GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE12713 Query DataSets for GSE12713
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
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.
Overall design 100 CHM samples collected throughout Japan were analyzed by Affymetrix Genechip Mapping 500K Set array.
Contributor(s) Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K
Citation(s) 19424418
Submission date Sep 09, 2008
Last update date May 17, 2017
Contact name Kenshi Hayashi
Phone +81-92-642-6171
Organization name Kyushu University
Department Medical Institute of Bioregulation
Street address Maidashi 3-1-1, Higashi-ku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (200)
GSM318925 CHM001Nsp
GSM318926 CHM001Sty
GSM318927 CHM002Nsp
BioProject PRJNA112647

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap