Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing

Human Mutation

Volumn 36, Issue 1, 2015, Pages 151-159

  Ralf, Arwin ^a   van Oven, Mannis ^a   Zhong, Kaiyin ^a   Kayser, Manfred ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Haplogroup; Ion torrent PGM; Male lineage identification; Next generation sequencing; Y chromosome; Y SNPs

Indexed keywords

COMPUTER PROGRAM; DEVICES; DNA SEQUENCE; ECONOMICS; GENETICS; HAPLOTYPE; HUMAN; MALE; PROCEDURES; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME;

CHROMOSOMES, HUMAN, Y; HAPLOTYPES; HUMANS; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84920075650     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22713     Document Type: Article

References (43)

1. Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, et al. 2011. Parallel evolution of genes and languages in the Caucasus region. Mol Biol Evol 28:2905-2920.
2. Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, Myres NM, King RJ, Rootsi S, Marjanovic D, Primorac D, Hadziselimovic R, Vidovic S, et al. 2009. Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. Eur J Hum Genet 17:820-830.
3. Cadenas AM, Zhivotovsky LA, Cavalli-Sforza LL, Underhill PA, Herrera RJ. 2008. Y-chromosome diversity characterizes the Gulf of Oman. Eur J Hum Genet 16:374-386.
4. Chennakrishnaiah S, Perez D, Gayden T, Rivera L, Regueiro M, Herrera RJ. 2013. Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India. Gene 526:96-106.
5. Cordaux R, Aunger R, Bentley G, Nasidze I, Sirajuddin SM, Stoneking M. 2004. Independent origins of Indian caste and tribal paternal lineages. Curr Biol 14:231-235.
6. Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, et al. 2002. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am J Hum Genet 70:1197-1214.
7. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, et al. 2013. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341:565-569.
8. Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusmão L. 2010. Digging deeper into East African human Y chromosome lineages. Hum Genet 127:603-613.
9. Hammer MF, Zegura SL. 2002. The human Y chromosome haplogroup tree: nomenclature and phylogeography of its major divisions. Annu Rev Anthropol 31:303-321.
10. Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P. 2007. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA 104:8726-8730.
11. Jobling MA, Tyler-Smith C. 2003. The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598-612.
12. Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, Hammer MF. 2010. Major east-west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol 27:1833-1844.
13. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830-838.
14. Kayser M, Brauer S, Cordaux R, Casto A, Lao O, Zhivotovsky LA, Moyse-Faurie C, Rutledge RB, Schiefenhoevel W, Gil D, Lin AA, Underhill PA, et al. 2006. Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Mol Biol Evol 23:2234-2244.
15. Kayser M, Brauer S, Weiss G, Schiefenhövel W, Underhill P, Shen P, Oefner P, Tommaseo-Ponzetta M, Stoneking M. 2003. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am J Hum Genet 72:281-302.
16. Kayser M, de Knijff P. 2011. Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet 12:179-192.
17. Lacau H, Gayden T, Regueiro M, Chennakrishnaiah S, Bukhari A, Underhill PA, Garcia-Bertrand RL, Herrera RJ. 2012. Afghanistan from a Y-chromosome perspective. Eur J Hum Genet 20:1063-1070.
18. Lao O, Altena E, Becker C, Brauer S, Kraaijenbrink T, van Oven M, Nürnberg P, de Knijff P, Kayser M. 2013. Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history. Investig Genet 4:9.
19. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
20. Luis JR, Rowold DJ, Regueiro M, Caeiro B, Cinnioğlu C, Roseman C, Underhill PA, Cavalli-Sforza LL, Herrera RJ. 2004. The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations. Am J Hum Genet 74:532-544.
21. Malyarchuk B, Derenko M, Denisova G, Maksimov A, Wozniak M, Grzybowski T, Dambueva I, Zakharov I. 2011. Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. J Hum Genet 56:583-588.
