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Exploring of new Y-chromosome SNP loci using Pyrosequencing and the SNaPshot methods

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Abstract

The single nucleotide polymorphisms on the Y chromosome (Y-SNP) have been considered to be important in forensic casework. However, Y-SNP loci were mostly population specific and lacked biallelic polymorphisms in the Asian population. In this study, we developed a strategy for seeking and genotyping new Y-SNP markers based on both Pyrosequencing and the SNaPshot methods. As results, 34 new biallelic markers were observed to be polymorphic in the Chinese Han population by estimation of allele frequencies of 103 candidate’s Y-SNP loci in DNA pools using Pyrosequencing technology. Then, a multiplex system with 20 Y-SNP loci was genotyped using the SNaPshot™ multiplex kit. Twenty Y-SNP loci defined 56 different haplotypes, and the haplotype diversity was estimated to be 0.9539. Our result demonstrated that the strategy could be used as an efficient tool to search and genotype biallelic markers from a large amount of candidate loci. In addition, 20 Y-SNP loci constructed a multiplex system, which could provide supplementary information for forensic identification.

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References

  1. Bruce B, Frederick RB, Arthur JE (2005) Forensic aspects of mass disasters: strategic considerations for DNA-based human identification. Leg Med 7:230–243

    Article  Google Scholar 

  2. Prinz M, Carracedo A, Mayr WR, Morling N, Parsons TJ, Sajantila A, Scheithauer R, Schmitter H, Schneider PM (2007) DNA Commission of the International Society for Forensic Genetics (ISFG): Recommendations regarding the role of forensic genetics for disaster victim identification (DVI). Forensic Sci Int Genetics 1:3–12

    Article  CAS  Google Scholar 

  3. Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW (2000) Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci USA 97:7360–7365

    Article  PubMed  CAS  Google Scholar 

  4. Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 32:135–142

    Article  PubMed  CAS  Google Scholar 

  5. The Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348

    Article  Google Scholar 

  6. 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

    Article  PubMed  CAS  Google Scholar 

  7. 1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073

    Article  CAS  Google Scholar 

  8. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307:1072–1079

    Article  PubMed  CAS  Google Scholar 

  9. Lavebratt C, Sengul S (2006) Single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools using Pyrosequencing. Nat Protoc 1:2573–2582

    Article  PubMed  CAS  Google Scholar 

  10. Su B, Xiao J, Underhill P, Deka R, Zhang W, Akey J, Huang W, Shen D, Lu D, Luo J, Chu J, Tan J, Shen P, Davis R, Cavalli-Sforza L, Chakraborty R, Xiong M, Du R, Oefner P, Chen Z, Jin L (1999) Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am J Hum Genet 65:1718–1724

    Article  PubMed  CAS  Google Scholar 

  11. Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A (2006) Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci Int 157:23–35

    Article  PubMed  CAS  Google Scholar 

  12. Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, Jin L, Su B (2005) Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet 77:408–419

    Article  PubMed  CAS  Google Scholar 

  13. Brión M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Børsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2005) Introduction of a single nucleodite polymorphism-based “Major Y-chromosome haplogroup typing kit” suitable for predicting the geographical origin of male lineages. Electrophoresis 26:4411–4420

    Article  PubMed  Google Scholar 

  14. Kaderali L, Deshpande A, Nolan JP, White PS (2003) Primer-design for multiplexed genotyping. Nucleic Acids Res 31:1796–1802

    Article  PubMed  CAS  Google Scholar 

  15. Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194

    Article  PubMed  CAS  Google Scholar 

  16. Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics 3:77–96

    Article  Google Scholar 

  17. Gruber JD, Colligan PB, Wolford JK (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using Pyrosequencing. Hum Genet 110:395–401

    Article  PubMed  CAS  Google Scholar 

  18. Wasson J, Skolnick G, Love-Gregory L, Permutt MA (2002) Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by Pyrosequencing™ technology. Biotechniques 32:1144–1152

