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

Yoji Kukita, Koji Yahara, Tomoko Tahira, Koichiro Higasa, Miki Sonoda, Ken Yamamoto, Kiyoko Kato, Norio Wake, Kenshi Hayashi

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)918-928
Number of pages11
JournalAmerican journal of human genetics
Volume86
Issue number6
DOIs
Publication statusPublished - Jul 11 2010

Fingerprint

Haploidy
Hydatidiform Mole
Haplotypes
Genome
Single Nucleotide Polymorphism
Oligonucleotide Array Sequence Analysis
Diploidy
Spermatozoa
Population

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events. / Kukita, Yoji; Yahara, Koji; Tahira, Tomoko; Higasa, Koichiro; Sonoda, Miki; Yamamoto, Ken; Kato, Kiyoko; Wake, Norio; Hayashi, Kenshi.

In: American journal of human genetics, Vol. 86, No. 6, 11.07.2010, p. 918-928.

Research output: Contribution to journalArticle

Kukita, Yoji ; Yahara, Koji ; Tahira, Tomoko ; Higasa, Koichiro ; Sonoda, Miki ; Yamamoto, Ken ; Kato, Kiyoko ; Wake, Norio ; Hayashi, Kenshi. / A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events. In: American journal of human genetics. 2010 ; Vol. 86, No. 6. pp. 918-928.
@article{46cceeed3d0b431fac3609f910fba60d,
title = "A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events",
abstract = "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.",
author = "Yoji Kukita and Koji Yahara and Tomoko Tahira and Koichiro Higasa and Miki Sonoda and Ken Yamamoto and Kiyoko Kato and Norio Wake and Kenshi Hayashi",
year = "2010",
month = "7",
day = "11",
doi = "10.1016/j.ajhg.2010.05.003",
language = "English",
volume = "86",
pages = "918--928",
journal = "American Journal of Human Genetics",
issn = "0002-9297",
publisher = "Cell Press",
number = "6",

}

TY - JOUR

T1 - A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events

AU - Kukita, Yoji

AU - Yahara, Koji

AU - Tahira, Tomoko

AU - Higasa, Koichiro

AU - Sonoda, Miki

AU - Yamamoto, Ken

AU - Kato, Kiyoko

AU - Wake, Norio

AU - Hayashi, Kenshi

PY - 2010/7/11

Y1 - 2010/7/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=77953121808&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77953121808&partnerID=8YFLogxK

U2 - 10.1016/j.ajhg.2010.05.003

DO - 10.1016/j.ajhg.2010.05.003

M3 - Article

C2 - 20537301

AN - SCOPUS:77953121808

VL - 86

SP - 918

EP - 928

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 6

ER -