publication . Article . Other literature type . 2004

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs.

Joshua M. Akey; Jing Huang; Vibhor Sonpar; Esteban J. Parra; Mark D. Shriver; Keith W. Jones; Giulia C. Kennedy; Heather A. Lawson;
Open Access English
  • Published: 01 May 2004 Journal: Human Genomics (issn: 1479-7364, Copyright policy)
  • Publisher: BMC
Abstract
<p>Abstract</p> <p>Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering according to population, with the root branching from the African-American clade. The African-American cluster is much less star-like than European-American ...
Subjects
free text keywords: population genomics, population genetics, microarray, genotyping, evolution, admixture, Medicine, R, Genetics, QH426-470, Primary Research, Human genetics, Population, education.field_of_study, education, Biology, Clade, Single-nucleotide polymorphism, Genome
Funded by
NIH| CONSTRUCTION AND APPLICATION OF A US ADMIXTURE MAP
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002154-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
42 references, page 1 of 3

Risch, N, Burchard, E, Ziv, E. 'Categorization of humans in biomedical research: Genes, race and disease'. Genome Biol. 2002; 3: 1-12 [OpenAIRE]

Schork, N, Fallin, D, Tiwari, HK. 'Pharmacogenetics'. Handbook of Statistical Genetics. 2001: 741-764

Burroughs, VJ, Maxey, RW, Levy, RA. 'Racial and ethnic differences in response to medicines: Towards individualized pharmaceutical treatment'. J Natl Med Assoc. 2002; 94: 1-26 [OpenAIRE] [PubMed]

Bowcock, AM, Ruiz-Linares, A, Tomfohrde, J. 'High resolution of human evolutionary trees with polymorphic microsatellites'. Natur. 1994; 368: 455-457 [OpenAIRE] [DOI]

Rosenberg, NA, Pritchard, JK, Weber, JL. 'Genetic structure of human populations'. Science. 2002; 298: 2381-2385 [OpenAIRE] [PubMed] [DOI]

Cavali-Sforza, LL. 'Population structure and human evolution'. Proc R Soc Lond B Biol Sci. 1966; 164: 362-379 [OpenAIRE] [PubMed] [DOI]

Black, WC, Baer, CF, Antolin, MF. 'Population genomics: Genome-wide sampling of insect populations'. Annu Rev Entomol. 2001; 46: 441-469 [OpenAIRE] [PubMed] [DOI]

Kennedy, GC, Matsuzaki, H, Dong, S. 'Large-scale genotyping of complex DNA'. Nat Biotechnol. 2003; 21: 1233-1237 [OpenAIRE] [PubMed] [DOI]

Akey, JM, Zhang, G, Zhang, K. 'Interrogating a high-density SNP map for signatures of natural selection'. Genome Res. 2002; 12: 1805-1814 [OpenAIRE] [PubMed] [DOI]

Chee, M, Yang, R, Hubbell, E. 'Accessing genetic information with high-density DNA arrays'. Science. 1996; 274: 610-614 [OpenAIRE] [PubMed] [DOI]

Chakraborty, R, Jin, L. A unified approach to study hypervariable polymorphisms: Statistical considerations of determining relatedness and population distances DNA Fingerprinting: Current State of the Science. 1993; 67: 153-175

Saitou, N, Nei, M. 'The neighbor-joining method: A new method for reconstructing phylogenetic trees'. Mol Biol Evol. 1987; 4: 406-425 [PubMed]

Kumar, S, Tamura, K, Jakobesen, IB. 'MEGA2: Molecular evolutionary genetics analysis software'. Bioinformatics. 2001; 17: 1244-1245 [OpenAIRE] [PubMed] [DOI]

Rohlf, FJ. 1992

Pritchard, JK, Stephens, M, Donelly, P. 'Inference of population structure from multilocus genotype data'. Genetics. 2000; 155: 945-959 [OpenAIRE] [PubMed]

42 references, page 1 of 3
Abstract
<p>Abstract</p> <p>Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single nucleotide polymorphisms (SNPs) in 84 individuals from four populations: African-American, European-American, Chinese and Japanese. Individual relationships were reconstructed using the allele sharing distance and the neighbour-joining tree making method. Trees show clear clustering according to population, with the root branching from the African-American clade. The African-American cluster is much less star-like than European-American ...
Subjects
free text keywords: population genomics, population genetics, microarray, genotyping, evolution, admixture, Medicine, R, Genetics, QH426-470, Primary Research, Human genetics, Population, education.field_of_study, education, Biology, Clade, Single-nucleotide polymorphism, Genome
Funded by
NIH| CONSTRUCTION AND APPLICATION OF A US ADMIXTURE MAP
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002154-02
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
42 references, page 1 of 3

Risch, N, Burchard, E, Ziv, E. 'Categorization of humans in biomedical research: Genes, race and disease'. Genome Biol. 2002; 3: 1-12 [OpenAIRE]

Schork, N, Fallin, D, Tiwari, HK. 'Pharmacogenetics'. Handbook of Statistical Genetics. 2001: 741-764

Burroughs, VJ, Maxey, RW, Levy, RA. 'Racial and ethnic differences in response to medicines: Towards individualized pharmaceutical treatment'. J Natl Med Assoc. 2002; 94: 1-26 [OpenAIRE] [PubMed]

Bowcock, AM, Ruiz-Linares, A, Tomfohrde, J. 'High resolution of human evolutionary trees with polymorphic microsatellites'. Natur. 1994; 368: 455-457 [OpenAIRE] [DOI]

Rosenberg, NA, Pritchard, JK, Weber, JL. 'Genetic structure of human populations'. Science. 2002; 298: 2381-2385 [OpenAIRE] [PubMed] [DOI]

Cavali-Sforza, LL. 'Population structure and human evolution'. Proc R Soc Lond B Biol Sci. 1966; 164: 362-379 [OpenAIRE] [PubMed] [DOI]

Black, WC, Baer, CF, Antolin, MF. 'Population genomics: Genome-wide sampling of insect populations'. Annu Rev Entomol. 2001; 46: 441-469 [OpenAIRE] [PubMed] [DOI]

Kennedy, GC, Matsuzaki, H, Dong, S. 'Large-scale genotyping of complex DNA'. Nat Biotechnol. 2003; 21: 1233-1237 [OpenAIRE] [PubMed] [DOI]

Akey, JM, Zhang, G, Zhang, K. 'Interrogating a high-density SNP map for signatures of natural selection'. Genome Res. 2002; 12: 1805-1814 [OpenAIRE] [PubMed] [DOI]

Chee, M, Yang, R, Hubbell, E. 'Accessing genetic information with high-density DNA arrays'. Science. 1996; 274: 610-614 [OpenAIRE] [PubMed] [DOI]

Chakraborty, R, Jin, L. A unified approach to study hypervariable polymorphisms: Statistical considerations of determining relatedness and population distances DNA Fingerprinting: Current State of the Science. 1993; 67: 153-175

Saitou, N, Nei, M. 'The neighbor-joining method: A new method for reconstructing phylogenetic trees'. Mol Biol Evol. 1987; 4: 406-425 [PubMed]

Kumar, S, Tamura, K, Jakobesen, IB. 'MEGA2: Molecular evolutionary genetics analysis software'. Bioinformatics. 2001; 17: 1244-1245 [OpenAIRE] [PubMed] [DOI]

Rohlf, FJ. 1992

Pritchard, JK, Stephens, M, Donelly, P. 'Inference of population structure from multilocus genotype data'. Genetics. 2000; 155: 945-959 [OpenAIRE] [PubMed]

42 references, page 1 of 3
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