SNP haplotype tagging from DNA pools of two individuals

被引：15

作者：

Hoh, J

Matsuda, F

Peng, X

Markovic, D

Lathrop, MG

Ott, J

机构：

[1] Rockefeller Univ, Lab Stat Genet, New York, NY 10021 USA

[2] Ctr Natl Genotypage, F-91057 Evry, France

来源：

BMC BIOINFORMATICS | 2003年 / 4卷 / 1期

关键词：

D O I：

10.1186/1471-2105-4-14

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers. Results: We present an algorithm for reconstructing haplotypes (alleles for multiple SNPs on same chromosome) from pools of two individual DNAs, in which Hardy-Weinberg equilibrium conditions or other assumptions are not required. The program outputs, in addition to inferred haplotypes, a minimal number of haplotype-tagging SNPs that are identified after an exhaustive search procedure. Conclusion: Our method and algorithms lead to a significant reduction in genotyping effort, for example, in case-control disease association studies while maintaining the possibility of reconstructing haplotypes under very general conditions.

引用

收藏

页数：5

相关论文

共 18 条

[1] USE OF POOLED DNA SAMPLES TO DETECT LINKAGE DISEQUILIBRIUM OF POLYMORPHIC RESTRICTION FRAGMENTS AND HUMAN-DISEASE - STUDIES OF THE HLA CLASS-II LOCI [J].

ARNHEIM, N ;

STRANGE, C ;

ERLICH, H .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1985, 82 (20) :6970-6974

[2] Fine genetic mapping using haplotype analysis and the missing data problem [J].

Chiano, MN ;

Clayton, DG .

ANNALS OF HUMAN GENETICS, 1998, 62 :55-60

[3]

CLARK AG, 1990, MOL BIOL EVOL, V7, P111

[4] The detection of defective members of large populations [J].

Dorfman, R .

ANNALS OF MATHEMATICAL STATISTICS, 1943, 14 :436-440

[5] ESTIMATION OF THE PREVALENCE OF A RARE DISEASE, PRESERVING THE ANONYMITY OF THE SUBJECTS BY GROUP-TESTING - APPLICATION TO ESTIMATING THE PREVALENCE OF AIDS ANTIBODIES IN BLOOD-DONORS [J].

GASTWIRTH, JL ;

HAMMICK, PA .

JOURNAL OF STATISTICAL PLANNING AND INFERENCE, 1989, 22 (01) :15-27

[6] Optimal selection strategies for QTL mapping using pooled DNA samples [J].

Jawaid, A ;

Bader, JS ;

Purcell, S ;

Cherny, SS ;

Sham, P .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2002, 10 (02) :125-132

[7] Haplotype tagging for the identification of common disease genes [J].

Johnson, GCL ;

Esposito, L ;

Barratt, BJ ;

Smith, AN ;

Heward, J ;

Di Genova, G ;

Ueda, H ;

Cordell, HJ ;

Eaves, IA ;

Dudbridge, F ;

Twells, RCJ ;

Payne, F ;

Hughes, W ;

Nutland, S ;

Stevens, H ;

Carr, P ;

Tuomilehto-Wolf, E ;

Tuomilehto, J ;

Gough, SCL ;

Clayton, DG ;

Todd, JA .

NATURE GENETICS, 2001, 29 (02) :233-237

[8] The impact of genotyping error on haplotype reconstruction and frequency estimation [J].

Kirk, KM ;

Cardon, LR .

EUROPEAN JOURNAL OF HUMAN GENETICS, 2002, 10 (10) :616-622

[9] Haplotype inference in random population samples [J].

Lin, S ;

Cutler, DJ ;

Zwick, ME ;

Chakravarti, A .

AMERICAN JOURNAL OF HUMAN GENETICS, 2002, 71 (05) :1129-1137

[10] Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium [J].

Pfeiffer, RM ;

Rutter, JL ;

Gail, MH ;

Struewing, J ;

Gastwirth, JL .

GENETIC EPIDEMIOLOGY, 2002, 22 (01) :94-102