A second generation human haplotype map of over 3.1 million SNPs

  title={A second generation human haplotype map of over 3.1 million SNPs},
  author={Kelly A. Frazer and Dennis Ballinger and David R. Cox and David A. Hinds and Laura L. Stuve and Richard A. Gibbs and John W. Belmont and Andrew A. Boudreau and Paul Hardenbol and Suzanne M. Leal and Shiran Pasternak and David A. Wheeler and Tom Willis and Fuli Yu and Huanming Yang and Changqing Zeng and Yang Gao and Haoran Hu and Weitao Hu and Chaohua Li and Wei Lin and Siqi Liu and Hao Pan and Xiaoli Tang and Jian Wang and Wei Wang and Jun Yu and Bo Zhang and Qingrun Zhang and Hongbin Zhao and Hui-Ping Zhao and Jun Zhou and S. Gabriel and Rachel Barry and Brendan S. Blumenstiel and Amy L. Camargo and Matthew Defelice and Maura Faggart and Marie-Anne Goyette and Supriya Gupta and Jamie M Moore and Huy Nguyen and Roberto Onofrio and Melissa Parkin and Jessica Roy and Erich Stahl and Ellen Winchester and Liuda Ziaugra and David Altshuler and Yan Shen and Zhijian Yao and Wei Huang and Xun Chu and Yungang He and Li Jin and Yangfan Liu and Yayun Shen and Weiwei Sun and Haifeng Wang and Yi Wang and Ying Wang and Xiao-yan Xiong and Liang Xu and Mary Miu Yee Waye and Stephen Kwok‐Wing Tsui and Hong Xue and Jeffrey Tze-Fei Wong and Luana Galver and Jian-Bing Fan and Kevin L. Gunderson and Sarah Shaw Murray and Arnold R. Oliphant and Mark S. Chee and Alexandre Montpetit and Fanny Chagnon and Vincent Ferretti and Martin Leboeuf and Jean-François Olivier and Michael S. Phillips and St{\'e}phanie Roumy and Cl{\'e}mentine Sall{\'e}e and Andrei Verner and Thomas J. Hudson and Pui-Yan Kwok and Dongmei Cai and Daniel C. Koboldt and Raymond D. Miller and Ludmila Pawlikowska and Patricia Taillon-Miller and Ming Xiao and Lap Chee Tsui and William Mak and You-Qiang Song and Paul Kwong-Hang Tam and Yusuke Nakamura and Takahisa Kawaguchi and Takuya Kitamoto and Takashi Morizono and Atsushi Nagashima and Yozo Ohnishi and Akihiro Sekine and Toshihiro Tanaka and Tatsuhiko Tsunoda and Panos Deloukas and Christine P. Bird and Marcos Delgado and Emmanouil T. Dermitzakis and Rhian Gwilliam and Sarah E. Hunt and Jonathan Morrison and Don Powell and Barbara E. Stranger and Pamela Whittaker and D. R. Bentley and Mark J. Daly and Paul I. W. de Bakker and Jeffrey C. Barrett and Yves R Chretien and Julian B. Maller and Steven Mccarroll and Nick J. Patterson and Itsik Pe’er and Alkes L. Price and Shaun M Purcell and Daniel J. Richter and Pardis C Sabeti and Richa Saxena and Stephen F. Schaffner and Pak Chung Sham and Patrick Varilly and Lincoln D. Stein and Lalitha Krishnan and Albert Vernon Smith and Marcela Karey Tello-Ruiz and Gudmundur A. Thorisson and Aravinda Chakravarti and Peter E. Chen and David J. Cutler and Carl S. Kashuk and Shin Lin and Gonçalo R. Abecasis and Weihua Guan and Yun Li and Heather M. Munro and Zhaohui S. Qin and Daryl J. Thomas and Gil McVean and Adam Auton and Leonardo Bottolo and Niall J Cardin and Susana Eyheramendy and Colin Freeman and Jonathan Marchini and Simon R. Myers and Chris C. A. Spencer and Matthew Stephens and Peter Donnelly and Lon R. Cardon and Geraldine M. Clarke and David M. Evans and Andrew P. Morris and Bruce S. Weir and James C. Mullikin and Stephen T. Sherry and Michael Feolo and Andrew Skol and Houcan Zhang and Ichiro Matsuda and Yoshimitsu Fukushima and Darryl R. J. Macer and Eiko Suda and Charles N. Rotimi and Clement A Adebamowo and Ike Oluwapo Oyeneye Ajayi and Toyin Aniagwu and Patricia A. Marshall and Chibuzor Nkwodimmah and Charmaine D. M. Royal and M. Leppert and Missy Dixon and Andy Peiffer and Renzong Qiu and Alastair Kent and Kazuto Kato and Norio Niikawa and Isaac F. Adewole and Bartha Maria Knoppers and Morris W Foster and Ellen Wright Clayton and Jessica Watkin and Donna M. Muzny and Lynne V. Nazareth and Erica Sodergren and George M. Weinstock and Imtaz Yakub and Bruce W. Birren and Richard K. Wilson and Lucinda L. Fulton and Jane Rogers and John Burton and Nigel P. Carter and Chris Clee and Mark Griffiths and Matthew C. Jones and Kirsten McLay and Robert W. Plumb and Mark T. Ross and Sarah Sims and David L. Willey and Zhu Chen and Hua Han and Le Kang and Martin Godbout and J. Wallenburg and P. L'Archev{\^e}que and Guy Bellemare and Koji Saeki and Hongguang Wang and Daochang An and Hongbo Fu and Qing Li and Zhen Wang and Ren-hao Wang and Arthur L. Holden and Lisa D. Brooks and Jean E Mcewen and Mark Guyer and Vivian Ota Wang and Jane Peterson and Michael Shi and Jack Spiegel and Lawrence M. Sung and Lynn F. Zacharia and Francis S. Collins and Karen L Kennedy and Ruth Jamieson and John Stewart},
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… 

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

Two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature are identified.

Integrating common and rare genetic variation in diverse human populations

An expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

HapMap coverage for SNPs in the Japanese population

The HapMap coverage appears to be high although not thorough for SNPs in the Japanese population as compared to its coverage reported in Caucasians, and this needs to be considered when the authors interpret association results.

An integrated map of genetic variation from 1,092 human genomes

It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites.

A global reference for human genetic variation

  • Taras K. OleksykAdam Gonçalo R. David M. Richard M. Gonçalo R. David R. Auton Abecasis Altshuler Durbin Abecasis Bentley C Shane A. McCarthy
  • Biology
  • 2015
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.

A map of human genome variation from population-scale sequencing

The pilot phase of the 1000 Genomes Project is presented, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms, and the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants are described.

Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms

There are already ample opportunities to retrospectively impute indels for prior genome-wide association studies and to incorporate indel imputation into future case/control studies, and further scope exists to improve the imputation of low frequency indels.

Genomics: HapMap Phase II unveiled

It is proposed that recombination might be favoured in regions that are exposed to recurrent selection (for example, from the environment or by pathogens) and integrating SNP information with structural variation.

High-resolution haplotype block structure in the cattle genome

This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples, revealing unexpected similarities between some beef and dairy breeds, and suggesting that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds and ~580,000 SNP would be needed to characterize the haplotypes block structure across the complete cattle genome.



A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HAPMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

Measures of human population structure show heterogeneity among genomic regions.

Estimates of genetic population structure (F(ST) were constructed from all autosomes in two large SNP data sets, and it is shown that individual-marker estimates are too variable to be useful.

Genome-Wide Associations of Gene Expression Variation in Humans

The results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans.

A haplotype map of the human genome

A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.

A haplotype map of the human genome.

A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.

Interrogating a high-density SNP map for signatures of natural selection.

An analysis of single nucleotide polymorphisms with allele frequencies that were determined in three populations provides a first generation natural selection map of the human genome and provides compelling evidence that selection has shaped extant patterns of human genomic variation.

Genome-wide detection and characterization of positive selection in human populations

‘Long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are developed.

Common deletion polymorphisms in the human genome

This work describes a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome.

Extended tracts of homozygosity in outbred human populations.

The results suggest that multiple-megabase-scale ancestral haplotypes persist in outbred human populations in broad genomic regions which have lower than average recombination rates.

Evaluating and improving power in whole-genome association studies using fixed marker sets

The extent to which the sets of SNPs contained on three whole-genome genotyping arrays capture common SNPs across the genome is evaluated, and it is found that the majority of commonSNPs are well captured by these products either directly or through linkage disequilibrium.