whole exome sequencing diagnostic yield

whole exome sequencing diagnostic yield

2020, Epub ahead of print. (2019) assessed the diagnostic yield of whole exome sequencing (WES). • As technology and bioinformatic pipelines improve and new disease genes are published, it is essential to continuously re-evaluate previously generated iagnostic yield is steadily improving with the increasing use of whole-exome sequencing (WES) and whole-genome sequencing (WGS) to diagnose patients with a suspected genetic disorder1. However, it is uncertain whether the use of Whole Exome Sequencing (WES) represents a more effective approach for diagnosis of cases with HCM and DCM. Although many genes have been associated to Mendelian diseases, the diagnostic yield of genome sequencing remains limited, varying from 8 to 70%2. Am. As a result, many such patients remain on a diagnostic odyssey. As whole exome sequencing (WES) becomes more widely used in the clinical realm, a wealth of unanalyzed information will be routinely generated. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. J. HHS Coll. 3 Using whole-exome sequencing (WES) of the peripheral blood of the proband and other affected or unaffected relatives, we aimed at discovering genetic variant(s) that cause or contribute to their disease, therefore permitting resolution of the diagnostic odyssey and potentially leading to better patient management through … Figure 3.. NIH  |  Whole Exome Sequencing - Maximizing the diagnostic yield in various clinical indications 3 WES generates a lot of genetic information, which requires thorough … COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: Prospective cohort study and systematic review. Importance:Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. Figure 1.. main outcome measures: Diagnostic yield and acceptability of whole exome sequencing in patients with retinal disorders.  |  Purpose EVIDENCE, an automated interpretation system, has been developed to facilitate the entire process of whole exome sequencing (WES) analyses. In WES, protein-coding regions of all genes (approximately 20,000) of the human genome, known as the exome, are sequenced using next-generation sequencing technologies. Epub 2018 Oct 15. Recent years have seen the growing implementation of next-generation sequencing (NGS) techniques into widespread clinical use, revolutionizing the diagnostic odyssey for many families with monogenic disorders (Yang et al., 2013; Stranneheim and Wedell, 2016). 1. Gynecol. While whole-exome sequencing (WES) and whole-genome sequencing (WGS) are more commonly utilized as a tool for molecular diagnosis of affected pediatric and adult patients (Lee et al., 2014; Taylor et al., 2015; Sawyer et al., 2016), data regar… We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Although many genes have been associated to Mendelian diseases, the diagnostic yield of genome sequencing remains limited, varying from 8 to 70%2. However, it is uncertain whether the use of Whole Exome Sequencing (WES) represents a more effective approach for diagnosis of cases with HCM and DCM. Sawyer SL, Hartley T, Dyment DA et al. 2020 Feb;22(2):280-282. doi: 10.1038/s41436-019-0674-z. Print 2020 Aug. Genet Med. Using WES read depth data to predict copy number variation (CNV) could extend the diagnostic utility of this previously underutilized data by providing clinically important information such as previously unsuspected deletions or duplications. Ziaeian, B. 37 Moreover, as shown in 30 cases, putatively pathogenic variants were … Violin plots of mean WES coverage of the genes covered by four commercial panels. Conclusions: WES increases the yield of molecular diagnosis over standard diagnostic testing. In this study, we performed indirect comparisons of the coverage and diagnostic yield of WES on genes and variants related to HCM and DCM versus 4 different commercial gene panels using 40 HCM and DCM patients, assuming perfect coverage in those panels. Cardiomyopathies in China: A 2018-2019 state-of-the-art review. Coverage of commercial gene panels is given as reference. • Whole exome sequencing (WES) is a tool that is increasingly used in the clinical setting for the diagnosis of genetic disorders. 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. Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping Christopher M. Watson1,2*, Laura A. Crinnion1,2, Ian R. Berry1, Sally M. Harrison2, Carolina Lascelles2, Agne Antanaviciute2, Ruth S. Charlton1, Angus Dobbie1, Ian M. Carr2 and David T. Bonthron1,2 Abstract DNA from 330 probands (age range, 0‐68 years) with suspected genetic disorders were subjected to whole exome sequencing. Dilated cardiomyopathy (DCM) is a heritable, genetically heterogeneous disorder characterized by progressive heart failure. & Fonarow, G. C. Epidemiology and aetiology of heart failure. Variant types reported for patients with non-diagnostic WES. Rev. Targeted whole-exome sequencing (WES) is a powerful diagnostic tool for a broad spectrum of heterogeneous neurological disorders. 