Einzeltreffer — DigiBib

Whole-genome and exome data sets continue to be produced at a frenetic pace, resulting in massively large catalogs of human genomic variation. However, a clear picture of the characteristics and patterns of neutral and deleterious variation within and between populations has yet to emerge, given that recent large-scale sequencing studies have often emphasized different aspects of the data and sometimes appear to have conflicting conclusions. Here, we comprehensively studied characteristics of protein-coding variation in high-coverage exome sequence data from 6,515 European American (EA) and African American (AA) individuals. We developed an unbiased approach to identify putatively deleterious variants and investigated patterns of neutral and deleterious single-nucleotide variants and alleles between individuals and populations. We show that there are substantial differences in the composition of genotypes between EA and AA populations and that small but statistically significant differences exist in the average number of deleterious alleles carried by EA and AA individuals. Furthermore, we performed extensive simulations to delineate the temporal dynamics of deleterious alleles for a broad range of demographic models and use these data to inform the interpretation of empirical patterns of deleterious variation. Finally, we illustrate that the effects of demographic perturbations, such as bottlenecks and expansions, often manifest in opposing patterns of neutral and deleterious variation depending on whether the focus is on populations or individuals. Our results clarify seemingly disparate empirical characteristics of protein-coding variation and provide substantial insights into how natural selection and demographic history have patterned neutral and deleterious variation within and between populations.

