A second generation human haplotype map of over 3.1 million SNPs. International HapMap Consortium, Frazer, K A, Ballinger, D G, Cox, D R, Hinds, D A, Stuve, L L, Gibbs, R A, Belmont, J W, Boudreau, A, Hardenbol, P, Leal, S M, Pasternak, S, Wheeler, D A, Willis, T D, Yu, F, Yang, H, Zeng, C, Gao, Y, Hu, H, Hu, W, Li, C, Lin, W, Liu, S, Pan, H, Tang, X, Wang, J, Wang, W, Yu, J, Zhang, B, Zhang, Q, Zhao, H, Zhao, H, Zhou, J, Gabriel, S B, Barry, R, Blumenstiel, B, Camargo, A, Defelice, M, Faggart, M, Goyette, M, Gupta, S, Moore, J, Nguyen, H, Onofrio, R C, Parkin, M, Roy, J, Stahl, E, Winchester, E, Ziaugra, L, Altshuler, D, Shen, Y, Yao, Z, Huang, W, Chu, X, He, Y, Jin, L, Liu, Y, Shen, Y, Sun, W, Wang, H, Wang, Y, Wang, Y, Xiong, X, Xu, L, Waye, M M, Tsui, S K, Xue, H, Wong, J T, Galver, L M, Fan, J B, Gunderson, K, Murray, S S, Oliphant, A R, Chee, M S, Montpetit, A, Chagnon, F, Ferretti, V, Leboeuf, M, Olivier, J F, Phillips, M S, Roumy, S, Sallée, C, Verner, A, Hudson, T J, Kwok, P Y, Cai, D, Koboldt, D C, Miller, R D, Pawlikowska, L, Taillon-Miller, P, Xiao, M, Tsui, L C, Mak, W, Song, Y Q, Tam, P K, Nakamura, Y, Kawaguchi, T, Kitamoto, T, Morizono, T, Nagashima, A, Ohnishi, Y, Sekine, A, Tanaka, T, Tsunoda, T, Deloukas, P, Bird, C P, Delgado, M, Dermitzakis, E T, Gwilliam, R, Hunt, S, Morrison, J, Powell, D, Stranger, B E, Whittaker, P, Bentley, D R, Daly, M J, de Bakker, P I, Barrett, J, Chretien, Y R, Maller, J, McCarroll, S, Patterson, N, Pe'er, I, Price, A, Purcell, S, Richter, D J, Sabeti, P, Saxena, R, Schaffner, S F, Sham, P C, Varilly, P, Altshuler, D, Stein, L D, Krishnan, L, Smith, A V, Tello-Ruiz, M K, Thorisson, G A, Chakravarti, A, Chen, P E, Cutler, D J, Kashuk, C S, Lin, S, Abecasis, G R, Guan, W, Li, Y, Munro, H M, Qin, Z S, Thomas, D J, McVean, G, Auton, A, Bottolo, L, Cardin, N, Eyheramendy, S, Freeman, C, Marchini, J, Myers, S, Spencer, C, Stephens, M, Donnelly, P, Cardon, L R, Clarke, G, Evans, D M, Morris, A P, Weir, B S, Tsunoda, T, Mullikin, J C, Sherry, S T, Feolo, M, Skol, A, Zhang, H, Zeng, C, Zhao, H, Matsuda, I, Fukushima, Y, Macer, D R, Suda, E, Rotimi, C N, Adebamowo, C A, Ajayi, I, Aniagwu, T, Marshall, P A, Nkwodimmah, C, Royal, C D, Leppert, M F, Dixon, M, Peiffer, A, Qiu, R, Kent, A, Kato, K, Niikawa, N, Adewole, I F, Knoppers, B M, Foster, M W, Clayton, E W, Watkin, J, Gibbs, R A, Belmont, J W, Muzny, D, Nazareth, L, Sodergren, E, Weinstock, G M, Wheeler, D A, Yakub, I, Gabriel, S B, Onofrio, R C, Richter, D J, Ziaugra, L, Birren, B W, Daly, M J, Altshuler, D, Wilson, R K, Fulton, L L, Rogers, J, Burton, J, Carter, N P, Clee, C M, Griffiths, M, Jones, M C, McLay, K, Plumb, R W, Ross, M T, Sims, S K, Willey, D L, Chen, Z, Han, H, Kang, L, Godbout, M, Wallenburg, J C, L'Archev\^eque, P, Bellemare, G, Saeki, K, Wang, H, An, D, Fu, H, Li, Q, Wang, Z, Wang, R, Holden, A L, Brooks, L D, McEwen, J E, Guyer, M S, Wang, V O, Peterson, J L, Shi, M, Spiegel, J, Sung, L M, Zacharia, L F, Collins, F S, Kennedy, K, Jamieson, R, & Stewart, J Nature, 449(7164):851-861, October, 2007.
A second generation human haplotype map of over 3.1 million SNPs [link]Paper  doi  abstract   bibtex   
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.
@article{hapmap2007second,
  abstract = {We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35\% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30\% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1\% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.
