Dataset Information


Definitive haplotypes from a collection of complete hydatidiform moles (CHMs)

ABSTRACT: The haplotype map constructed by the International HapMap Project is a valuable source for the studies of disease genes, population structure, and evolution. In the Project, haplotypes have been inferred from experimentally determined genotypes, and are fairly accurate for Caucasians and Africans since the inference was based on the genotypes of trios. However, the inference for the Asians populations was less accurate, because of the lack of familial information. Here we assessed how the error in the inference can affect downstream studies, especially the analysis of recent positive selections, by comparing the results of the analyses using the data of HapMap JPT and of definitive haplotypes (DHaplo-DB) determined by us from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. We found that the error in JPT was not uniform throughout the genome, and the statistics for recent positive selection was significantly affected. Keywords: Definitive haplotype determination using CHMs, which carry haploid genomes. 100 CHM samples collected throughout Japan were analyzed by Affymetrix Genechip Mapping 500K Set array.

ORGANISM(S): Homo sapiens

SUBMITTER: Kiyoko Kato 

PROVIDER: E-GEOD-12713 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions.

Higasa Koichiro K   Kukita Yoji Y   Kato Kiyoko K   Wake Norio N   Tahira Tomoko T   Hayashi Kenshi K  

PLoS genetics 20090508 5

The haplotype map constructed by the HapMap Project is a valuable resource in the genetic studies of disease genes, population structure, and evolution. In the Project, Caucasian and African haplotypes are fairly accurately inferred, based mainly on the rules of Mendelian inheritance using the genotypes of trios. However, the Asian haplotypes are inferred from the genotypes of unrelated individuals based on population genetics, and are less accurate. Thus, the effects of this inaccuracy on downs  ...[more]

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