A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.
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 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 because of inherent structural instability.
Division of Genome Analysis, Research Center for Genetic Information, Kyushu University, Fukuoka 812-8582, Japan.
Yoji
Y
Kukita
Koji
K
Yahara
Tomoko
T
Tahira
Koichiro
K
Higasa
Miki
M
Sonoda
Ken
K
Yamamoto
Kiyoko
K
Kato
Norio
N
Wake
Kenshi
K
Hayashi
D000782:Aneuploidy; D056915:DNA Copy Number Variations; D019992:Databases as Topic; D005260:Female; D005838:Genotype; D006238:Haploidy; D006239:Haplotypes; D006801:Humans; D006828:Hydatidiform Mole / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy