Assessment and implications of linkage disequilibrium in genome-wide single-nucleotide polymorphism and microsatellite panels

Genetic Epidemiology

Volumn 29, Issue SUPPL., 2005, Pages

  Goode, Ellen L ^a   Jarvik, Gail P ^b,c  

^a Mayo Clinic   (United States)

^b UNIVERSITY OF WASHINGTON MEDICAL CENTER   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Bias; Haplotype; Linkage analysis; Population substructure; X chromosome

Indexed keywords

ALCOHOLISM; AUTOSOME; COMPUTER SIMULATION; CONFERENCE PAPER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOME; HAPLOTYPE; HUMAN; MICROSATELLITE MARKER; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME;

ALCOHOLISM; CHROMOSOMES, HUMAN, X; CYTOGENETIC ANALYSIS; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 30344437026     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.20112     Document Type: Conference Paper

References (28)

1. 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.
2. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
3. Avery CL, Martin LJ, Williams JT, North KE. 2005. Accuracy of haplotype estimation in a region of low linkage disequilibrium. BMC Genet [Suppl] 6:80.
4. Beckmann L, Ziegler A, Duggal P, Bailey-Wilson JE. 2005. Haplotypes and tagging single-nucleotide polymorphisms: Presentation Group 8 of Genetic Analysis Workshop 14. Genet Epidemiol [Suppl] 29: this issue.
5. Cox ME, Campbell JK, Langefeld CD. 2005. An exploration of sex-specific linkage disequilibrium on chromosome X in Caucasians from the COGA Study. BMC Genet [Suppl] 6:81.
6. Edenberg HJ, Bierut LJ, Boyce P, Cao M, Cawley S, Chiles R, Doheny KF, Hansen M, Hinrichs T, Jones K, Kelleher M, Kennedy GC, Liu G, Marcus G, McBride C, Murray SS, Oliphant A, Pettengill J, Porjesz B, Pugh EW, Rice JP, Rubano T, Shannon S, Steeke R, Tischfield JA, Tsai YY, Zhang C, Begleiter H. 2005. Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for the Genetic Analysis Workshop 14. BMC Genet [Suppl] 6:2.
7. Goode EL, Badzioch MD, Jarvik GP. 2005. Bias of allele-sharing linkage statistics in the presence of intermarker linkage disequilibrium. BMC Genet [Suppl] 6:82.
8. Greenberg DA, Zhang J, Shmulewitz D, Strug LJ, Zimmerman R, Singh V, Marathe S. 2005. Construction of the model for the Genetic Analysis Workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype. BMC Genet [Suppl] 6:3.
9. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A. 2000. Allegro, a new computer program for multipoint linkage analysis. Nat Genet 25:12-23.
10. Hao K, Li C, Rosenow C, Wong WH. 2004. Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10 K array. Eur J Hum Genet 12:1001-1016.
11. Heath SC. 1997. Markov chain Monte Carlo methods for radiation hybrid mapping. J Comput Biol 4:505-515.
12. Heath SC, Snow GL, Thompson EA, Tseng C, Wijsman EM. 1997. MCMC segregation and linkage analysis. Genet Epidemiol 14:1011-1016.
13. Hirschhorn JN, Daly M. 2005. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108.
14. Huang Q, Shete S, Amos CI. 2004. Ignoring linkage disequilibrium among tightly linked markers induces false-positive evidence of linkage for affected sib pair analysis. Am J Hum Genet 75:1106-1112.
15. Huang Q, Shete S, Swartz M, Amos CI. 2005. Examining the effect of linkage disequilibrium on multipoint linkage analysis. BMC Genet [Suppl] 6:83.
16. Jorgenson E, Lin X, Witte JS. 2005. Case-control analyses: Geneopardy! Genet Epidemiol [Suppl] 29: this issue.
17. Kauwe JSK, Bertelsen S, Bierut LJ, Dunn G, Hinrichs AL, Jin CH, Suarez BK. 2005. The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure. BMC Genet [Suppl] 6:84.
18. Kong A, Cox NJ. 1997. Allele-sharing models: LOD scores and accurate linkage tests. Am J Hum Genet 61:1179-1188.
19. Markianos K, Daly MJ, Kruglyak L. 2001. Efficient multipoint linkage analysis through reduction of inheritance space. Am J Hum Genet 68:963-977.
20. Murray SS. 2005. Evaluation of linkage disequilibrium and its effect on nonparametric multipoint linkage analysis using two high density single-nucleotide polymorphism mapping panels. BMC Genet [Suppl] 6:85.
21. Ott J. 1992. Strategies for characterizing highly polymorphic markers in human gene mapping. Am J Hum Genet 51:283-290.
22. Peralta JM, Dyer TD, Warren DM, Blangero J, Almasy L. 2005. Linkage disequilibrium across two different single-nucleotide polymorphism genome scans. BMC Genet [Suppl] 6:86.
23. Pritchard JK, Donnelly P. 2001. Case-control studies of association in structured or admixed populations. Theor Popul Biol 60:227-237.
24. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
25. Schaid DJ. 2004. Genetic epidemiology and haplotypes. Genet Epidemiol 27:317-320.
26. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
27. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989.
28. Xu CF, Lewis K, Cantone KL, Khan P, Donnelly C, White N, Crocker N, Boyd PR, Zaykin DV, Purvis IJ. 2002. Effectiveness of computational methods in haplotype prediction. Hum Genet 11:148-156.