A 34-plex autosomal SNP single base extension assay for ancestry investigations

Methods in Molecular Biology

Volumn 830, Issue , 2012, Pages 109-126

  Phillips, C ^a   Fondevila, M ^a   Lareau, Maria Victoria ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

Bayesian analysis; Genetic ancestry; Population admixture; Population genetics; SNP AIM SNP

Indexed keywords

PRIMER DNA;

ARTICLE; BASE PAIRING; GENEALOGY; GENETIC DATABASE; GENETIC MARKER; GENETICS; HUMAN; HUMAN CHROMOSOME; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

BASE PAIRING; BASE SEQUENCE; CHROMOSOMES, HUMAN; DATABASES, GENETIC; DNA PRIMERS; GENEALOGY AND HERALDRY; GENETIC MARKERS; GENETICS, POPULATION; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REFERENCE STANDARDS;

EID: 84855867652     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-461-2_8     Document Type: Article

References (20)

1. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. (2002) Genetic structure of human populations. Science 298: 2381-5. (Pubitemid 36014209)
2. Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A, The SNPforID Consortium. (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1: 273-80. (Pubitemid 47376569)
3. Lao O, Vallone PM, Coble MD, Diegoli TM, van Oven M, van der Gaag KJ, Pijpe J, de Knijff P, Kayser M. (2010) Hum Mutat 31: E1875-93.
4. Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T. (2008) A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum Mutat 29: 648-58. (Pubitemid 351614589)
5. Fondevila M, Phillips C, Naveran N, Fernandez L, Cerezo M, Salas A, Carracedo A, Lareu MV. (2008) Case report: identifi cation of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur. Forensic Sci Int Genet 2: 212-8.
6. Phillips C, Prieto L, Fondevila M, Salas A, Gómez-Tato A, Alvarez-Dios J, Alonso A, Blanco-Verea A, Brión M, Montesino M, Carracedo A, Lareu MV. (2009) Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One 4: e6583.
7. Pritchard JK, Stephens M, Donnelly P. (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-59. (Pubitemid 30397141)
8. 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 identifi cation. Electrophoresis 27: 1713-24.
9. Phillips C. (2009) SNP databases. Methods Mol Biol 578: 43-71.
10. Amigo J, Phillips C, Lareu M, Carracedo A. (2008) The SNP for ID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med 122: 435-40.
11. Amigo J, Salas A, Phillips C, Carracedo A. (2008) SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics 9: 428.
12. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, Chen Z, Chu J, et al. (2002) A human genome diversity cell line panel. Science 296: 261-2. (Pubitemid 34303653)
13. Rosenberg NA, Li LM, Ward R, Pritchard JK. (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-22. (Pubitemid 38037431)
14. Liu N, Chen L, Wang S, Oh C, Zhao H. (2005) Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genet 30 Suppl 1: S26.
15. Haasl RJ, Payseur BA. (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106: 158-71.
16. Phillips C, Rodriguez A, Mosquera-Miguel A, Fondevila M, Porras-Hurtado L, Rondon F, Salas A, Carracedo A, Lareu MV. (2008) D9S1120, a simple STR with a common Native American-specifi c allele: forensic optimization, locus characterization and allele frequency studies. Forensic Sci Int Genet 3: 7-13.
17. Phillips C, Fernandez-Formoso L, Garcia-Magariños M, Porras L, Tvedebrink T, Amigo J, Fondevila M, Gomez-Tato A, Alvarez-Dios J, Freire-Aradas A, Gomez-Carballa A, Mosquera-Miguel A, Carracedo A, Lareu MV. (2010) Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. Forensic Sci Int Genet (Epub ahead of print) doi: 10.1016/j.fsigen. 2010.02.003 .
18. Falush D, Stephens M, Pritchard JK. (2003) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7: 574-8.
19. Falush D, Stephens M, Pritchard JK. (2007) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 4746-51.
20. Hubisz MJ, Falush D, Stephens M, Pritchard JK. (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resources 9: 1322-32.