The impact of population admixture on traditional linkage analysis

Ethnicity and Disease

Volumn 11, Issue 3, 2001, Pages 519-531

  Barnholtz Sloan, Jill S ^a,d   De Andrade, Mariza ^b   Chakraborty, Ranajit ^c  

^a WAYNE STATE UNIVERSITY   (United States)

^b MAYO CLINIC   (United States)

^c UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^d KARMANOS CANCER INSTITUTE   (United States)

Author keywords

Hardy Weinberg Equilibrium; Linkage Disequilibrium; LOD Score; Population Admixture

Indexed keywords

ALLELE; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC LINKAGE; GENETICS; HUMAN; MALE; PEDIGREE; PROSTATE TUMOR; STATISTICAL MODEL;

ALLELES; COMPUTER SIMULATION; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE (GENETICS); LOD SCORE; MALE; MODELS, GENETIC; PEDIGREE; PROSTATIC NEOPLASMS;

EID: 0035464898     PISSN: 1049510X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (50)

1. Bennett C, McKenney N, Harrison R. Racial classification issues concerning children in mixed-race households. Paper presented at: Annual Meeting of the Population Association of America; 1995.
2. United States Bureau of the Census. Current Population Survey Data, Current Population Reports, Series: Marital Status and Living Arrangements; 1998.
3. Risser DR, Epidemiologist III, Texas Cancer Registry, Austin, Texas (personal communication, August 1997).
4. Prout T. Appendix to JB Mitton and RK Koehn: population genetics of marine Pelecypods. III. epistasis between functionally related isoenzymes of Mytilus edulis. Genetics. 1973;73:487-496.
5. Nei M, Li W. Linkage disequilibrium in subdivided populations. Genetics. 1973;75:213-219.
6. Lathrop GM, Lalouel JM. Easy calculations of LOD scores and genetic risks on small computers. Am J Hum Genet. 1984;36:460-465.
7. Wahlund S. Zuzammensetzung von populationen und korrelation-serscheinungen von stand pundt der vererbungslehre aus betrachtet. Hereditas. 1928;11:65-106.
8. Nei M. Molecular Evolutionary Genetics. New York, NY: Columbia University Press; 1987.
9. Thompson EA. Pedigree Analysis in Human Genetics. Baltimore, Md: The Johns Hopkins University Press; 1986.
10. Chakraborty R, Weiss KM. Admixture as a tool for finding linked and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA. 1988;85:9119-9123.
11. Clerget-Darpoux F. Bias of the estimated recombination fraction and lod score due to an association between a disease gene and a marker gene. Ann Hum Genet. 1982;46:363-372.
12. Clerget-Darpoux F, Bonaiti-Pellie C, Hochez J. Effects of misspecifying genetic parameters in lod score analysis. Biometrics. 1986;42:393-399.
13. Risch N, Giuffra L. Model misspecification and multipoint linkage analysis. Hum Hered. 1992;42: 77-92.
14. Freimer NB, Sandkuijil LA, Blower SM. Incorrect specification of marker allele frequencies: effects on linkage analysis. Am J Hum Genet. 1993;52: 1102-1110.
15. Ott J. Strategies for characterizing highly polymorphic markers in human gene mapping. Am J Hum Genet. 1992;51:283-290.
16. American Cancer Society Inc. Cancer Facts and Figures 2000. Data sources: Vital Statistics of the United States of America, 1998 and NCI Surveillance, Epidemiology, and End Results Program, 1998. Publication No. 5008.99
17. Carter BS, Beaty TH, Steinberg GD, Childs B, Walsh PC. Mendelian inheritance of familial prostate cancer. Proc Natl Acad Sci USA. 1992;89: 3367-3371.
18. Gronberg H, Damber L, Damber LE, Iselius L. Segregation analysis of prostate cancer in Sweden: support for dominant inheritance. Am J Epidemiol. 1997a;146:552-557.
19. Schaid DJ, McDonnell SK, Blute ML, Thibodeau SN. Evidence for autosomal dominant inheritance of prostate cancer. Am J Hum Genet. 1998;62: 1425-1438.
20. Smith JR, Freije D, Carpten JD, et al. Major susceptibility locus on chromosome 1 suggested by a genome-wide search. Science. 1996;274(5291): 1371-1374.
21. Cooney KA, McCarthy JD, Lange E, et al. Prostate cancer susceptibility locus on chromosome 1q: a confirmatory study. J Natl Cancer Inst. 1997;89(13):955-959.
22. Hsieh CL, Oakley-Girvan I, Gallagher R, et al. Re: prostate cancer susceptibility locus on chromosome 1q: a confirmatory study. J Natl Cancer Inst. 1997;89:1893-1894.
