Insights into the Genetic Structure and Diversity of 38 South Asian Indians from Deep Whole-Genome Sequencing

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Indians of South Asia has long been a population of interest to a wide audience, due to its unique diversity. We have deep-sequenced 38 individuals of Indian descent residing in Singapore (SSIP) in an effort to illustrate their diversity from a whole-genome standpoint. Indeed, among Asians in our population panel, SSIP was most diverse, followed by the Malays in Singapore (SSMP). Their diversity is further observed in the population's chromosome Y haplogroup and mitochondria haplogroup profiles; individuals with European-dominant haplogroups had greater proportion of European admixture. Among variants (single nucleotide polymorphism and small insertions/deletions) discovered in SSIP, 21.69% were novel with respect to previous sequencing projects. In addition, some 14 loss-of-function variants (LOFs) were associated to cancer, Type II diabetes, and cholesterol levels. Finally, D statistic test with ancient hominids concurred that there was gene flow to East Asians compared to South Asians.

Vyšlo v časopise: Insights into the Genetic Structure and Diversity of 38 South Asian Indians from Deep Whole-Genome Sequencing. PLoS Genet 10(5): e32767. doi:10.1371/journal.pgen.1004377
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004377

Souhrn

Zdroje

1. MardisER (2011) A decade's perspective on DNA sequencing technology. Nature 470: 198–203.

2. AbecasisGR, AutonA, BrooksLD, DePristoMA, DurbinRM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65.

3. WongLP, OngRT, PohWT, LiuX, ChenP, et al. (2013) Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet 92: 52–66.

4. MeyerM, KircherM, GansaugeMT, LiH, RacimoF, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222–226.

5. GreenRE, KrauseJ, BriggsAW, MaricicT, StenzelU, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.

6. ReichD, GreenRE, KircherM, KrauseJ, PattersonN, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053–1060.

7. KellerA, GraefenA, BallM, MatzasM, BoisguerinV, et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3: 698.

8. DESA (2009) World population prospects: the 2008 revision. New York: Department for Economic and Social Affairs.

9. MacaulayV, HillC, AchilliA, RengoC, ClarkeD, et al. (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308: 1034–1036.

10. ThangarajK, ChaubeyG, KivisildT, ReddyAG, SinghVK, et al. (2005) Reconstructing the origin of Andaman Islanders. Science 308: 996.

11. ReichD, ThangarajK, PattersonN, PriceAL, SinghL (2009) Reconstructing Indian population history. Nature 461: 489–494.

12. MoorjaniP, ThangarajK, PattersonN, LipsonM, LohPR, et al. (2013) Genetic evidence for recent population mixture in India. Am J Hum Genet 93: 422–438.

13. Singstat (2012) Population Trends 2012. Singapore: Department of Statistics.

14. Leow BG, Singapore. Dept. of Statistics. (2001) Census of population 2000. Demographic characteristics. Singapore: Dept. of Statistics. 142 pp.

15. Periasamy M (2007) Indian Migration into Malaya and Singapore During the British Period. Singapore: Biblioasia.

16. Turnbull CM (2009) A History of Modern Singapore. Singapore: National University of Singapore Press.

17. CingolaniP, PlattsA, WangLL, CoonM, NguyenT, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3;. Fly 6: 80–92.

18. MacArthurDG, BalasubramanianS, FrankishA, HuangN, MorrisJ, et al. (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335: 823–828.

19. Kloss-BrandstätterA, PacherD, SchönherrS, WeissensteinerH, BinnaR, et al. (2011) HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Human Mutation 32: 25–32.

20. RajkumarR, BanerjeeJ, GunturiHB, TrivediR, KashyapVK (2005) Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol Biol 5: 26.

21. van OvenM, KayserM (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386–394.

22. ChandrasekarA, KumarS, SreenathJ, SarkarBN, UradeBP, et al. (2009) Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: dispersal of modern human in South Asian corridor. PLoS One 4: e7447.

23. MoorjaniP, ThangarajK, PattersonN, LipsonM, LohP-R, et al. (2013) Genetic Evidence for Recent Population Mixture in India. American journal of human genetics 93: 422–438.

24. WallJD, YangMA, JayF, KimSK, DurandEY, et al. (2013) Higher Levels of Neanderthal Ancestry in East Asians than in Europeans. Genetics 194: 199–209.

25. ChanSL, SuoC, LeeSC, GohBC, ChiaKS, et al. (2012) Translational aspects of genetic factors in the prediction of drug response variability: a case study of warfarin pharmacogenomics in a multi-ethnic cohort from Asia. Pharmacogenomics J 12: 312–318.

26. ChanSL, SuoC, ChiaKS, TeoYY (2012) The population attributable fraction as a measure of the impact of warfarin pharmacogenetic testing. Pharmacogenomics 13: 1247–1256.

27. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079.

28. DePristoMA, BanksE, PoplinR, GarimellaKV, MaguireJR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491–498.

29. McKennaA, HannaM, BanksE, SivachenkoA, CibulskisK, et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20: 1297–1303.

30. NgPC, HenikoffS (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research 31: 3812–3814.

31. AdzhubeiI, SchmidtS, PeshkinL, RamenskyV, GerasimovaA, et al. (2010) A method and server for predicting damaging missense mutations. Nature methods 7: 248–249.

32. Huang daW, ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1–13.

33. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, et al.. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet Chapter 10: Unit 10 11.

34. ForbesSA, BindalN, BamfordS, ColeC, KokCY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39: D945–950.

35. HindorffLA, SethupathyP, JunkinsHA, RamosEM, MehtaJP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362–9367.

36. Dayem UllahAZ, LemoineNR, ChelalaC (2012) SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). Nucleic Acids Res 40: W65–70.

37. ChenK, WallisJW, McLellanMD, LarsonDE, KalickiJM, et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Meth 6: 677–681.

38. HormozdiariF, HajirasoulihaI, DaoP, HachF, YorukogluD, et al. (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26: i350–i357.

39. YeK, SchulzMH, LongQ, ApweilerR, NingZ (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865–2871.

40. RauschT, ZichnerT, SchlattlA, StützAM, BenesV, et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333–i339.

41. IafrateAJ, FeukL, RiveraMN, ListewnikML, DonahoePK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.

42. PriceAL, PattersonNJ, PlengeRM, WeinblattME, ShadickNA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904–909.

43. TeoYY, SimX, OngRT, TanAK, ChenJ, et al. (2009) Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome Res 19: 2154–2162.

44. ReichD, ThangarajK, PattersonN, PriceAL, SinghL (2009) Reconstructing Indian population history. Nature 461: 489–494.

45. AlexanderDH, NovembreJ, LangeK (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19: 1655–1664.

46. DrmanacR, SparksAB, CallowMJ, HalpernAL, BurnsNL, et al. (2010) Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays. Science 327: 78–81.

47. Jostins L (2011) YFitter: a program for assigning haplogroups using maximum likelihood.

48. PattersonN, MoorjaniP, LuoY, MallickS, RohlandN, et al. (2012) Ancient Admixture in Human History. Genetics 192: 1065–1093.

49. ReichD, GreenRE, KircherM, KrauseJ, PattersonN, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053–1060.

50. MeyerM, KircherM, GansaugeM-T, LiH, RacimoF, et al. (2012) A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 338: 222–226.