22. Mendez FL, Karafet TM, Krahn T, Ostrer H, Soodyall H, Hammer MF. 2011. Increased resolution of Y chromosome haplogroup T defines relationships among populations of the Near East, Europe, and Africa. Hum Biol 83:39-53.
23. Myres NM, Rootsi S, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, et al. 2011. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 19:95-101.
24. Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P. 2013. Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree. J Hum Genet 58:195-201.
25. Poznik GD, Henn BM, Yee M-C, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD. 2013. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341:562-565.
26. Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barać L, Pericić M, Balanovsky O, Pshenichnov A, Dion D, et al. 2004. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe. Am J Hum Genet 75:128-137.
27. Rootsi S, Myres NM, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Varendi K, Sahakyan H, Behar DM, Khusainova R, et al. 2012. Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 20:1275-1282.
28. Rootsi S, Zhivotovsky LA, Baldovic M, Kayser M, Kutuev IA, Khusainova R, Bermisheva MA, Gubina M, Fedorova SA, Ilumäe A-M, Khusnutdinova EK, Voevoda MI, et al. 2007. A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. Eur J Hum Genet 15:204-211.
29. Rosa A, Ornelas C, Jobling MA, Brehm A, Villems R. 2007. Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective. BMC Evol Biol 7:124.
30. Scheinfeldt L, Friedlaender F, Friedlaender J, Latham K, Koki G, Karafet T, Hammer M, Lorenz J. 2006. Unexpected NRY chromosome variation in Northern Island Melanesia. Mol Biol Evol 23:1628-1641.
31. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, et al. 2004. Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023-1034.
32. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow C-ET, Lin AA, Mitra M, Sil SK, Ramesh A, Usha Rani MV, Thakur CM, et al. 2006. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 78:202-221.
33. Taylor D, Nagle N, Ballantyne KN, van Oorschot RAH, Wilcox S, Henry J, Turakulov R, Mitchell RJ. 2012. An investigation of admixture in an Australian Aboriginal Y-chromosome STR database. Forensic Sci Int Genet 6:532-538.
34. Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, King RJ, Lin AA, Chow C-ET, Semino O, Battaglia V, Kutuev I, Järve M, et al. 2010. Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 18:479-484.
35. van Oven M, Brauer S, Choi Y, Ensing J, Schiefenhövel W, Stoneking M, Kayser M. 2014a. Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea. Eur J Hum Genet doi:10.1038/ejhg.2014.38.
36. van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau MHD. 2014b. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat 35:187-191.
37. van Oven M, Ralf A, Kayser M. 2011. An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups. Int J Legal Med 125:879-885.
38. van Oven M, van den Tempel N, Kayser M. 2012. A multiplex SNP assay for the dissection of human Y-chromosome haplogroup O representing the major paternal lineage in East and Southeast Asia. J Hum Genet 57:65-69.
39. van Oven M, Toscani K, van den Tempel N, Ralf A, Kayser M. 2013. Multiplex genotyping assays for fine-resolution subtyping of the major human Y-chromosome haplogroups E, G, I, J, and R in anthropological, genealogical, and forensic investigations. Electrophoresis 34:3029-3038.
40. Wang C-C, Yan S, Qin Z-D, Lu Y, Ding Q-L, Wei L-H, Li S-L, Yang Y-J, Jin L, Li H, the Genographic Consortium. 2013. Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611: neolithic expansion of Y chromosomes in China. J Syst Evol 51:280-286.
41. Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y, Tyler-Smith C. 2013. A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23:388-395.
42. Wood ET, Stover DA, Ehret C, Destro-Bisol G, Spedini G, McLeod H, Louie L, Bamshad M, Strassmann BI, Soodyall H, Hammer MF. 2005. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes. Eur J Hum Genet 13:867-876.
43. Zegura SL, Karafet TM, Zhivotovsky LA, Hammer MF. 2004. High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas. Mol Biol Evol 21:164-175.