دورية أكاديمية
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De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population.

التفاصيل البيبلوغرافية
العنوان: De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population.
المؤلفون: Kessler MD; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201., Loesch DP; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201., Perry JA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201., Heard-Costa NL; Department of Neurology, Boston University School of Medicine, Boston, MA 02118.; Framingham Heart Study, Framingham, MA 01702., Taliun D; Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109., Cade BE; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115.; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142., Wang H; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115.; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142., Daya M; Department of Medicine, University of Colorado Denver, Aurora, CO 80045., Ziniti J; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115., Datta S; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115., Celedón JC; Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213., Soto-Quiros ME; Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica., Avila L; Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica., Weiss ST; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115.; Department of Medicine, Harvard Medical School, Boston, MA 02115., Barnes K; Department of Medicine, University of Colorado Denver, Aurora, CO 80045., Redline SS; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115.; Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115.; Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215., Vasan RS; Framingham Heart Study, Framingham, MA 01702., Johnson AD; Framingham Heart Study, Framingham, MA 01702.; Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702., Mathias RA; Division of Allergy and Clinical Immunology, The Johns Hopkins School of Medicine, Baltimore, MD 21224.; Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21218., Hernandez R; Quantitative Life Sciences, McGill University, Montreal, QC H3A OG4, Canada., Wilson JG; Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216., Nickerson DA; Department of Genome Sciences, University of Washington, Seattle, WA 98195., Abecasis G; School of Public Health, University of Michigan, Ann Arbor, MI 48109., Browning SR; Department of Biostatistics, University of Washington, Seattle, WA 98195., Zöllner S; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109.; Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109., O'Connell JR; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201., Mitchell BD; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201., O'Connor TD; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201; timothydoconnor@gmail.com.; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201.; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201.
مؤلفون مشاركون: National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group
المصدر: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2020 Feb 04; Vol. 117 (5), pp. 2560-2569. Date of Electronic Publication: 2020 Jan 21.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Washington, DC : National Academy of Sciences
مواضيع طبية MeSH: Genome, Human*, Amish/*genetics, Adult ; Cohort Studies ; DNA Mutational Analysis ; Female ; Genetics, Population ; Heterozygote ; Humans ; Male ; Mutation ; Pedigree ; Whole Genome Sequencing ; Young Adult
