scholarly journals HPO-driven virtual gene panel: a new efficient approach in molecular autopsy of sudden unexplained death

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ulrike Schön ◽  
Anna Holzer ◽  
Andreas Laner ◽  
Stephanie Kleinle ◽  
Florentine Scharf ◽  
...  
Keyword(s):  
Causal Variant ◽  
Mean Value ◽  
Gene Panel ◽  
Tissue Samples ◽  
Human Phenotype ◽  
Molecular Autopsy ◽  
Sudden Unexplained Death ◽  
Unexplained Death ◽  
Whole Exome ◽  
Genetic Assessment

Abstract Background Molecular autopsy represents an efficient tool to save the diagnosis in up to one-third of sudden unexplained death (SUD). A defined gene panel is usually used for the examination. Alternatively, it is possible to carry out a comprehensive genetic assessment (whole exome sequencing, WES), which also identifies rare, previously unknown variants. The disadvantage is that a dramatic number of variants must be assessed to identify the causal variant. To improve the evaluation of WES, the human phenotype ontology (HPO) annotation is used internationally for deep phenotyping in the field of rare disease. However, a HPO-based evaluation of WES in SUD has not been described before. Methods We performed WES in tissue samples from 16 people after SUD. Instead of a fixed gene panel, we defined a set of HPO terms and thus created a flexible “virtual gene panel”, with the advantage, that recently identified genes are automatically associated by HPO terms in the HPO database. Results We obtained a mean value of 68,947 variants per sample. Stringent filtering ended up in a mean value of 276 variants per sample. Using the HPO-driven virtual gene panel we developed an algorithm that prioritized 1.4% of the variants. Variant interpretation resulted in eleven potentially causative variants in 16 individuals. Conclusion Our data introduce an effective diagnostic procedure in molecular autopsy of SUD with a non-specific clinical phenotype.

scholarly journals Dealing With Unspecific Clinical Phenotypes in Molecular Autopsy - HPO-Driven Whole Exome Sequencing Analysis Versus Gene Panel Testing

2020 ◽  
Author(s):  
Ulrike Schoen ◽  
Anna Holzer ◽  
Andreas Laner ◽  
Stephanie Kleinle ◽  
Florentine Scharf ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Gene Panel ◽  
Sequencing Analysis ◽  
Tissue Samples ◽  
Human Phenotype ◽  
Versus Gene ◽  
Molecular Autopsy ◽  
Whole Exome ◽  
Gene Panel Testing

Abstract Background: Molecular autopsy represents an efficient tool to save the diagnosis in up to one-third of sudden unexplained death (SUD). A defined gene panel is usually used for the examination. Alternatively, it is possible to carry out a comprehensive genetic assessment (Whole Exome Sequencing, WES), which also identifies rare, previously unknown variants. The disadvantage is that a dramatic number of variants must be assessed to identify the causal variant. To improve the evaluation of WES, the Human Phenotype Ontology (HPO) annotation is used internationally for deep phenotyping in the field of rare disease. However, a HPO-based evaluation of WES in SUD has not been described before.Methods: We performed WES in tissue samples from 16 people after SUD. Instead of a fixed gene panel, we defined a set of HPO terms and thus created a flexible “virtual gene panel”, with the advantage, that recently identified genes are automatically associated by HPO terms in the HPO database.Results: We obtained a median value of 68,947 variants per sample. Stringent filtering ended up in a median value of 276 variants per sample. Using the HPO-driven virtual gene panel we developed an algorithm that prioritized 1.4% of the variants. Variant interpretation resulted in eleven potentially causative variants in 16 individuals. Conclusion: Our data introduce an effective diagnostic procedure in molecular autopsy of SUD with a non-specific clinical phenotype.

scholarly journals Whole-Exome Molecular Autopsy After Exertion-Related Sudden Unexplained Death in the Young

2016 ◽  
Vol 9 (3) ◽  
pp. 259-265 ◽  
Author(s):  
Jason H. Anderson ◽  
David J. Tester ◽  
Melissa L. Will ◽  
Michael J. Ackerman
Keyword(s):  
Molecular Autopsy ◽  
Sudden Unexplained Death ◽  
Unexplained Death ◽  
Whole Exome

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

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Elias L. Salfati ◽  
Emily G. Spencer ◽  
Sarah E. Topol ◽  
Evan D. Muse ◽  
Manuel Rueda ◽  
...  
Keyword(s):  
Sudden Death ◽  
Rare Disease ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Diagnostic Yield ◽  
Molecular Diagnostic ◽  
Sudden Unexplained Death ◽  
Unexplained Death ◽  
Pathogenic Variants ◽  
Whole Exome

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.

P4172Prevalence and potential genetic determinants of young sudden unexplained death victims with suspected arrhythmogenic mitral valve prolapse

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
J Giudicessi ◽  
D Tester ◽  
M Ackerman
Keyword(s):  
Mitral Valve ◽  
Mitral Valve Prolapse ◽  
Molecular Mechanisms ◽  
Age At Death ◽  
Genetic Determinants ◽  
Contributing Factors ◽  
Benign Condition ◽  
Sudden Unexplained Death ◽  
Unexplained Death ◽  
Whole Exome

Abstract Background Mitral valve prolapse (MVP) is largely considered a benign condition. Recently, arrhythmogenic MVP, a sudden cardiac death (SCD)-predisposing condition characterized clinically by frequent/complex ventricular arrhythmias likely secondary to prolapsing leaflet-induced fibrosis of the left ventricle (LV), has emerged as an underappreciated cause of sudden unexplained death in the young (SUDY). Objective To determine the prevalence and potential genetic underpinnings of suspected arrhythmogenic MVP in a referral cohort of SUDY cases. Methods In this retrospective necropsy study, the medical records, autopsy reports, and whole exome molecular autopsy (WEMA) results for 77 SUDY victims (27 females; average age at death 20.6±8.9 years) were reviewed. Evidence of myxomatous MVP and concomitant LV pathology were noted. Variants detected in the pre-specified 164 WEMA gene panel with a frequency <0.001 in public exomes were classified using the 2015 American College of Medical Genetics (ACMG) guidelines. Results Overall, 6/77 (7.8%; 2 females; average age at death 20.7±6.9 years) SUDY cases had MVP as the lone abnormal post-mortem finding. The majority had bileaflet involvement (5/6; 83%) and microscopic LV fibrosis (5/6; 83%). Two SUDY cases (33%) were diagnosed with MVP by echocardiography prior to death. No gross hypertrophy, myocyte disarray, or fibrofatty replacement was noted. Unexpectedly, an ACMG pathogenic/likely pathogenic (P/LP) was more likely to be detected in SUDY cases with MVP than those without [3/6 (50%) vs 9/71 (13%); p<0.05]. Interestingly, the three variants identified in MVP-positive SUDY cases localized to genes associated previously with a cardiomyopathy/channelopathy predisposition (p.E1518fsX25-DMD, p.S285N-RYR2, and p.R109X-TTN). Conclusion This WEMA series provides additional evidence that the combination of bileaflet MVP and microscopic LV fibrosis underlies an unexpected number of SUDY cases. Whether P/LP variants in cardiomyopathy/channelopathy-susceptibility genes function as contributing factors or if unrelated, but poorly understood, molecular mechanisms account for the distinct cardiomyopathy-like phenotype observed in arrhythmogenic MVP requires further investigation.

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

Circulation ◽  
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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