Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA

Tomonari Sasaki, T. Tahira, A. Suzuki, K. Higasa, Y. Kukita, Shingo Baba, K. Hayashi

研究成果: ジャーナルへの寄稿記事

81 引用 (Scopus)

抄録

We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10%) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8%). We found that as many as 40% of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential - for example, in linkage disequilibrium analysis.

元の言語英語
ページ(範囲)214-218
ページ数5
ジャーナルAmerican journal of human genetics
68
発行部数1
DOI
出版物ステータス出版済み - 1 1 2001

Fingerprint

Single-Stranded Conformational Polymorphism
Gene Frequency
Single Nucleotide Polymorphism
DNA
Linkage Disequilibrium
Alleles

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

これを引用

Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA. / Sasaki, Tomonari; Tahira, T.; Suzuki, A.; Higasa, K.; Kukita, Y.; Baba, Shingo; Hayashi, K.

:: American journal of human genetics, 巻 68, 番号 1, 01.01.2001, p. 214-218.

研究成果: ジャーナルへの寄稿記事

@article{dab28da07e984ad891e0677c17b9609d,
title = "Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA",
abstract = "We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10{\%}) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8{\%}). We found that as many as 40{\%} of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential - for example, in linkage disequilibrium analysis.",
author = "Tomonari Sasaki and T. Tahira and A. Suzuki and K. Higasa and Y. Kukita and Shingo Baba and K. Hayashi",
year = "2001",
month = "1",
day = "1",
doi = "10.1086/316928",
language = "English",
volume = "68",
pages = "214--218",
journal = "American Journal of Human Genetics",
issn = "0002-9297",
publisher = "Cell Press",
number = "1",

}

TY - JOUR

T1 - Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA

AU - Sasaki, Tomonari

AU - Tahira, T.

AU - Suzuki, A.

AU - Higasa, K.

AU - Kukita, Y.

AU - Baba, Shingo

AU - Hayashi, K.

PY - 2001/1/1

Y1 - 2001/1/1

N2 - We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10%) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8%). We found that as many as 40% of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential - for example, in linkage disequilibrium analysis.

AB - We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10%) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8%). We found that as many as 40% of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential - for example, in linkage disequilibrium analysis.

UR - http://www.scopus.com/inward/record.url?scp=0035158426&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035158426&partnerID=8YFLogxK

U2 - 10.1086/316928

DO - 10.1086/316928

M3 - Article

C2 - 11083945

AN - SCOPUS:0035158426

VL - 68

SP - 214

EP - 218

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 1

ER -