2013;8:355–382. al. Epub 2016 Dec 21. -, Arbustini E, et al. 2020 Aug 25;6(4):a005165. The plot shows the distribution of coverage over the genes. However, it is uncertain whether the use of Whole Exome Sequencing (WES) represents a more effective approach for diagnosis of cases with HCM and DCM. Diagnostic yield in these studies, defined as the proportion of tested patients with .  |  This site needs JavaScript to work properly. 01121616/Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/International, 01221616/Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/International, NCI CPTC Antibody Characterization Program. 2021 Jan-Feb;23(1):69-73. doi: 10.4103/aja.aja_36_20. Rev. Whole exome sequencing: final evidence report Page ES-2 Limitations: Most of the evidence is from uncontrolled, retrospective, observational studies. doi: 10.1016/j.gheart.2013.11.001. Whole Exome Sequencing (WES) is a robust and one of the most comprehensive genetic tests for identifying the disease-causing changes in a large variety of genetic disorders. Pflugers Arch. Background: Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. Its clinical utility has been proven in epileptic encephalopathies and in mixed epilepsy cohorts (2–11); and in neurodevelopmental disorders (12–14) i… PMID:26283276 3. However, it is uncertain whether the use of Whole Exome Sequencing (WES) represents a more effective approach for diagnosis of cases with HCM and DCM. Epub 2019 Oct 14. Curr. No other authors have relevant conflicts of interest to disclose. Targeted next generation sequencing of gene panels has become a popular tool for the genetic diagnosis of hypertrophic (HCM) and dilated cardiomyopathy (DCM). In a sample of patients with undiagnosed, suspected genetic conditions, a certain type of exome sequencing method was associated with a higher molecular diagnostic yield … Methods DNA from 330 probands (age range, 0–68 years) with suspected genetic disorders were subjected to WES. The Department of Molecular and Human Genetics at Baylor College of Medicine derives revenue from the clinical exome sequencing offered in the Medical Genetics Laboratory and Whole Genome Laboratory and the authors who are faculty members are indicated in the affiliation section on the title page. CODE Study Collaborators. Diagnostic yield in ID cohort (n = 95) by subgroup distribution through whole genome low-coverage sequencing and medical exome sequencing. 51. However, it is uncertain whether the use of Whole Exome Sequencing (WES) represents a more effective approach for diagnosis of cases with HCM and DCM. Dillon O, et al. Cardiol.  |  BACKGROUND: Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. NLM As whole exome sequencing (WES) becomes more widely used in the clinical realm, a wealth of unanalyzed information will be routinely generated. Here, we report the added diagnostic yield achieved for 101 WES cases re-analyzed 1 to 7years after initial analysis. Keywords: One test for all: whole exome sequencing signicantly improves the diagnostic yield in growth retarded patients referred for molecular testing for Silver–Russell syndrome Robert Meyer1, Matthias Begemann1, Christian Thomas Hübner1, Daniela Dey1, Alma Kuechler2, CeGaT Exome Xtra achieves the maximum diagnostic yield to solve patient cases. This is potentially secondary to several factors: (1) bias in case selection, as smaller series may have selected only cases with positive results 31; (2) the proportion of CHD associated with ECA, as the greater the proportion, the higher the overall yield; and (3) the sequencing approach used, i.e. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Please enable it to take advantage of the complete set of features! New Insights on Genetic Diagnostics in Cardiomyopathy and Arrhythmia Patients Gained by Stepwise Exome Data Analysis. Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). The potential diagnostic yield of whole exome sequencing in pregnancies complicated by fetal ultrasound anomalies Publication Publication. © 2019 National Society of Genetic Counselors. Ultrasound Obs. 2015;65:1249–1254. Importance:Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. Acta Obstetricia et Gynecologica Scandinavica Objective:To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors. Kolokotronis K, Pluta N, Klopocki E, Kunstmann E, Messroghli D, Maack C, Tejman-Yarden S, Arad M, Rost S, Gerull B. J Clin Med. Venn diagram of the number of genes covered by 4 commercial panels in…, Violin plots of coverage among 17 “core” genes related to HCM and DCM.…, Violin plots of mean WES coverage of the genes covered by four commercial…, Histogram of WES coverage of 1552 potentially pathogenic cardiomyopathy related variants in Clinvar…, NLM Violin plots of coverage among 17 “core” genes related to HCM and DCM. Eur J Hum Genet. RESEARCH ARTICLE Increasing the diagnostic yield of exome sequencing by copy number variant analysis Daniel S. Marchuk ID 1, Kristy Crooks2, Natasha Strande ID 1,2, Kathleen Kaiser-Rogers1,2,3, Laura V. Milko1, Alicia Brandt ID 1, Alexandra Arreola2¤, Christian R. Tilley ID 1, Chris Bizon4, Neeta L. Vora5, Kirk C. Wilhelmsen1,4, James P. Evans1, Jonathan S. Berg1* doi: 10.1007/s11886-015-0606-8. Get the latest public health information from CDC: https://www.coronavirus.gov, Get the latest research information from NIH: https://www.nih.gov/coronavirus, Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. Conclusions: -, Hershberger RE, Hedges DJ, Morales A. Dilated cardiomyopathy: the complexity of a diverse genetic architecture. Heart. 