Family-based association tests for quantitative traits using pooled DNA

European Journal of Human Genetics

Volumn 10, Issue 12, 2002, Pages 870-878

  Bader, Joel S ^a   Sham, Pak ^b  

^a CURAGEN CORPORATION   (United States)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

Association; DNA pooling; Genotyping; Linkage; Quantitative trait locus (QTL); Single nucleotide polymorphism (SNP)

Indexed keywords

DNA;

ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; FAMILY; FEASIBILITY STUDY; GENE FREQUENCY; GENETIC SCREENING; GENOME ANALYSIS; GENOTYPE; HUMAN; MEASUREMENT; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

CHROMOSOME MAPPING; DNA; FEMALE; GENE FREQUENCY; GENOME, HUMAN; HUMANS; MALE; QUANTITATIVE TRAIT LOCI;

EID: 0036926785     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5200893     Document Type: Article

References (34)

1. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 1996; 273: 1516-1517.
2. Ott J: Analysis of Human Genetic Linkage. 3rd edn. Baltimore: Johns Hopkins University Press, 1999; pp 306-329.
3. Sham PC, Cherny SS, Purcell S et al: Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data. Am J Hum Gen 2000; 66: 1616-1630.
4. Ardlie KG, Kruglyak L, Seielstad M: Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2000; 3: 299-309.
5. Collins FS, Guyer MS, Chakarvarti A: Variations on a theme: cataloguing human DNA sequence variation. Science 1997; 274: 1580-1581.
6. Abecasis GR, Noguchi E, Heinzmann A et al: Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Gen 2001; 68: 191-197.
7. Reich DE, Cargill M, Bolk S et al: Linkage disequilibrium in the human genome. Nature 2001; 411: 199-204.
8. Patil N, Berno AJ, Hinds DA et al: Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001; 294: 1719-1723.
9. Gabriel SB, Schaffner SF, Nguyen H et al: The structure of haplotype blocks in the human genome. Science 2002; 296: 2225-2229.
10. Dawson E, Abecasis GR, Bumpstead S et al: A first-generation linkage disequilibrium map of human chromosome 22. Nature 2002; 418: 544-548.
11. Barcellos LF, Klitz W, Field LL et al: Association mapping of disease loci, by use of a pooled DNA genomic screen. Am J Hum Gen 1997; 61: 734-747.
12. Daniels J, Holmans P, Williams N et al: A simple method for analysing microsatellite allele image patterns generated from DNA pools and its applications to allelic association studies. Am J Hum Gen 1998; 62: 1189-1197.
13. Shaw SH, Carrasquillo MM, Kashuk C et al: Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res 1998; 8: 111-123.
14. Stockton DW, Lewis RA, Abboud EB et al: A novel locus for Leber congenital amaurosis on chromosome 14q24. Hum Gen 1998; 103: 328-333.
15. Suzuki K, Bustos T, Spritz RA: Linkage disequilibrium mapping of the gene for Margarita Island ectodermal dysplasia (ED4) to 11q23. Am J Hum Gen 1998; 63: 1102-1107.
16. Fisher PJ, Turic D, Williams NM et al: DNA pooling identifies QTLs on chromosome 4 for general cognitive ability in children. Hum Mol Gen 1999; 8: 915-922.
17. Hill L, Craig IW, Asherson P et al: DNA pooling and dense marker maps: a systematic search for genes for cognitive ability. Neuroreport 1999; 10: 843-848.
18. Risch N, Teng J: The relative power of family-based and case control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling. Genome Res 1998; 8: 1273-1288.
19. Bader JS, Bansal A, Sham P: Efficient SNP-based tests of association for quantitative phonotypes using pooled DNA. Genescreen 2001; 1: 143-150.
20. Mosteller F: On some useful 'inefficient' statistics. Annals of Mathematical Statistics 1946; 17: 377-408.
21. Jawaid A, Bader JS, Purcell S et al: Optimal selection strategies for QTL mapping using pooled DNA samples. Eur J Hum Gen 2002; 10: 125-132.
22. Beutow KH, Edmonson M, MacDonald R et al: High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 2001; 98: 581-584.
23. Grupe A, Germer S, Usuka J et al: In silico mapping of complex disease-related traits in mice. Science 2001; 292: 1915-1918.
24. Devlin B, Roeder K: Genomic control for association studies. Biometrics 1999; 55: 788-808.
25. Pritchard JK, Rosenberg NA: Use of unliked genetic markers to detect population stratification in association studies. Am J Hum Gen 1999; 65: 220-228.
26. Pritchard JK, Stephens M, Rosenberg NA et al: Inference of population structure using multilocus genotype data. Genetics 2000; 155: 945-959.
27. Zhang S, Zhao H: Quantitative similarity-based association tests using population samples. Am J Hum Gen 2001; 69: 601-614.
28. Satten GA, Flanders DW, Yang Q; Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Gen 2001; 68: 466-477.
29. Falconer DS, MacKay TFC: Introduction to quantitative genetics. Boston: Addison-Wesley, 1996; pp 153.
30. Hill WG: Design and efficiency of selection experiments for estimating genetic parameters. Biomerics 1971; 27: 293-311.
31. Kimura M, Crow JF: Effect of overall phenotypic selection on genetic change at individual loci. Proc Natl Acad Sci USA 1978; 75: 6168-6171.
32. Darvasi A, Soller M: Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 1994; 138: 1365-1373.
33. Ollivier L, Messer LA, Rothschild MF et al: The use of selection experiments for detecting quantitative trait loci. Genet Res, Camb 1997; 69: 227-232.
34. Le Hellard S, Ballereau SJ, Visscher PM et al: SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 2002; 30: e74, (electronic preprint).