مستخلص: De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains <1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability ( h 2 ), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
Competing Interests: The authors declare no competing interest.
(Copyright © 2020 the Author(s). Published by PNAS.)
التعليقات: Erratum in: Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):. (PMID: 33649245)
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معلومات مُعتمدة: R35 HG010692 United States HG NHGRI NIH HHS; R01 HL120393 United States HL NHLBI NIH HHS; U24 AG021886 United States AG NIA NIH HHS; HHSN268201500001C United States HL NHLBI NIH HHS; R01 HL113338 United States HL NHLBI NIH HHS; R01 AI079139 United States AI NIAID NIH HHS; U01 HL137181 United States HL NHLBI NIH HHS; R37 HL066289 United States HL NHLBI NIH HHS; K08 HL141601 United States HL NHLBI NIH HHS; HHSN268201500001I United States HL NHLBI NIH HHS; R01 HG005701 United States HG NHGRI NIH HHS; T32 CA154274 United States CA NCI NIH HHS; P30 DK020595 United States DK NIDDK NIH HHS; K01 HL135405 United States HL NHLBI NIH HHS; P30 DK040561 United States DK NIDDK NIH HHS; U01 HL137183 United States HL NHLBI NIH HHS; K01 AG059898 United States AG NIA NIH HHS; R01 HL121007 United States HL NHLBI NIH HHS; T32 HL007698 United States HL NHLBI NIH HHS; R01 HL092577 United States HL NHLBI NIH HHS; R01 DK113003 United States DK NIDDK NIH HHS; OT3 OD025459 United States OD NIH HHS; P50 HL118006 United States HL NHLBI NIH HHS; R01 HL066216 United States HL NHLBI NIH HHS; T32 HG000040 United States HG NHGRI NIH HHS; R01 HL138737 United States HL NHLBI NIH HHS; U24 AG056270 United States AG NIA NIH HHS; R01 HL141845 United States HL NHLBI NIH HHS; R01 AR072199 United States AR NIAMS NIH HHS; R35 HL135818 United States HL NHLBI NIH HHS; R01 HL098433 United States HL NHLBI NIH HHS; R01 HL104608 United States HL NHLBI NIH HHS; R01 HL148239 United States HL NHLBI NIH HHS; U01 HL072515 United States HL NHLBI NIH HHS; R01 HL117626 United States HL NHLBI NIH HHS; P20 GM121334 United States GM NIGMS NIH HHS; R01 HL135129 United States HL NHLBI NIH HHS; P01 HL132825 United States HL NHLBI NIH HHS; R01 HL118267 United States HL NHLBI NIH HHS; R01 AG018728 United States AG NIA NIH HHS
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Y Park; M Parker; A Parsa; J Patel; S Patel; A Patel; B Paten; C Patterson; G Peloso; J Manuel; P Alexandre; PM Perez; J Perry; U Peters; P Peyser; N Pezant; S Phillips; LS Phillips; S Pipe; J Pirruccello; A Pitsillides; C Pohl; L Polfus; T Pollin; B Porneala; W Post; JP Becker; K Pratte; M Preethi; BM Preuss; A Price; J Pritchard; A Prizment; D Prokopenko; M Province; B Psaty; S Purcell; JA Purnell; S Purves; P Qasba; Q Qi; H Qian; Y Qian; D Qiao; Z Qin; H Qu; C Quick; D Rader; N Rafaels; L Raffel; L Raffield; D Raftery; S Raghavan; MF Ragland; DC Rao; L Rasmussen-Torvik; D Rastogi; A Ratan; D Ray; S Raychaudhuri; S Redline; R Reed; E Regan; AD Reily; A Reiner; K Rexrode; J Rhodes; K Rice; S Rich; M Rienstra; LL Rinke; N Robine; C Robinson-Cohen; A Rock; D Roden; B Andrew; T Rodriguez; A Rodriguez; KK Roll; J Rosand; C Roselli; Y Rosen; S Rosenthal; J Rotter; I Ruczinski; M Rueschman; A Runko; E Russell; P Russell; S Ruuska; K Ryan; EC Sabino; A Sabo; N Saccone; V Sachdev; S Sahni; P Sakornsakolpat; D Saleheen; R Salem; W Salerno; S Salimi; J Salomon-Andonie; S Salzberg; JL Sanders; K Sandow; V Sankaran; C Sarnowski; C Satizabal; G Saunders; R Saxena; G Schellenberg; A Schoech; J Schoenberg; C Schramm; D Schrider; K