SNaPshot ® minisequencing analysis of multiple ancestry-informative Y-SNPs using capillary electrophoresis

Methods in Molecular Biology

Volumn 830, Issue , 2012, Pages 127-140

  Geppert, Maria ^a   Roewer, Lutz ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

AIM; Capillary electrophoresis; Minisequencing; Multiplex PCR; SNaPshot ; Y SNP

Indexed keywords

PRIMER DNA;

ARTICLE; BASE PAIRING; CAPILLARY ELECTROPHORESIS; DNA SEQUENCE; GENEALOGY; GENETICS; GEOGRAPHY; HAPLOTYPE; HUMAN; MALE; METABOLISM; METHODOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS; Y CHROMOSOME;

BASE PAIRING; CHROMOSOMES, HUMAN, Y; DNA PRIMERS; ELECTROPHORESIS, CAPILLARY; GENEALOGY AND HERALDRY; GEOGRAPHY; HAPLOTYPES; HUMANS; MALE; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; STATISTICS AS TOPIC;

EID: 84855867653     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-461-2_9     Document Type: Article

References (23)

1. Sobrino, B., and Carracedo, A. (2005) SNP typing in forensic genetics: a review, Methods Mol Biol 297 , 107-126.
2. Sanchez, J. J., Phillips, C., Borsting, C., Balogh, K., Bogus, M., Fondevila, M., Harrison, C. D., Musgrave-Brown, E., Salas, A., Syndercombe-Court, D., Schneider, P. M., Carracedo, A., and Morling, N. (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identifi cation, Electrophoresis 27 , 1713-1724.
3. Brandstatter, A., Parsons, T. J., and Parson, W. (2003) Rapid screening of mtDNA coding region SNPs for the identifi cation of west European Caucasian haplogroups, Int J Legal Med 117 , 291-298. (Pubitemid 37356103)
4. Walsh, S., Liu, F., Ballantyne, K. N., van Oven, M., Lao, O., and Kayser, M. (2011) IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information, Forensic Sci Int Genet . 5(3), 170-80.
5. A map of human genome variation from population-scale sequencing, Nature 467 , 1061-1073.
6. Jobling, M. A. (2001) Y-chromosomal SNP haplotype diversity in forensic analysis, Forensic Sci Int 118 , 158-162. (Pubitemid 32331906)
7. Underhill, P. A., Passarino, G., Lin, A. A., Shen, P., Mirazon Lahr, M., Foley, R. A., Oefner, P. J., and Cavalli-Sforza, L. L. (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations, Ann Hum Genet 65 , 43-62. (Pubitemid 32390189)
8. (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups, Genome Res 12 , 339-348.
9. Karafet, T. M., Mendez, F. L., Meilerman, M. B., Underhill, P. A., Zegura, S. L., and Hammer, M. F. (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree, Genome Res 18 , 830-838. (Pubitemid 351645073)
10. Jobling, M. A., and Tyler-Smith, C. (2003) The human Y chromosome: an evolutionary marker comes of age, Nat Rev Genet 4 , 598-612. (Pubitemid 36917502)
11. Bouakaze, C., Keyser, C., Amory, S., Crubezy, E., and Ludes, B. (2007) First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA, Int J Legal Med 121 , 493-499. (Pubitemid 47573394)
12. Brion, M., Sobrino, B., Blanco-Verea, A., Lareu, M. V., and Carracedo, A. (2005) Hierarchical analysis of 30 Y-chromosome SNPs in European populations, Int J Legal Med 119 , 10-15.
13. Sanchez, J. J., Borsting, C., Hallenberg, C., Buchard, A., Hernandez, A., and Morling, N. (2003) Multiplex PCR and minisequencing of SNPs-a model with 35 Y chromosome SNPs, Forensic Sci Int 137 , 74-84. (Pubitemid 37188770)
