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Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE18642: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix) GSE18663: Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina) Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Kenshi Hayashi

PROVIDER: E-GEOD-18701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.

Kukita Yoji Y Yahara Koji K Tahira Tomoko T Higasa Koichiro K Sonoda Miki M Yamamoto Ken K Kato Kiyoko K Wake Norio N Hayashi Kenshi K

American journal of human genetics 20100527 6

The majority of complete hydatidiform moles (CHMs) harbor duplicated haploid genomes that originate from sperm. This makes CHMs more advantageous than conventional diploid cells for determining haplotypes of SNPs and copy-number variations (CNVs), because all of the genetic variants in a CHM genome are homozygous. Here we report SNP and CNV haplotype structures determined by analysis of 100 CHMs from Japanese subjects via high-density DNA arrays. The obtained haplotype map should be useful as a ...[more]

PMID: 20537301

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Whole-genome definitive haplotypes of SNPs and CNVs determined by genotyping duplicated haploid genomes

Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 97 complete hydatidiform moles (CHMs) tissues collected throughout Japan.

2014-02-13 | E-GEOD-54948 | biostudies-arrayexpress

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

Project description:Copy number variations (CNVs) are abundant, possibly variable among populations, and can confer various phenotypic variations such as risk to complex disease. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes that originated from single sperm, and have advantages as materials over conventional diploid cells in detecting CNVs by hybridization, because greater S/N ratios are expected, and overlapping CNV segments are independently detected without being bothered by possible heterozygous situations. Overall occupancy of CNV segments per haploid found here was at a level similar to previous reports. Approximately a half of our polymorphic CNV regions have not been described in the previous report for Asians, but the frequencies of most of these new CNV regions were low. The limited number of examined samples is likely to be the reason that they have escaped detection in the previous report. Many common CNV regions are resolvable to clusters of CNV segmets (that is, CNV events) on the basis of mutual overlap of the segments. The similarity of haplotype backgrounds surrounding different CNV events within the same CNV regions suggests that ancestral recurrences of CNV events were predominantly haplotype preferential. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 5 complete hydatidiform moles (CHMs) tissues collected throughout Japan.

2010-05-17 | E-GEOD-18663 | biostudies-arrayexpress

Whole-genome definitive haplotypes of SNPs and CNVs determined by genotyping duplicated haploid genomes

2014-02-13 | GSE54948 | GEO

Project description:Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles

| PRJNA121489 | ENA

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

2010-05-17 | GSE18663 | GEO

Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix)

2010-05-17 | GSE18642 | GEO

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

Project description: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.

2010-04-05 | E-GEOD-12713 | biostudies-arrayexpress

Homo sapiens

Project description:Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix)

| PRJNA123815 | ENA

Homo sapiens

Project description:Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Illumina)

| PRJNA123805 | ENA

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

2009-05-12 | GSE12713 | GEO