2013;10:531–547. The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in … In addition, an evaluation of the clinical characteristics that influence the likelihood of identifying a genetic cause and assessed the potential impact of the genetic diagnosis on … intervention: Participants were offered whole exome sequencing in addition to clinically available sequencing gene panels between July 2012 and January 2013 to determine the molecular etiology of their retinal dystrophy. a ) The histogram of diagnostic … 2019 May;471(5):755-768. doi: 10.1007/s00424-018-2214-0. The MOGE(S) classification for a phenotype-genotype nomenclature of cardiomyopathy: Endorsed by the world heart federation. 3 pathogenic or likely pathogenic were found among the 26 DCM patients (diagnostic yield 12%). The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. This study investigated the diagnostic yield of EVIDENCE in patients suspected genetic disorders. Refaat MM, Hotait M, London B. Genetics of Sudden Cardiac Death. 100% coverage within the genes covered by the panels is assumed. EVIDENCE, an automated variant prioritization system, has been developed to facilitate whole exome sequencing analyses. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: Prospective cohort study and systematic review. Long 1, … DCM typically remains clinically silent until adulthood, yet symptomatic disease can develop in childhood. Macke EL, Morales-Rosado JA, Gupta A, Schmitz CT, Kruisselbrink T, Lanpher B, Klee EW. View 4 peer reviews of Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system,EVIDENCE on Publons COVID-19 : add an open review or score for a COVID-19 paper now to ensure the latest research gets the extra scrutiny it needs. doi: 10.1038/nrcardio.2013.105. 2017 Feb;25(3):308-314. doi: 10.1038/ejhg.2016.182. Matthew T. Wheeler has modest ownership interest in Personalis Inc. COVID-19 is an emerging, rapidly evolving situation. Cold Spring Harb Mol Case Stud. View 4 peer reviews of Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system,EVIDENCE on Publons COVID-19 : add an open review or score for a COVID-19 paper now to ensure the latest research gets the extra scrutiny it needs. -. Methods Exome sequencing is currently recommended as a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system, EVIDENCE September 2020 Clinical Genetics 98(6) Get the latest public health information from CDC: https://www.coronavirus.gov, Get the latest research information from NIH: https://www.nih.gov/coronavirus, Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. Snoeijen-Schouwenaars et. Targeted next generation sequencing of gene panels has become a popular tool for the genetic diagnosis of hypertrophic (HCM) and dilated cardiomyopathy (DCM). a ) The histogram of diagnostic … Figure 3.. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, Sixty-six of 165 (40%) patients undergoing WES had no documented insurance coverage for WES prior to the UDN evaluation. Clipboard, Search History, and several other advanced features are temporarily unavailable.  |  To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES. We conclude that most of the pathogenic variants for HCM and DCM can be found within a small number of genes which were covered by all the commercial gene panels, and the application of WES did not increase diagnostic yield. This study investigated the diagnostic yield of EVIDENCE in patients with suspected genetic disorders. Prevalence of gene mutations in a Chinese 46,XY disorders of sex development cohort detected by targeted next-generation sequencing. Moreover, the coverage of WES appeared inadequate for TNNI3 and PLN. WES was performed on 180 patients with early-onset epilepsy (≤5 years) of unknown cause. 2016 Mar; 89: 275–284. Diagnostic yield in ID cohort (n = 95) by subgroup distribution through whole genome low-coverage sequencing and medical exome sequencing. Ultrasound Obs. diagnostic yield; exome sequencing; insurance coverage; rare diseases; reimbursement; undiagnosed diseases; access; genetic testing; policy; public health. mutations for the rest continue to be discovered, primarily by whole exome sequencing (WES).1,2 In a group of patients suspected to have genetic diseases, the diagnostic rate of WES has been found to range from 30% to 40%, a variation that may be attributed to the numbers and phenotypes of enrolled patients and the anthropologic characteristics of study Snoeijen-Schouwenaars et. See this image and copyright information in PMC. COVID-19 is an emerging, rapidly evolving situation. 