Guidelines for genotyping in genomewide linkage studies: Single-nucleotide-polymorphism maps versus microsatellite maps

American Journal of Human Genetics

Volumn 75, Issue 4, 2004, Pages 687-692

  Evans, David M ^a   Cardon, Lon R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY; GENE FREQUENCY; GENETIC LINKAGE; GENOTYPE; HETEROZYGOSITY; INHERITANCE; MATHEMATICAL COMPUTING; MICROSATELLITE MARKER; PRIORITY JOURNAL; REVIEW; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 4544335122     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/424696     Document Type: Article

References (26)

1. Abecasis GR, Cherny SS, Cardon LR (2001) The impact of genotyping error on family-based analysis of quantitative traits. Eur J Hum Genet 9:130-134
2. Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101
3. Altmüller J, Palmer LJ, Fischer G, Scherb H, Wjst M (2001) Genomewide scans of complex human diseases: true linkage is hard to find. Am J Hum Genet 69:936-950
4. Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet 63:861-869
5. Daw EW, Thompson EA, Wijsman EM (2000) Bias in multipoint linkage analysis arising from map misspecification. Genet Epidemiol 19:366-380
6. Dawson E, Abecasis G, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, et al (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548
7. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152-154
8. Dolan CV, Boomsma DI, Neale MC (1999) A note on the power provided by sibships of sizes 2, 3, and 4 in genetic covariance modeling of a codominant QTL. Behav Genet 29:163-170
9. Douglas JA, Boehnke M, Lange K (2000) A multipoint method for detecting genotype errors and mutations in sibling-pair linkage data. Am J Hum Genet 66:1287-1297
10. Goddard KAB, Wijsman EM (2002) Characteristics of genetic markers and maps for cost-effective genome screens using diallelic markers. Genet Epidemiol 22:205-220
11. Helgadottir A, Manolescu A, Thorleifsson G, Gretasdottir S, Jonsdottir H, Thorsteinsdottir G, Samani NJ, et al (2004) The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke. Nat Genet 36:233-239
12. John S, Shephard N, Liu G, Zeggini E, Cao M, Chen W, Vasavda N, Mills T, Barton A, Hinks A, Eyre S, Jones KW, Oilier W, Silman A, Gibson N, Worthington J, Kennedy GC (2004) Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. Am J Hum Genet 75:54-64
13. Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet 13:577-588
14. 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 (2003) Large scale genotyping of complex DNA. Nat Biotechnol 21:1233-1237
15. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K (2002) A high-resolution map of the human genome. Nat Genet 31:241-247
16. Kostanje R, Paigen B (2002) From QTL to gene: the harvest begins. Nat Genet 31:235-236
17. Kruglyak L (1997) The use of a genetic map of biallelic markers in linkage studies. Nat Genet 17:21-24
18. Kruglyak L, Lander ES (1995) Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am J Hum Genet 57:439-454
19. Matise TC, Sachidanandam R, Clark AG, Kruglyak L, Wijsman E, Kakol J, Buyske S, et al (2003) A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet 73:271-284
20. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R (2004) Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 14:414-425
21. Middleton FA, Pato MT, Gentile KL, Morley CP, Zhao X, Eisner A, Brown A, Petryshen TL, Kirby AN, Medeiros H, Carvalho C, Macedo A, Dourado A, Coelho I, Valente J, Scares MJ, Ferreira CP, Lei M, Azevedo MH, Kennedy JL, Daly MJ, Sklar P, Pato CN (2004) 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 74:886-897
22. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques Suppl:56-58, 60-61
23. Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, et al (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 33:382-387
24. Schaid DJ, McDonnell SK, Wang L, Cunningham JM, Thibodeau SN (2002) Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Am J Hum Genet 71:992-995
25. Williams JT, Blangero J (1999) The power of variance component linkage analysis to detect quantitative trait loci. Ann Hum Genet 63:545-563
26. Wilson AF, Sorant AJ (2000) Equivalence of single- and multilocus markers: power to detect linkage with composite markers derived from biallelic loci. Am J Hum Genet 66:1610-1615