rare idiopathic disease cases and 50 were postmortem “molecular autopsy” cases of early sudden unexplained death. Variants considered for reporting were prioritized and classified into three groups: (1) diagnostic variants, pathogenic and likely pathogenic variants in genes known to cause the phenotype of interest; (2) possibly diagnostic variants, possibly pathogenic variants in genes known to cause the phenotype of interest or pathogenic variants in genes possibly causing the phenotype of interest; and (3) variants of uncertain diagnostic significance, potentially deleterious variants in genes possibly causing the phenotype of interest. Results Initial analysis revealed diagnostic variants in 13 rare disease cases (25.4%) and 5 sudden death cases (10%). Re-analysis resulted in the identification of additional diagnostic variants in 3 rare disease cases (5.9%) and 1 sudden unexplained death case (2%), which increased our molecular diagnostic yield to 31.4% and 12%, respectively. Conclusions The basis of new findings ranged from improvement in variant classification tools, updated genetic databases, and updated clinical phenotypes. Our findings highlight the potential for re-analysis to reveal diagnostic variants in cases that remain undiagnosed after initial WES.

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Abstract 15841: Whole Exome Sequencing and Analysis for Sudden Unexplained Death in the Young: A Case Series

Circulation ◽

10.1161/circ.130.suppl_2.15841 ◽

2014 ◽

Vol 130 (suppl_2) ◽

Author(s):

Nupoor Narula ◽

David J Tester ◽

Anna Paulmichl ◽

Joseph J Maleszewski ◽

Michael J Ackerman

Keyword(s):

Sudden Death ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Effective Means ◽

Susceptibility Gene ◽

Case Series ◽

Susceptibility Genes ◽

Sudden Unexplained Death ◽

Unexplained Death ◽

Whole Exome

Introduction: Annually, thousands of sudden deaths in individuals under the age of 35 years remain unexplained following a medico-legal autopsy and are termed autopsy negative sudden unexplained death in the young (SUDY). Cardiomyopathies, channelopathies, and metabolic disorders may underlie a significant number of SUDY cases. Previously, we demonstrated that 25% of autopsy-negative SUDY cases had mutations in the 4 major cardiac ion channel genes ( KCNQ1, KCNH2, SCN5A , and RYR2 ). However, over 100 sudden death-susceptibility genes have been discovered and may be implicated in SUDY. Objective: We explored the utility of whole exome sequencing (WES) followed by gene-specific surveillance as an efficient and effective means of performing post-mortem genetic testing in SUDY. Methods: Postmortem WES was performed on 14 consecutively-referred white SUDY victims (57% men; average age at death 17.4 ± 8.6 years) using the Agilent SureSelect Human All Exon V4+UTR capture kit and an Illumina HiSeq 2000 sequencer. Following variant alignment (hg19) and annotation, 117 cardiac channelopathy-, cardiomyopathy-, and metabolic disorder-susceptibility genes were surveyed to identify putative SUDY-associated mutations. Potentially pathogenic variants had to be non-synonymous and ultra-rare [i.e. absent in all 3 evaluated exome databases (1,000 Genome Project, the NHLBI GO Exome Sequencing Project, and Exome Chip Design)]. Results: On average, each SUDY case had 12,758 ± 2016 non-synonymous variants, of which 79 ± 15 localized to the 117 evaluated genes. Overall, 8 unique, ultra-rare variants (7 missense, 1 in-frame insertion) identified in 6 genes (3 in TTN ; 1 each in CACNA1C, JPH2, MYH7, VCL, RYR2 ) were detected in 7 of 14 cases (50%). Of the 7 missense alterations, 2 (T171M- CACNA1C , I22160T- TTN ) were predicted damaging by 3 in-silico tools. Conclusions: Although WES and gene-specific surveillance is an efficient and effective strategy to detect rare, potentially lethal, genetic variants, the accurate interpretation of each variant is daunting. Importantly, rarity, even ultra-rarity, does not equal pathogenicity even when the ultra-rare variant resides within a so-called sudden death-susceptibility gene.

