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Genome Res. 15:1511-1518, 2005
©2005 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/05 $5.00
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Letter

Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles

Yoji Kukita1,4, Katsuyuki Miyatake1,4, Renee Stokowski2,4, David Hinds2,4, Koichiro Higasa1,4, Norio Wake3, Toshio Hirakawa3, Hidenori Kato3, Takao Matsuda3, Krishna Pant2, David Cox2, Tomoko Tahira1 and Kenshi Hayashi1,5

1 Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan 2 Perlegen Sciences Inc., Mountain View, California 94043, USA 3 Division of Molecular and Cell Therapeutics, Medical Institute of Bioregulation, Kyushu University, Beppu, Oita 874-0838, Japan

We present genome-wide definitive haplotypes, determined using a collection of 74 Japanese complete hydatidiform moles, each carrying a genome derived from a single sperm. The haplotypes incorporate 281,439 common SNPs, genotyped with a high throughput array-based oligonucleotide hybridization technique. Comparison of haplotypes inferred from pseudoindividuals (constructed from randomized mole pairs) with those of moles showed some switch errors in resolution of phases by the computational inference method. The effects of these errors on local haplotype structure and selection of tag SNPs are discussed. We also show that definitive haplotypes of moles may be useful for elucidation of long-range haplotype structure, and should be more effective for detecting extended haplotype homozygosity indicative of positive selection.

[Supplemental material is available online at www.genome.org.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.4371105. Freely available online through the Genome Research Immediate Open Access option.

4 These authors contributed equally to this work.

5 Corresponding author.
E-mail khayashi{at}gen.kyushu-u.ac.jp; fax +81-92-632-2375.


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