Titel:	Characteristics of neutral and deleterious protein-coding variation among individuals and populations.
Autor/in / Beteiligte Person:	Fu, W ; Gittelman, RM ; Bamshad, MJ ; Akey, JM
Link:	Full Text Finder (Volltext)
Zeitschrift:	American journal of human genetics, Jg. 95 (2014-10-02), Heft 4, S. 421-36
Veröffentlichung:	2008- : [Cambridge, MA] : Cell Press ; <i>Original Publication</i>: Baltimore, American Society of Human Genetics., 2014
Medientyp:	academicJournal
ISSN:	1537-6605 (electronic)
DOI:	10.1016/j.ajhg.2014.09.006
Schlagwort:	Africa ethnology Europe ethnology Evolution, Molecular Genetic Drift Genome, Human Humans Models, Theoretical Selection, Genetic Black People genetics Exome genetics Exons genetics Genetics, Population Polymorphism, Single Nucleotide genetics Proteins genetics White People genetics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Am J Hum Genet] 2014 Oct 02; Vol. 95 (4), pp. 421-36. MeSH Terms: Genetics, Population* ; Black People / genetics ; Exome / genetics ; Exons / genetics ; Polymorphism, Single Nucleotide / genetics ; Proteins / genetics ; White People / genetics ; Africa / ethnology ; Europe / ethnology ; Evolution, Molecular ; Genetic Drift ; Genome, Human ; Humans ; Models, Theoretical ; Selection, Genetic Comments: Comment in: Nat Rev Genet. 2014 Dec;15(12):777. (PMID: 25352302) References: Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):12035-9. (PMID: 8876258) ; Mol Ecol. 2013 Dec;22(24):5972-82. (PMID: 24102784) ; Science. 2001 Oct 5;294(5540):169-73. (PMID: 11588264) ; Nat Genet. 2014 Mar;46(3):220-4. (PMID: 24509481) ; Am J Hum Genet. 2012 Nov 2;91(5):809-22. (PMID: 23103233) ; Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):13994-4001. (PMID: 15292512) ; Hum Biol. 1958 Feb;30(1):1-13. (PMID: 13513111) ; Nature. 2013 Jan 10;493(7431):216-20. (PMID: 23201682) ; Science. 2012 Jul 6;337(6090):100-4. (PMID: 22604722) ; Genetics. 1963 Oct;48:1303-12. (PMID: 14071753) ; Nature. 2012 Nov 1;491(7422):56-65. (PMID: 23128226) ; Nature. 2010 Oct 28;467(7319):1061-73. (PMID: 20981092) ; Nat Genet. 2007 Oct;39(10):1251-5. (PMID: 17828266) ; Proc Natl Acad Sci U S A. 1956 Nov;42(11):855-63. (PMID: 16589958) ; Nature. 2008 Feb 21;451(7181):994-7. (PMID: 18288194) ; Bioinformatics. 2012 Jul 15;28(14):1919-20. (PMID: 22576172) ; PLoS Comput Biol. 2010 Dec 02;6(12):e1001025. (PMID: 21152010) ; Annu Rev Genomics Hum Genet. 2008;9:403-33. (PMID: 18593304) ; Genome Res. 2009 Sep;19(9):1553-61. (PMID: 19602639) ; Genetics. 2011 Aug;188(4):907-13. (PMID: 21527780) ; Cell. 2012 Aug 3;150(3):457-69. (PMID: 22840920) ; Evolution. 1975 Mar;29(1):1-10. (PMID: 28563291) ; Mol Biol Evol. 2007 Aug;24(8):1792-800. (PMID: 17545186) ; Genetics. 2012 Apr;190(4):1579-83. (PMID: 22267501) ; Am J Hum Genet. 2012 Oct 5;91(4):660-71. (PMID: 23040495) ; PLoS Genet. 2008 May 30;4(5):e1000083. (PMID: 18516229) ; Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):961-8. (PMID: 20080596) ; BMC Genomics. 2013 Jul 23;14:495. (PMID: 23875710) ; Am J Hum Genet. 1950 Jun;2(2):111-76. (PMID: 14771033) ; Nat Methods. 2010 Aug;7(8):575-6. (PMID: 20676075) ; Nature. 1973 Nov 9;246(5428):96-8. (PMID: 4585855) ; Science. 2012 May 11;336(6082):740-3. (PMID: 22582263) ; Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8. (PMID: 21730125) ; PLoS Genet. 2014 May 29;10(5):e1004379. (PMID: 24875776) ; Bioinformatics. 2008 Dec 1;24(23):2786-7. (PMID: 18842601) ; Am J Hum Genet. 2010 Jun 11;86(6):850-9. (PMID: 20560205) ; PLoS Genet. 2013;9(9):e1003815. (PMID: 24086152) ; Nat Genet. 2015 Feb;47(2):126-31. (PMID: 25581429) ; Mutat Res. 1997 Jun 9;377(1):61-2. (PMID: 9219579) ; Nat Commun. 2010 Nov 30;1:131. (PMID: 21119644) ; Nat Rev Genet. 2000 Oct;1(1):40-7. (PMID: 11262873) ; Nat Genet. 2014 Mar;46(3):310-5. (PMID: 24487276) ; Nat Genet. 1998 Jul;19(3):233-40. (PMID: 9662394) ; Cold Spring Harb Symp Quant Biol. 1955;20:33-53. (PMID: 13433553) ; Nat Methods. 2010 Apr;7(4):248-9. (PMID: 20354512) ; Science. 2012 Jul 6;337(6090):64-9. (PMID: 22604720) ; Hum Hered. 2012;74(3-4):118-28. (PMID: 23594490) ; Am J Hum Genet. 2014 May 1;94(5):710-20. (PMID: 24768551) ; Science. 2003 Feb 28;299(5611):1391-4. (PMID: 12610304) ; Genome Res. 2010 Jan;20(1):110-21. (PMID: 19858363) ; Am J Hum Genet. 2013 Jul 11;93(1):90-102. (PMID: 23746547) ; Genetics. 2013 Nov;195(3):969-78. (PMID: 23979573) ; Nat Protoc. 2009;4(7):1073-81. (PMID: 19561590) ; Curr Opin Genet Dev. 2014 Dec;29:139-46. (PMID: 25461617) Substance Nomenclature: 0 (Proteins) Entry Date(s): Date Created: 20141004 Date Completed: 20141209 Latest Revision: 20221207 Update Code: 20231215 PubMed Central ID: PMC4185119

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Characteristics of neutral and deleterious protein-coding variation among individuals and populations.