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Whole-exome sequencing accuracy in the diagnosis of primary ciliary dyskinesia

ERJ Open Research ◽

10.1183/23120541.00213-2020 ◽

2020 ◽

Vol 6 (4) ◽

pp. 00213-2020

Author(s):

Alex Gileles-Hillel ◽

Hagar Mor-Shaked ◽

David Shoseyov ◽

Joel Reiter ◽

Reuven Tsabari ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Primary Ciliary Dyskinesia ◽

Diagnostic Yield ◽

Characteristic Curve ◽

Transmission Electron Microscopy Analysis ◽

Alternative Diagnosis ◽

Pathogenic Variants ◽

Whole Exome ◽

Ciliary Dyskinesia

The diagnosis of primary ciliary dyskinesia (PCD) relies on clinical features and sophisticated studies. The detection of bi-allelic disease-causing variants confirms the diagnosis. However, a standardised genetic panel is not widely available and new disease-causing genes are continuously identified.To assess the accuracy of untargeted whole-exome sequencing (WES) as a diagnostic tool for PCD, patients with symptoms highly suggestive of PCD were consecutively included. Patients underwent measurement of nasal nitric oxide (nNO) levels, ciliary transmission electron microscopy analysis (TEM) and WES. A confirmed PCD diagnosis in symptomatic patients was defined as a recognised ciliary ultrastructural defect on TEM and/or two pathogenic variants in a known PCD-causing gene.Forty-eight patients (46% male) were enrolled, with a median age of 10.0 years (range 1.0–37 years). In 36 patients (75%) a diagnosis of PCD was confirmed, of which 14 (39%) patients had normal TEM. A standalone untargeted WES had a diagnostic yield of 94%, identifying bi-allelic variants in 11 known PCD-causing genes in 34 subjects. A nNO<77 nL·min was nonspecific when including patients younger than 5 years (area under the receiver operating characteristic curve (AUC) 0.75, 95% CI 0.60–0.90). Consecutive WES considerably improved the diagnostic accuracy of nNO in young children (AUC 0.97, 95% CI 0.93–1). Finally, WES established an alternative diagnosis in four patients.In patients with clinically suspected PCD and low nNO levels, WES is a simple, beneficial and accurate next step to confirm the diagnosis of PCD or suggest an alternative diagnosis, especially in preschool-aged children in whom nNO is less specific.

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Post-mortem whole-exome sequencing (WES) with a focus on cardiac disease-associated genes in five young sudden unexplained death (SUD) cases

International Journal of Legal Medicine ◽

10.1007/s00414-016-1317-4 ◽

2016 ◽

Vol 130 (4) ◽

pp. 1011-1021 ◽

Cited By ~ 13

Author(s):

Jacqueline Neubauer ◽

Cordula Haas ◽

Christine Bartsch ◽

Argelia Medeiros-Domingo ◽

Wolfgang Berger

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Cardiac Disease ◽

Post Mortem ◽

Sudden Unexplained Death ◽

Unexplained Death ◽

Whole Exome ◽

Disease Associated Genes

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Using whole exome sequencing and bioformatics in the molecular autopsy of a sudden unexplained death syndrome (SUDS) case

Forensic Science International ◽

10.1016/j.forsciint.2015.08.022 ◽

2015 ◽

Vol 257 ◽

pp. e20-e25 ◽

Cited By ~ 5

Author(s):

Chun Wang ◽

Shan Duan ◽

Guoli Lv ◽

Xiaoping Lai ◽

Rui Chen ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Molecular Autopsy ◽

Sudden Unexplained Death ◽

Unexplained Death ◽

Whole Exome

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Confirmation of Cause of Death Via Comprehensive Autopsy and Whole Exome Molecular Sequencing in People With Epilepsy and Sudden Unexpected Death

Journal of the American Heart Association ◽

10.1161/jaha.121.021170 ◽

2021 ◽

Cited By ~ 1

Author(s):

C. Anwar A. Chahal ◽

David J. Tester ◽

Ahmed U. Fayyaz ◽

Keerthi Jaliparthy ◽

Nadeem A. Khan ◽

...