Schwander; C Schwartz; D Schwartz; M Schwarz; F Sciurba; J Seidman; C Seidman; E Selvin; M Seo; V Seplyarskiy; S Seshadri; A Seyerle; A Shadyab; S Shah; P Shah; A Sharma; JR Shaw; V Sheehan; CJ Sheldahl; S Sherman; S Sherry; A Shetty; WH Sheu; K Shianna; D Shimbo; MB Shoemaker; P Sholinsky; MI Short; L Silsbee; B Silver; E Silverman; J Simino; N Simon; M Sinner; N Sinnott; AC Sitlani; R Sladek; P Sleiman; C Smail; G Smith; J Smith; B Smith; N Smith; J Smith; AV Smith; S Smoller; S Snitker; B Snively; M Snyder; T Sofer; M Sohail; S Sokolow; K Soldano; W Song; N Sotoodehnia; M Spear; D Spies; S Spivack; C Spracklen; P Srinivas; V Srinivasasainagendra; D Srivastava; D Steinberg; D Stern; A Stilp; A Stine; N Stitziel; E Streeten; A Sturcke; JL Su; P Sullivan; A Sulovari; P Sumazin; C Summarell; R Sun; X Sun; HK Sun; A Sundaresan; YJ Sung; SR Sunyaev; I Surakka; T Suzuki; M Sweet; M Szeto; Z Szpiech; A Szpiro; C Sztalryd; D Taliun; H Tang; W Tang; M Taub; KD Taylor; RE Taylor; M Taylor; S Taylor; JG Taylor; BT Vi; M Telen; JG Terry; E Thompson; A Thomson; TA Thornton; B Thyagarajan; A Tin; L Tinker; D Tirschwell; S Tishkoff; H Tiwari; D Tobias; D Tong; R Torres; R Tracy; M Tristani; M Trottier; M Tsai; C Tsao; D Vaidya; D Van Den Berg; M Van Oene; P VandeHaar; L VanWagner; J Vargas; RS Vasan; M Verbanck; KA Viaud; MP Visscher; A Von; HS Vrieze; M Wagner; J Waligorski; T Walker; R Wallace; A Walts; E Wan; Z Wang; T Wang; FF Wang; BB Wang; P Wang; Y Wang; F Wang; H Wang; K Watson; DE Weeks; K Wehr; G Wei; J Weinstock; BW Scott; WF Wen; LC Weng; S Wenric; E Werner; J Wessel; M Wheeler; M White; W White; P White; N Whitehead; K Wiggins; C Willer; C Williams; K Williams; LK Williams; S Williams; J Williams-Nguyen; J Wilson; C Wilson; MK Wing; K Winters; M Wojczynski; B Wolford; Q Wong; P Wu; J Wu; A Wu; L Xia; C Xiao; S Xiao; H Xu; W Xu; S Xu; H Xu; L Yanek; YC Yang; C Yang; Q Yang; I Yang; Y Yano; J Yao; E Yaschenko; M Yau; X Yin; S Yoneyama; B Young; H Young; K Young; T Young; K Young; M Youngblood; B Yu; C Yu; N Zaghloul; M Zalokar-Newton; H Zare; J Zein; M Zekavat; G Man Zhang; W Zhang; X Zhang; Y Zhang; J Zhang; X Zhang; J Zhang; X Zhang; Y Zhang; SX Zhao; LP Zhao; X Zhao; W Zhao; Y Zheng; X Zheng; D Zhi; H Zhou; L Zhou; X Zhou; Y Zhou; L Zhu; X Zhu; M Zody; S Zoellner; B Zorman; D Beame; M Bowers; S Browning; L Challagundla; M Conomos; M Daya; M de Andrade; R Deka; R Do; L Emery; L Francioli; Y Gao; S Gazal; S Gogarten; M Gutierrez-Arcelus; I Hall; D Harris; K Harris; K Hartman; R Hernandez; C Hodonsky; KR Iyer; D Jain; J Jiang; A Johnson; R Johnston; D Jordan; A Justice; HM Kang; A Keely; T Kelly; M Kessler; C Laurie; X Liu; D Loesch; Y Luo; D MacArthur; A Manichaikul; R Mathias; C McHugh; J Mikulla; RL Minster; JC Mychaleckyj; R Nassir; SC Nelson; D Nickerson; J O'Connell; T O'Connor; G Page; G Papanicolaou; A Price; D Prokopenko; JA Purnell; S Raychaudhuri; J Rotter; A Schoech; D Schrider; V Seplyarskiy; A Shetty; T Sofer; M Sohail; W Song; N Sotoodehnia; M Spear; P Sullivan; SR Sunyaev; Z Szpiech; H Tang; KD Taylor; TA Thornton; H Tiwari; D Tong; R Torres; D Vaidya; M Verbanck; K Wehr; B Weir; S Wenric; Q Wong; L Yanek; Q Yang; D Zhi; M Zody; S Zoellner
Keywords: Amish; de novo mutations; diversity; mutation rate; recombination
تواريخ الأحداث: Date Created: 20200123 Date Completed: 20200615 Latest Revision: 20240603
رمز التحديث: 20240603
مُعرف محوري في PubMed: PMC7007577
DOI: 10.1073/pnas.1902766117
PMID: 31964835
قاعدة البيانات: MEDLINE
الوصف
تدمد:1091-6490
DOI:10.1073/pnas.1902766117