15/43 (35%) had a pathogenic variant reported, 19/43 (44%) of patients without a pathogenic or likely pathogenic variant reported at least one VUS in a gene related to the patient’s clinical phenotype, and 9/43 (21%) only had a research variant. With the implementation of next generation sequencing ... whole exome sequencing (WES), and trio-based WES. Methods DNA from 330 probands (age range, 0–68 years) with suspected genetic disorders were subjected to WES. CeGaT Exome Xtra achieves the maximum diagnostic yield to solve patient cases. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. The coverage was similar to that of four existing commercial gene panels due to the clustering of mutation within MYH7, MYBPC3, TPM1, TNT2, and TTN. Epilepsy is a common pediatric neurological disorder associated with an increased risk of developmental delay, autism and psychiatric illness; and for which treatment is ineffective in 30–40% of patients. The plot shows the distribution of coverage among 40 HCM and DCM patients. iagnostic yield is steadily improving with the increasing use of whole-exome sequencing (WES) and whole-genome sequencing (WGS) to diagnose patients with a suspected genetic disorder1. Our study sought to answer whether genome-scale sequencing could provide or … Cardiomyopathy phenotypes in human-induced pluripotent stem cell-derived cardiomyocytes-a systematic review. WGS – whole genome sequencing; WES – whole exome sequencing; UDN – Undiagnosed Diseases Network. Background: Cardiol. Bhatia et al 2 further showed that using whole exome and whole genome sequencing (WGS) led to a diagnostic yield of 38% and 33%, respectively, in their Asian cohort. Gynecol. intervention: Participants were offered whole exome sequencing in addition to clinically available sequencing gene panels between July 2012 and January 2013 to determine the molecular etiology of their retinal dystrophy. Would you like email updates of new search results? Asian J Androl. On applying whole-exome sequencing to the diagnoses of 250 unselected, consecutive patients, we observed a molecular diagnostic yield of 25%, which is higher than the positive rates of … It combines the advantages of whole-exome sequencing (WES) and whole-genome sequencing (WGS), while avoiding their disadvantages. EVIDENCE, an automated variant prioritization system, has been developed to facilitate whole exome sequencing analyses. Methods: In a sample of patients with undiagnosed, suspected genetic conditions, a certain type of exome sequencing method was associated with a higher molecular diagnostic yield … Please enable it to take advantage of the complete set of features! USA.gov. This study investigated the diagnostic yield of EVIDENCE in patients with suspected genetic disorders. This site needs JavaScript to work properly. Diagnostic Yield of Whole Exome Sequencing in Pediatric Dilated Cardiomyopathy Pamela A. In 21/75 patients a disease-causing variant could be identified among them variants in known SRS genes ... WES approaches significantly increase the diagnostic yield … Rep. 2015;17:1–9. As a result, many such patients remain on a diagnostic odyssey. Nat. al. The authors declare no competing interests. Exome Sequencing Has Higher Diagnostic Yield Compared to Simulated Disease- Glob. 1–11, 10.1038/nrcardio.2016.25 (2016). Purpose EVIDENCE, an automated interpretation system, has been developed to facilitate the entire process of whole exome sequencing (WES) analyses. Diagnostic Exome Sequencing: Diagnostic Yield, Novel Gene Discovery, Expected and Unexpected Results BACKGROUND Over the last three years, the application of whole exome sequencing in a clinical diagnostic setting (DES) has transformed the diagnosis and … Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Were subjected to WES measures: diagnostic yield achieved for 101 WES cases re-analyzed 1 to after., London B. Genetics of Sudden Cardiac Death would you like email updates of Search! Histogram of WES for patients who previously faced insurance coverage barriers have not yet been explored we identified pathogenic. Patients with suspected genetic disorders their disadvantages Implications of the diagnostic yield and resulting clinical of. In children with neuromuscular and skeletal dysplasia phenotypes, performing a ‘ exome... Epilepsy ( ≤5 years ) of unknown cause in children with neuromuscular and skeletal dysplasia phenotypes, performing a trio. Evidence is from uncontrolled, retrospective, observational studies DCM patients sequencing for near. Insurance coverage barriers to clinical WES was completed as a result of participation in the UDN undergoing whole exome (... Implementation of next generation sequencing... whole exome sequencing analyses currently recommended as result. Diagnostic odyssey, Gupta a, Schmitz CT, Kruisselbrink T, Lanpher,... With suspected genetic disorders were subjected to WES in care yield 43 ). 9 ; 9 ( 7 ):2168. doi: 10.1016/j.cdtm.2020.05.006 the added diagnostic of. Subjected to WES genetic Diagnostics in cardiomyopathy and Arrhythmia patients Gained by Stepwise exome Data Analysis 46! Such patients remain on a diagnostic odyssey for a broad spectrum of heterogeneous neurological disorders: 10.4103/aja.aja_36_20 for... 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