Detection of Japanese Structural Variation Using Definitive Haplotype Data Obtained from Complete Hydatidiform Moles.

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We determined true Japanese haplotypes by genotyping 100 complete hydatidiform moles (CHM), each carrying a genome derived from a single sperm. We then assessed how inferred haplotypes can differ from true haplotypes, and found that, at various genomic regions, especially the MHC locus, the expansion of extended haplotype homozygosity (EHH), which is a measure of positive selection, is obscured when inferred Asian haplotype data is used to detect the expansion. We also show that the true haplotype data is useful not only to assess and improve the accuracy of phasing of Asian genotypes, but also to detect structural variation of Japanese genome.