Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses
Tóm tắt
We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage results from the dense Affymetrix SNP markers and less densely spaced Illumina SNP markers are very similar. The linkage analysis results from microsatellite and SNP markers are generally similar, but the match is not perfect. Strong linkage peaks were found on chromosome 7 in three sets of linkage analyses using both SNP and microsatellite marker data. We also observed that for SNP markers, using the given genetic map and using the map by converting 1 megabase pair (1 Mb) to 1 centimorgan (cM), did not change the linkage results. We recommend the use of the 1 Mb-to-1 cM converted map in a first round of linkage analysis with SNP markers in which map integration is an issue.
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Tài liệu tham khảo
Wilson AF, Sorant AJM: Equivalence of single- and multilocus markers: power to detect linkage with composite markers derived from biallelic loci. Am J Hum Genet. 2000, 66: 1610-1615. 10.1086/302889.
Hodge SE, Boehnke M, Spence MA: Loss of information due to ambiguous haplotyping of SNPs. Nat Genet. 1999, 21: 360-361. 10.1038/7687.
Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones KW: Large-scale genotyping of complex DNA. Nat Biotechnol. 2003, 21: 1233-1237. 10.1038/nbt869.
Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di XJ, Liu WM, Yang G, Liu GY, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R: Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 2004, 14: 414-425. 10.1101/gr.2014904.
Middleton FA, Pato MT, Gentile KL, Morley CP, Zhao X, Eisener AF, Brown A, Petryshen TL, Kirby AN, Medeiros H, Carvalho C, Macedo A, Dourado A, Coelho I, Valente J, Soares MJ, Ferreira CP, Lei M, Azevedo MH, Kennedy JL, Daly MJ, Sklar P, Pato CN: Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22. Am J Hum Genet. 2004, 74: 886-897. 10.1086/420775.
John S, Shephard N, Liu GY, Zeggini E, Cao MQ, Chen WW, Vasavda N, Mills T, Barton A, Hinks A, Eyre S, Jones KW, Ollier W, Silman A, Gibson N, Worthington J, Kennedy GC: Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. Am J Hum Genet. 2004, 75: 54-64. 10.1086/422195.
Sham P: Statistics in Human Genetics. 1998, London: Arnold Publications
Goring HH, Terwilliger JD: Linkage analysis in the presence of errors. I. complex-valued recombination fractions and complex phenotypes. Am J Hum Genet. 2000, 66: 1095-1106. 10.1086/302797.
Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002, 30: 97-101. 10.1038/ng786.
Whittemore AS, Halpern J: A class of tests for linkage using affected pedigree members. Biometrics. 1994, 50: 118-127. 10.2307/2533202.
Leykin I, Hao K, Cheng JS, Meyer N, Pollak MR, Smith RJH, Wong WH, Rosenow C, Li C: Comparative linkage analysis and visualization of high- density oligonucleotide SNP array data. BMC Genet. 2005, 6: 7-10.1186/1471-2156-6-7.
Kong A, Cox NJ: Allele-sharing models: LOD scores and accurate linkage tests. Am J Hum Genet. 1997, 61: 1179-1188. 10.1086/301592.
Evans DM, Cardon LR: Guidelines for genotyping in genomewide linkage studies: single-nucleotide-polymorphism maps versus microsatellite maps. Am J Hum Genet. 2004, 75: 687-692. 10.1086/424696.