14. Onofri, V., Alessandrini, F., Turchi, C., Pesaresi, M., Buscemi, L., and Tagliabracci, A. (2006) Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs, Forensic Sci Int 157 , 23-35. (Pubitemid 43117197)
15. King, T. E., and Jobling, M. A. (2009) Founders, drift, and infi delity: the relationship between Y chromosome diversity and patrilineal surnames, Mol Biol Evol 26 , 1093-1102.
16. Sanchez, J. J., Brion, M., Parson, W., Blanco-Verea, A. J., Borsting, C., Lareu, M., Niederstatter, H., Oberacher, H., Morling, N., and Carracedo, A. (2004) Duplications of the Y-chromosome specifi c loci P25 and 92R7 and forensic implications, Forensic Sci Int 140 , 241-250. (Pubitemid 38230058)
17. Adams, S. M., King, T. E., Bosch, E., and Jobling, M. A. (2006) The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion, Forensic Sci Int 159 , 14-20.
18. Lindblad-Toh, K., Winchester, E., Daly, M. J., Wang, D. G., Hirschhorn, J. N., Laviolette, J. P., Ardlie, K., Reich, D. E., Robinson, E., Sklar, P., Shah, N., Thomas, D., Fan, J. B., Gingeras, T., Warrington, J., Patil, N., Hudson, T. J., and Lander, E. S. (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse, Nat Genet 24 , 381-386. (Pubitemid 30187437)
19. Protocol: ABI PRISM ® SNaPshot ® Multiplex System http://www3.appliedbiosystems.com/cms/groups/mcb-support/documents/ generaldocuments/cms-041203.pdf.
20. SNaPshot ® Kit Analysis -Getting Started Guide, http://www3. appliedbiosystems.com/cms/groups/mcb-support/documents/generaldocuments/ cms-042037.pdf
21. Semino, O., Passarino, G., Oefner, P. J., Lin, A. A., Arbuzova, S., Beckman, L. E., De Benedictis, G., Francalacci, P., Kouvatsi, A., Limborska, S., Marcikiae, M., Mika, A., Mika, B., Primorac, D., Santachiara-Benerecetti, A. S., Cavalli-Sforza, L. L., and Underhill, P. A. (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective, Science 290 , 1155-1159.
22. Rosser, Z. H., Zerjal, T., Hurles, M. E., Adojaan, M., Alavantic, D., Amorim, A., Amos, W., Armenteros, M., Arroyo, E., Barbujani, G., Beckman, G., Beckman, L., Bertranpetit, J., Bosch, E., Bradley, D. G., Brede, G., Cooper, G., Corte-Real, H. B., de Knijff, P., Decorte, R., Dubrova, Y. E., Evgrafov, O., Gilissen, A., Glisic, S., Golge, M., Hill, E. W., Jeziorowska, A., Kalaydjieva, L., Kayser, M., Kivisild, T., Kravchenko, S. A., Krumina, A., Kucinskas, V., Lavinha, J., Livshits, L. A., Malaspina, P., Maria, S., McElreavey, K., Meitinger, T. A., Mikelsaar, A. V., Mitchell, R. J., Nafa, K., Nicholson, J., Norby, S., Pandya, A., Parik, J., Patsalis, P. C., Pereira, L., Peterlin, B., Pielberg, G., Prata, M. J., Previdere, C., Roewer, L., Rootsi, S., Rubinsztein, D. C., Saillard, J., Santos, F. R., Stefanescu, G., Sykes, B. C., Tolun, A., Villems, R., Tyler-Smith, C., and Jobling, M. A. (2000) Y-chromosomal diversity in Europe is clinical and infl uenced primarily by geography, rather than by language, Am J Hum Genet 67 , 1526-1543.
23. Myres, N. M., Rootsi, S., Lin, A. A., Jarve, M., King, R. J., Kutuev, I., Cabrera, V. M., Khusnutdinova, E. K., Pshenichnov, A., Yunusbayev, B., Balanovsky, O., Balanovska, E., Rudan, P., Baldovic, M., Herrera, R. J., Chiaroni, J., Di Cristofaro, J., Villems, R., Kivisild, T., and Underhill, P. A. (2011) A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe, Eur J Hum Genet . 19(1), 95-101