دورية أكاديمية
أعرض في EDS

Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects.

التفاصيل البيبلوغرافية
العنوان: Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects.
المؤلفون: Foley JF; Division of National Toxicology Program, NIEHS, Durham, North Carolina, USA., Elgart B; Sciome, LLC, Durham, North Carolina, USA., Alex Merrick B; Division of National Toxicology Program, NIEHS, Durham, North Carolina, USA., Phadke DP; Sciome, LLC, Durham, North Carolina, USA., Cook ME; Division of Intramural Research, NIEHS, Durham, North Carolina, USA., Malphurs JA; Division of Intramural Research, NIEHS, Durham, North Carolina, USA., Solomon GG; Division of Intramural Research, NIEHS, Durham, North Carolina, USA., Shah RR; Sciome, LLC, Durham, North Carolina, USA., Fessler MB; Division of Intramural Research, NIEHS, Durham, North Carolina, USA., Miller FW; Division of Intramural Research, NIEHS, Durham, North Carolina, USA., Gerrish KE; Division of Intramural Research, NIEHS, Durham, North Carolina, USA.
المصدر: Physiological reports [Physiol Rep] 2021 Aug; Vol. 9 (15), pp. e14993.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural
اللغة: English
بيانات الدورية: Publisher: published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society Country of Publication: United States NLM ID: 101607800 Publication Model: Print Cited Medium: Internet ISSN: 2051-817X (Electronic) Linking ISSN: 2051817X NLM ISO Abbreviation: Physiol Rep Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [Malden MA] : published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society, 2013-
مواضيع طبية MeSH: Genome, Human* , Mutation*, Cell-Free Nucleic Acids/*blood , Cell-Free Nucleic Acids/*genetics , Chromosomes, Human/*genetics , Whole Genome Sequencing/*methods, Humans
مستخلص: Cell-free DNA circulates in plasma at low levels as a normal by-product of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can lead to increased circulating cell-free DNA (ccfDNA) levels. Plasma DNA studies frequently employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/ml) of ccfDNA in the blood. Here, we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two human plasma samples from normal, healthy subjects, representative of limited clinical samples at <1 ml. Amplification was sufficiently robust with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. A high prevalence of C>T and T>C mutations was present along with a strong concordance of variants shared between the germline genome databases; gnomAD (81.1%) and the 1000 Genome Project (93.6%). This study demonstrates isolation and amplification procedures from low input ccfDNA samples that can detect sequence variants across the whole genome from amplified human plasma ccfDNA that can translate to multiple clinical research disciplines.
(© 2021 The Authors. Physiological Reports published by Wiley Periodicals LLC on behalf of The Physiological Society and the American Physiological Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)
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معلومات مُعتمدة: HHSN273201700001C United States ES NIEHS NIH HHS
فهرسة مساهمة: Keywords: circulating cell-free DNA; genomic sequencing; plasma DNA; variants
المشرفين على المادة: 0 (Cell-Free Nucleic Acids)
تواريخ الأحداث: Date Created: 20210805 Date Completed: 20220228 Latest Revision: 20230920
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC8339531
DOI: 10.14814/phy2.14993
PMID: 34350716
قاعدة البيانات: MEDLINE
الوصف
تدمد:2051-817X
DOI:10.14814/phy2.14993