},
  added-at = {2012-07-13T19:44:19.000+0200},
  author = {{International HapMap Consortium} and Frazer, K A and Ballinger, D G and Cox, D R and Hinds, D A and Stuve, L L and Gibbs, R A and Belmont, J W and Boudreau, A and Hardenbol, P and Leal, S M and Pasternak, S and Wheeler, D A and Willis, T D and Yu, F and Yang, H and Zeng, C and Gao, Y and Hu, H and Hu, W and Li, C and Lin, W and Liu, S and Pan, H and Tang, X and Wang, J and Wang, W and Yu, J and Zhang, B and Zhang, Q and Zhao, H and Zhao, H and Zhou, J and Gabriel, S B and Barry, R and Blumenstiel, B and Camargo, A and Defelice, M and Faggart, M and Goyette, M and Gupta, S and Moore, J and Nguyen, H and Onofrio, R C and Parkin, M and Roy, J and Stahl, E and Winchester, E and Ziaugra, L and Altshuler, D and Shen, Y and Yao, Z and Huang, W and Chu, X and He, Y and Jin, L and Liu, Y and Shen, Y and Sun, W and Wang, H and Wang, Y and Wang, Y and Xiong, X and Xu, L and Waye, M M and Tsui, S K and Xue, H and Wong, J T and Galver, L M and Fan, J B and Gunderson, K and Murray, S S and Oliphant, A R and Chee, M S and Montpetit, A and Chagnon, F and Ferretti, V and Leboeuf, M and Olivier, J F and Phillips, M S and Roumy, S and Sall{\'e}e, C and Verner, A and Hudson, T J and Kwok, P Y and Cai, D and Koboldt, D C and Miller, R D and Pawlikowska, L and Taillon-Miller, P and Xiao, M and Tsui, L C and Mak, W and Song, Y Q and Tam, P K and Nakamura, Y and Kawaguchi, T and Kitamoto, T and Morizono, T and Nagashima, A and Ohnishi, Y and Sekine, A and Tanaka, T and Tsunoda, T and Deloukas, P and Bird, C P and Delgado, M and Dermitzakis, E T and Gwilliam, R and Hunt, S and Morrison, J and Powell, D and Stranger, B E and Whittaker, P and Bentley, D R and Daly, M J and de Bakker, P I and Barrett, J and Chretien, Y R and Maller, J and McCarroll, S and Patterson, N and Pe'er, I and Price, A and Purcell, S and Richter, D J and Sabeti, P and Saxena, R and Schaffner, S F and Sham, P C and Varilly, P and Altshuler, D and Stein, L D and Krishnan, L and Smith, A V and Tello-Ruiz, M K and Thorisson, G A and Chakravarti, A and Chen, P E and Cutler, D J and Kashuk, C S and Lin, S and Abecasis, G R and Guan, W and Li, Y and Munro, H M and Qin, Z S and Thomas, D J and McVean, G and Auton, A and Bottolo, L and Cardin, N and Eyheramendy, S and Freeman, C and Marchini, J and Myers, S and Spencer, C and Stephens, M and Donnelly, P and Cardon, L R and Clarke, G and Evans, D M and Morris, A P and Weir, B S and Tsunoda, T and Mullikin, J C and Sherry, S T and Feolo, M and Skol, A and Zhang, H and Zeng, C and Zhao, H and Matsuda, I and Fukushima, Y and Macer, D R and Suda, E and Rotimi, C N and Adebamowo, C A and Ajayi, I and Aniagwu, T and Marshall, P A and Nkwodimmah, C and Royal, C D and Leppert, M F and Dixon, M and Peiffer, A and Qiu, R and Kent, A and Kato, K and Niikawa, N and Adewole, I F and Knoppers, B M and Foster, M W and Clayton, E W and Watkin, J and Gibbs, R A and Belmont, J W and Muzny, D and Nazareth, L and Sodergren, E and Weinstock, G M and Wheeler, D A and Yakub, I and Gabriel, S B and Onofrio, R C and Richter, D J and Ziaugra, L and Birren, B W and Daly, M J and Altshuler, D and Wilson, R K and Fulton, L L and Rogers, J and Burton, J and Carter, N P and Clee, C M and Griffiths, M and Jones, M C and McLay, K and Plumb, R W and Ross, M T and Sims, S K and Willey, D L and Chen, Z and Han, H and Kang, L and Godbout, M and Wallenburg, J C and L'Archev{\^e}que, P and Bellemare, G and Saeki, K and Wang, H and An, D and Fu, H and Li, Q and Wang, Z and Wang, R and Holden, A L and Brooks, L D and McEwen, J E and Guyer, M S and Wang, V O and Peterson, J L and Shi, M and Spiegel, J and Sung, L M and Zacharia, L F and Collins, F S and Kennedy, K and Jamieson, R and Stewart, J},
  biburl = {https://www.bibsonomy.org/bibtex/2ef1e93daf6bae3c39765971754c5ae13/peter.ralph},
  description = {A second generation human haplotype map of over 3.1 m... [Nature. 2007] - PubMed - NCBI},
  doi = {10.1038/nature06258},
  interhash = {3b97f2a3dcd2e73e572fa7eefc3688b3},
  intrahash = {ef1e93daf6bae3c39765971754c5ae13},
  journal = {Nature},
  keywords = {data_source haplotype hapmap},
  month = oct,
  number = 7164,
  pages = {851-861},
  pmid = {17943122},
  timestamp = {2012-07-13T19:44:55.000+0200},
  title = {A second generation human haplotype map of over 3.1 million {SNPs}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/17943122},
  volume = 449,
  year = 2007
}
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