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| Status |
Public on May 12, 2009 |
| Title |
Definitive haplotypes from a collection of complete hydatidiform moles (CHMs) |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
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.
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| Overall design |
100 CHM samples collected throughout Japan were analyzed by Affymetrix Genechip Mapping 500K Set array.
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| Contributor(s) |
Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K |
| Citation(s) |
19424418 |
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| Submission date |
Sep 09, 2008 |
| Last update date |
May 17, 2017 |
| Contact name |
Kenshi Hayashi |
| E-mail(s) |
hayashi.kenshi@gmail.com
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| Phone |
+81-92-642-6171
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| Organization name |
Kyushu University
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| Department |
Medical Institute of Bioregulation
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| Street address |
Maidashi 3-1-1, Higashi-ku
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| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
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| Platforms (2) |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
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| Samples (200)
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| Relations |
| BioProject |
PRJNA112647 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12713_RAW.tar |
4.9 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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