A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events

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  • Kukita, Yoji
    Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases
  • Yahara, Koji
    Division of Life Science System, Fujitsu Kyushu Systems Inc.
  • Tahira, Tomoko
    Division of Genome Analysis, Research Center for Genetic Information, Kyushu University
  • Higasa, Koichiro
    Division of Genome Analysis, Research Center for Genetic Information, Kyushu University
  • Sonoda, Miki
    Division of Molecular Population Genetics, Kyushu University
  • Yamamoto, Ken
    Division of Molecular Population Genetics, Kyushu University
  • Kato, Kiyoko
    Division of Molecular and Cell Therapeutics, Medical Institute of Bioregulation, Kyushu University
  • Wake, Norio
    Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University
  • Hayashi, Kenshi
    Division of Genome Analysis, Research Center for Genetic Information, Kyushu University

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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 single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) as all of the genetic variants in a CHM genome are homozygous. Here we report SNP/CNV haplotype structures determined by analyzing 100 CHMs from Japanese subjects using high-density DNA arrays. The obtained haplotype map should be useful as a reference for the haplotype structure of Asian populations. We resolved common CNV regions (merged CNV segments across the examined samples) into CNV events (clusters of CNV segments) on the basis of mutual overlap and found that the haplotype backgrounds of different CNV events within the same CNV region were predominantly similar, perhaps due to inherent structural instability.

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