Keyword(s):

Cardiac Arrest ◽

Sudden Death ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Cause Of Death ◽

Sudden Cardiac Arrest ◽

Sudden Unexpected Death ◽

Unexpected Death ◽

Pathogenic Variants ◽

Whole Exome

Background Sudden cardiac arrest is the leading mode of death in the United States. Epilepsy affects 1% of Americans; yet epidemiological data show a prevalence of 4% in cases of sudden cardiac arrest. Sudden unexpected death in epilepsy (SUDEP) may share features with sudden cardiac arrest. The objective of this study was to report autopsy and genomic findings in a large cohort of SUDEP cases. Methods and Results Mayo Clinic Sudden Death Registry containing cases (ages 0–90 years) of sudden unexpected and unexplained deaths 1960 to present was queried. Exome sequencing performed on decedent cases. From 13 687 cases of sudden death, 656 (4.8%) had a history of seizures, including 368 confirmed by electroencephalography, 96 classified as SUDEP, 58 as non‐SUDEP, and 214 as unknown (insufficient records). Mean age of death in SUDEP was 37 (±19.7) years; 56 (58.3%) were male; 65% of deaths occurred at night; 54% were found in bed; and 80.6% were prone. Autopsies were obtained in 83 cases; bystander coronary artery disease was frequently reported as cause of death; nonspecific fibrosis was seen in 32.6% of cases, in structurally normal hearts. There were 4 cases of Dravet syndrome with pathogenic variants in SCN1A gene. Using whole exome sequencing in 11 cases, 18 ultrarare nonsynonymous variants were identified in 6 cases including CACNB2, RYR2, CLNB, CACNA1H, and CLCN2 . Conclusions This study examined one of the largest single‐center US series of SUDEP cases. Several cases were reclassified as SUDEP, 15% had an ECG when alive, and 11 (11.4%) had blood for whole exome sequencing analysis. The most frequent antemortem genetic finding was pathogenic variants in SCN1A ; postmortem whole exome sequencing identified 18 ultrarare variants.

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Abstract 12059: Incidental Findings in Cardiomyopathy and Channelopathy Genes Among 5891 Individuals Undergoing Whole-exome Sequencing. What Should be Reported?

Circulation ◽

10.1161/circ.132.suppl_3.12059 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Elisa Mastantuono ◽

Thomas Wieland ◽

Riccardo Berutti ◽

Peter Lichtner ◽

Tim Strom ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Incidental Findings ◽

Genetic Disorders ◽

Molecular Diagnostic ◽

Minor Genes ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Whole Exome ◽

Unknown Significance

Background: Whole-exome-sequencing (WES) is becoming a common molecular diagnostic test for patients with genetic disorders. However, this technique allows the identification not only of mutations responsible for the disease under investigation, but also of variants potentially causing other diseases, the so called “incidental findings” (IFs). The American College of Medical Genetics and Genomics (ACMG) stated that IFs should be reported based on clinical validity and utility and indicated a list of 56 actionable genes. Among these, nearly half (20/56) are major genes associated with channelopathies and cardiomyopathies. Despite these recommendations, most of the studies so far published, reported also mutations in minor genes among the actionable findings. Methods: WES was performed in 5891 individuals without known channelopathies or cardiomyopathies. Exome data were first filtered based on genotype quality. Subsequently, a frequency filter was applied, considering 1000 Genomes, ExAC and our internal exome database. Variants reported as pathogenic in ClinVar or novel but expected to be pathogenic (nonsense, frameshift and splice) were further investigated, following the ACMG guidelines. Major (20) and minor (73) genes associated with channelopathies and cardiomyopathies were evaluated. Results: We identified 3514 variants in the 93 genes under investigation, after applying the quality and frequency filters. Eight variants were classified as pathogenic and 52 as likely pathogenic and they were detected in around 1% of the individuals. The vast majority (85%) of pathogenic or likely pathogenic variants were located in the 20 actionable genes indicated by ACMG. The inclusion of minor genes increased the number of variants of unknown significance (VUS), from 865 to 3454. Conclusion: Our data support the ACMG recommendations in reporting only IFs identified in the 20 major cardiac actionable genes. Indeed, the inclusion of minor genes is mainly increasing the number of VUS, without significantly impacting the number of pathogenic and likely pathogenic variants. The percentage of individuals with potentially clinical relevant variants in these genes is too high in relation to the disease-prevalence: a cardiologic evaluation is warranted.

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Erratum to: Post-mortem whole-exome sequencing (WES) with a focus on cardiac disease-associated genes in five young sudden unexplained death (SUD) cases

International Journal of Legal Medicine ◽

10.1007/s00414-016-1346-z ◽

2016 ◽

Vol 130 (4) ◽

pp. 1023-1023 ◽

Cited By ~ 1

Author(s):

Jacqueline Neubauer ◽

Cordula Haas ◽

Christine Bartsch ◽

Argelia Medeiros-Domingo ◽

Wolfgang Berger

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Cardiac Disease ◽

Post Mortem ◽

Sudden Unexplained Death ◽

Unexplained Death ◽

Whole Exome ◽

Disease Associated Genes

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Unveiling a sudden unexplained death case by whole exome sequencing and bioinformatic analysis

Molecular Genetics & Genomic Medicine ◽

10.1002/mgg3.1182 ◽

2020 ◽

Vol 8 (4) ◽

Author(s):

Martina Modena ◽

Vincenzo Castiglione ◽

Paolo Aretini ◽

Chiara M. Mazzanti ◽

Enrica Chiti ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Bioinformatic Analysis ◽

Sudden Unexplained Death ◽

Unexplained Death ◽

Death Case ◽

Whole Exome

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B.06 Whole exome sequencing in genetic ataxias associated with cerebellar atrophy: the Canadian experience

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/cjn.2019.95 ◽

2019 ◽

Vol 46 (s1) ◽

pp. S11

Author(s):

L Gauquelin ◽

T Hartley ◽

M Tarnopolsky ◽

DA Dyment ◽

B Brais ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Diagnostic Yield ◽

Genetic Diseases ◽

Genetic Diagnosis ◽

Cerebellar Atrophy ◽

Clinical Findings ◽

Disease Genes ◽

Pathogenic Variants ◽

Whole Exome

Background: Cerebellar atrophy is characterized by loss of cerebellar tissue, with evidence on brain imaging of enlarged interfolial spaces compared to the foliae. Genetic ataxias associated with cerebellar atrophy are a heterogeneous group of disorders. We investigated the prevalence in Canada and the diagnostic yield of whole exome sequencing (WES) for this group of conditions. Methods: Between 2011 and 2017, WES was performed in 91 participants with cerebellar atrophy as part of one of two national research programs, Finding of Rare Genetic Disease Genes (FORGE) or Enhanced Care for Rare Genetic Diseases in Canada (Care4Rare). Results: A genetic diagnosis was established in 58% of cases (53/91). Pathogenic variants were found in 24 known genes, providing a diagnosis for 46/53 participants (87%), and in four novel genes, accounting for 7/53 cases (13%). 38/91 cases (42%) remained unsolved. The most common diagnoses were channelopathies in 12/53 patients (23%) and mitochondrial disorders in 9/53 (17%). Inheritance was autosomal recessive in the majority of cases. Additional clinical findings provided useful clues to some of the diagnoses. Conclusions: This is the first report on the prevalence of genetic ataxias associated with cerebellar atrophy in Canada, and the utility of WES for this group of conditions.

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