ArticleGenome medicine2013
Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy.
Article in Genome medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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100 citing papers in PubMed, 142 citations in OpenAlex.
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- Exome Sequencing Implicates DGKZ , ESRRA , and GXYLT1 for Modulating Granuloma Formation in Crohn Disease.Journal of pediatric gastroenterology and nutrition · 2023Article
- Use of whole genome sequencing to determine the genetic basis of visceral myopathies including Prune Belly syndrome.Journal of rare diseases (Berlin, Germany) · 2023Article
- An ELF4 hypomorphic variant results in NK cell deficiency.JCI insight · 2022Article
- Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine.Trends in genetics : TIG · 2022Review
- Genetic errors of immunity distinguish pediatric nonmalignant lymphoproliferative disorders.The Journal of allergy and clinical immunology · 2022Article
- PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation.Genome biology · 2021Article
- Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression.NPJ genomic medicine · 2021Article
- Rare deleterious germline variants and risk of lung cancer.NPJ precision oncology · 2021Article
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- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Identification of potential crucial genes associated with the pathogenesis and prognosis of pancreatic adenocarcinoma.Oncology letters · 2020Article
- Human NK cell deficiency as a result of biallelic mutations in MCM10.The Journal of clinical investigation · 2020Article
- Recurrent arginine substitutions in the ACTG2 gene are the primary driver of disease burden and severity in visceral myopathy.Human mutation · 2020Article
- Identifying a Minor Histocompatibility Antigen in Mauritian Cynomolgus Macaques Encoded byFrontiers in immunology · 2020Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.
methodsWe investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).
resultsWe compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.
conclusionsES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.