    PubMed  CAS  Google Scholar 

  19. Neve B, Froguel L, Corset L, Vaillant E, Vatin V, Boutin P (2002) Rapid SNP allele frequency determination in genomic DNA pools by Pyrosequencing™. Biotechniques 32:1138–1142

    PubMed  CAS  Google Scholar 

  20. Lavebratt C, Sengul S, Jansson M, Schalling M (2004) Pyrosequencing-based SNP allele frequency estimation in DNA pools. Hum Mutat 23:92–97

    Article  PubMed  CAS  Google Scholar 

  21. Alderborn A, Kristofferson A, Hammerling U (2000) Determination of single nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 10:1249–1258

    Article  PubMed  CAS  Google Scholar 

  22. Fakhrai-Rad H, Pourmand N, Ronaghi M (2002) Pyrosequencing™: an accurate detection platform for single nucleotide polymorphisms. Hum Mutat 19:479–485

    Article  PubMed  CAS  Google Scholar 

  23. Palmieri O, Toth S, Ferraris A, Andriulli A, Latiano A, Annese V, Dallapiccola B, Vecchi M, Devoto M, Surrey S, Fortina P (2003) CARD15 genotyping in inflammatory bowel disease patients by multiplex Pyrosequencing. Clin Chem 49:1675–1679

    Article  PubMed  CAS  Google Scholar 

  24. Zhou GH, Gotou M, Kajiyama T, Kambara H (2005) Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI). Nucleic Acids Res 33:e133

    Article  PubMed  Google Scholar 

  25. Brandstätter A, Salas A, Niederstätter H, Gassner C, Carracedo A, Parson W (2006) Dissection of mitochondrial superhaplogroup H using coding region SNPs. Electrophoresis 27:2541–2550

    Article  PubMed  Google Scholar 

  26. Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724

    Article  PubMed  CAS  Google Scholar 

  27. Lessig R, Zoledziewska M, Fahr K, Edelmann J, Kostrzewa M, Dobosz T, Kleemann WJ (2005) Y-SNP-genotyping—a new approach in forensic analysis. Forensic Sci Int 154:128–136

    Article  PubMed  CAS  Google Scholar 

  28. Sanchez JJ, Børsting C, Hallenberg C, Buchard A, Hernandez A, Morling N (2003) Multiplex PCR and minisequencing of SNPs—a model with 35 Y chromosome SNPs. Forensic Sci Int 137:74–84

    Article  PubMed  CAS  Google Scholar 

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Acknowledgement

This study was supported by grants (30872917 and 81072510) from the National Nature Science Foundation, China.

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Authors and Affiliations

  1. Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu, 610041, Sichuan, China

    Wei Wei, Hai-Bo Luo, Jing Yan & Yi-Ping Hou

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  1. Wei Wei
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  2. Hai-Bo Luo
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  3. Jing Yan
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  4. Yi-Ping Hou
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Corresponding author

Correspondence to Yi-Ping Hou.

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Table S1

Allele frequencies of 103 Y-SNP loci in DNA pools by Pyrosequencing in the Chinese Han population samples (n = 54) (DOC 111 kb)

Table S2

Twenty 20 Y-SNP primer sequences and concentrations for multiplex PCR amplifications (DOC 56 kb)

Table S3

Twenty Y-SNP primer sequences and concentrations for multiplied minisequencing reactions (DOC 54 kb)

Table S4

Allele for 34 Y-Chromosomal SNPs in the Chinese Han population sample using Pyrosequencing in individual sample (n = 54) (DOC 132 kb)

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Wei, W., Luo, HB., Yan, J. et al. Exploring of new Y-chromosome SNP loci using Pyrosequencing and the SNaPshot methods. Int J Legal Med 126, 825–833 (2012). https://doi.org/10.1007/s00414-011-0603-4

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  • DOI: https://doi.org/10.1007/s00414-011-0603-4

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