Analysis of the Prader–Willi syndrome imprinting center using droplet digital PCR and next‐generation whole‐exome sequencing

Next-generation sequencing has become more widely used to reveal genetic defect in monogenic disorders. Retinitis pigmentosa (RP), the leading cause of hereditary blindness worldwide, has been attributed to more than 67 disease-causing genes. Due to the extreme genetic heterogeneity, using general molecular screening alone is inadequate for identifying genetic predispositions in susceptible individuals. In order to identify underlying mutation rapidly, we utilized next-generation sequencing in a four-generation Chinese family with RP. Two affected patients and an unaffected sibling were subjected to whole exome sequencing. Through bioinformatics analysis and direct sequencing confirmation, we identified p.R135W transition in the rhodopsin gene. The mutation was subsequently confirmed to cosegregate with the disease in the family. In this study, our results suggest that whole exome sequencing is a robust method in diagnosing familial hereditary disease.

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MSI-WES: a simple approach for microsatellite instability testing using whole exome sequencing

Future Oncology ◽

10.2217/fon-2021-0132 ◽

2021 ◽

Author(s):

Henry O Ebili ◽

Adedeji OJ Agboola ◽

Emad Rakha

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Methylation Status ◽

Molecular Targets ◽

Next Generation ◽

Variant Call ◽

Whole Exome ◽

Generation Sequencing

Aim: To demonstrate that MSI-WES is an accurate testing method for microsatellite instability (MSI). Materials & methods: Microsatellite-based indels were counted in the variant call-formatted whole exome sequencing (WES) data of 441 gastric cancer cases using Unix-based algorithms, and the counts expressed as a fraction of the genome sequenced to obtain next-generation sequencing-based MSI indices. Results: The next-generation sequencing-based MSI indices showed a near-perfect concordance with PCR-based MSI status, and moderate to good correlations with the molecular targets of MSI index, MLH1 expression and MLH1 methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and molecular targets of MSI index/ MLH1 expression and methylation. Conclusion: MSI-WES is a valid, adequate and sensitive approach for testing MSI in cancer.

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Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2016-3414 ◽

2017 ◽

Vol 102 (5) ◽

pp. 1529-1537 ◽

Cited By ~ 13

Author(s):

David R. Murdock ◽

Frank X. Donovan ◽

Settara C. Chandrasekharappa ◽

Nicole Banks ◽

Carolyn Bondy ◽

...

Keyword(s):

Next Generation Sequencing ◽

Newborn Screening ◽

Exome Sequencing ◽

Turner Syndrome ◽

Whole Exome Sequencing ◽

Genomic Research ◽

Next Generation ◽

Low Level ◽

Whole Exome ◽

Generation Sequencing

Abstract Context: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities. Objectives: This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health. Female control subjects (n = 37) and male subjects (n = 27) also underwent WES. Copy number variation was evaluated using EXCAVATOR2 and B allele frequency was calculated from informative single nucleotide polymorphisms. Simulated WES data were generated for detection of low-level mosaicism and complex structural chromosome abnormalities. Results: We detected monosomy for chromosome X in all 27 TS samples, including 1 mosaic for 45,X/46,XX and another with previously unreported material on chromosome Y. Sensitivity and specificity were both 100% for the diagnosis of TS with no false-positive or false-negative results. Using simulated WES data, we detected isochromosome Xq and low-level mosaicism as low as 5%. Conclusion: We present an accurate method of diagnosing TS using WES, including cases with low-level mosaicism, isochromosome Xq, and cryptic Y-chromosome material. Given the potential use of next-generation sequencing for NBS in many different diseases and syndromes, we propose WES can be used as a screening test for TS in newborns.

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Genetic landscape of pediatric movement disorders and management implications

Neurology Genetics ◽

10.1212/nxg.0000000000000265 ◽

2018 ◽

Vol 4 (5) ◽

pp. e265 ◽

Cited By ~ 8

Author(s):

Dawn Cordeiro ◽

Garrett Bullivant ◽

Komudi Siriwardena ◽

Andrea Evans ◽

Jeff Kobayashi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Movement Disorder ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Movement Disorders ◽

Genetic Diagnosis ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Whole Exome ◽

Generation Sequencing

ObjectiveTo identify underlying genetic causes in patients with pediatric movement disorders by genetic investigations.MethodsAll patients with a movement disorder seen in a single Pediatric Genetic Movement Disorder Clinic were included in this retrospective cohort study. We reviewed electronic patient charts for clinical, neuroimaging, biochemical, and molecular genetic features. DNA samples were used for targeted direct sequencing, targeted next-generation sequencing, or whole exome sequencing.ResultsThere were 51 patients in the Pediatric Genetic Movement Disorder Clinic. Twenty-five patients had dystonia, 27 patients had ataxia, 7 patients had chorea-athetosis, 8 patients had tremor, and 7 patients had hyperkinetic movements. A genetic diagnosis was confirmed in 26 patients, including in 20 patients with ataxia and 6 patients with dystonia. Targeted next-generation sequencing panels confirmed a genetic diagnosis in 9 patients, and whole exome sequencing identified a genetic diagnosis in 14 patients.ConclusionsWe report a genetic diagnosis in 26 (51%) patients with pediatric movement disorders seen in a single Pediatric Genetic Movement Disorder Clinic. A genetic diagnosis provided either disease-specific treatment or effected management in 10 patients with a genetic diagnosis, highlighting the importance of early and specific diagnosis.

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Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives

Clinical Reviews in Allergy & Immunology ◽

10.1007/s12016-021-08838-5 ◽

2021 ◽

Author(s):

Emil E. Vorsteveld ◽

Alexander Hoischen ◽

Caspar I. van der Made

Keyword(s):

Next Generation Sequencing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Diagnostic Yield ◽

Primary Immunodeficiencies ◽

Next Generation ◽

Inborn Errors ◽

New Genes ◽

Whole Exome ◽

Generation Sequencing

AbstractPrimary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of the genetic and molecular basis of genetic diseases, thereby also leading to a sharp increase in the discovery of new genes associated with primary immunodeficiencies. In this review, we discuss the current diagnostic yield of this generic diagnostic approach by evaluating the studies that have employed next-generation sequencing techniques in cohorts of patients with primary immunodeficiencies. The average diagnostic yield for primary immunodeficiencies is determined to be 29% (range 10–79%) and 38% specifically for whole-exome sequencing (range 15–70%). The significant variation between studies is mainly the result of differences in clinical characteristics of the studied cohorts but is also influenced by varying sequencing approaches and (in silico) gene panel selection. We further discuss other factors contributing to the relatively low yield, including the inherent limitations of whole-exome sequencing, challenges in the interpretation of novel candidate genetic variants, and promises of exploring the non-coding part of the genome. We propose strategies to improve the diagnostic yield leading the way towards expanded personalized treatment in PIDs.

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Impact of Next-Generation Whole-Exome sequencing in molecular diagnostics

Drug Invention Today ◽

10.1016/j.dit.2013.07.005 ◽

2013 ◽

Vol 5 (4) ◽

pp. 327-334 ◽

Cited By ~ 3

Author(s):

Anuraj Nayarisseri ◽

Mukesh Yadav ◽

Mayuri Bhatia ◽

Ankita Pandey ◽

Arundhati Elkunchwar ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Molecular Diagnostics ◽

Next Generation ◽

Whole Exome

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Next-generation sequencing refines the genetic architecture of Greek GnRH-deficient patients

Endocrine Connections ◽

10.1530/ec-19-0010 ◽

2019 ◽

Vol 8 (5) ◽

pp. 468-480 ◽

Cited By ~ 2

Author(s):

M I Stamou ◽

P Varnavas ◽

L Plummer ◽

V Koika ◽

N A Georgopoulos

Keyword(s):

Genetic Variation ◽

Next Generation Sequencing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Sanger Sequencing ◽

Wide Spectrum ◽

Next Generation ◽

Whole Exome ◽

Low Prevalence ◽

Generation Sequencing

Isolated gonadotropin-releasing hormone (GnRH) deficiency (IGD) is a rare disease with a wide spectrum of reproductive and non-reproductive clinical characteristics. Apart from the phenotypic heterogeneity, IGD is also highly genetically heterogeneous with >35 genes implicated in the disease. Despite this genetic heterogeneity, genetic enrichment in specific subpopulations has been described. We have previously described low prevalence of genetic variation in the Greek IGD cohort discovered with utilization of Sanger sequencing in 14 known IGD genes. Here, we describe the expansion of genetic screening in the largest IGD Greek cohort that has ever been studied with the usage of whole-exome sequencing, searching for rare sequencing variants (RSVs) in 37 known IGD genes. Even though Sanger sequencing detected genetic variation in 21/81 IGD patients in 7/14 IGD genes without any evidence of oligogenicity, whole exome sequencing (WES) revealed that 27/87 IGD patients carried a rare genetic change in a total of 15 genes with 4 IGD cases being oligogenic. Our findings suggest that next-generation sequencing (NGS) techniques can discover previously undetected variation, making them the standardized method for screening patients with rare and/or more common disorders.

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