23. Gronberg H, Xu J, Smith JR, et al. Early age at diagnosis in families providing evidence of linkage to the hereditary prostate cancer locus (HPC1) on chromosome 1. Cancer Res. 1997b;57:4707-4709.
24. Gronberg H, Smith J, Emanuelsson M, et al. In Swedish families with heredity prostate cancer, linkage to the HPC1 locus on chromosome 1q24-25 is restricted to families with early-onset prostate cancer. Am J Hum Genet. 1999;65:134-140.
25. Eeles RA, Durocher F, Edwards S, et al, and The Cancer Research Campaign/British Prostate Group U.K. Familial Prostate Cancer Study Collaborators. Linkage analysis of chromosome 1q markers in 136 prostate cancer families. Am J Hum Genet. 1998;62:653-658.
26. Xu J, and the International Consortium for Prostate Cancer Genetics. Combined analysis of hereditary prostate cancer linkage to 1q24-25: results from 772 hereditary prostate cancer families from the International Consortium for Prostate Cancer Genetics. Am J Hum Genet. 2000;66:945-957.
27. Goode EL, Stanford JL, Chakrabarti L, et al. Linkage analysis of 150 high-risk prostate cancer families at 1q24-25. Genet Epidemiol. 2000;18:251-275.
28. McIndoe RA, Stanford JL, Gibbs M, et al. Linkage analysis of 49 high-risk families does not support a common familial prostate cancer-susceptibility gene at 1q24-25. Am J Hum Genet. 1997; 61:347-353.
29. Berthon P, Valeri A, Cohen-Akenine A, et al. Predisposing gene for early-onset prostate cancer, localized on chromosome 1q42.2-43. Am J Hum Genet. 1998;62:1416-1424.
30. Gibbs M, Chakrabarti L, Stanford JL, et al. Analysis of chromosome 1q42.2-43 in 152 families with high risk of prostate cancer. Am J Hum Genet. 1999b;64:1087-1095.
31. Whittemore AS, Lin IG, Oakley-Girvan I, et al. No evidence for linkage for chromosome 1q42.2-43 in prostate cancer. Am J Hum Genet. 1999;65: 254-256.
32. Singh R, and the ACTANE consortium. No evidence of linkage to chromosome 1q42.2-43 in 131 prostate cancer families from the ACTANE consortium. Anglo, Canada, Texas, Australia, Norway, EU Biomed. Br J Cancer. 2000;83:1654-1658.
33. Suarez BK, Lin J, Witte JS, et al. Replication linkage study for prostate cancer susceptibility genes. Prostate. 2000;45:106-114.
34. Berry R, Schaid DJ, Smith JR, et al. Linkage analyses at the chromosome 1 loci 1q24-25 (HPC1), 1q42.2-43 (PCAP), and 1p36 (CAPB) in families with hereditary prostate cancer. Am J Hum Genet. 2000;66:539-546.
35. Gibbs M, Stanford JL, Jarvik GP, et al. A genomic scan of families with prostate cancer identifies multiple regions of interest. Am J Hum Genet. 2000;67:100-109.
36. Gibbs M, Stanford JL, McIndoe RA, et al. Evidence for a rare prostate cancer-susceptibility locus at chromosome 1p36. Am J Hum Genet. 1999a;64:776-787.
37. Badzioch M, Eeles R, Leblanc G, et al. Suggestive evidence for a site specific prostate cancer gene on chromosome 1p36. The CRC/BPG UK Familial Prostate Cancer Study Coordinators and Collaborators. The EU Biomed Collaborators. J Med Genet. 2000;37:947-949.
38. Devgan SA, Henderson BE, Yu MC, et al. Genetic variation of 3β-hydroxysteroid dehydrogenase type II in three racial/ethnic groups: implications for prostate cancer risk. Prostate. 1997;33:9-12.
39. Xu J, Meyers D, Freije D, et al. Evidence for a prostate cancer susceptibility locus on the X chromosome. Nat Genet. 1998;20:175-179.
40. Lange EM, Chen H, Brierley K, et al. Linkage analysis of 153 prostate cancer families over a 30-cM region containing the putative susceptibility locus HPCX. Clin Cancer Res. 1999;5:4013-4020.
41. Peters MA, Jarvik GP, Janer M, et al. Genetic linkage analysis of prostate cancer families to Xq27-28. Hum Hered. 2001;51:107-113.
42. Berry R, Schroeder JJ, French AJ, et al. Evidence for a prostate cancer-susceptibility locus on chromosome 20. Am J Hum Genet. 2000;67:82-91.
43. Bock C, Cunningham J, McDonnell S, et al. Analysis of the prostate cancer-susceptibility locus hpc20 in 172 families affected by prostate cancer. Am J Hum Genet. 2001;68:795-801.
44. Tavtigian SV, Simard J, Teng DH, et al. A candidate prostate cancer susceptibility gene at chromosome 17p. Nat Genet. 2001;27:172-180.
45. Speer M, Terwilliger JD, Ott J. A chromosome-based method for rapid computer simulation. Am J Hum Genet Suppl. 1992;51:A202.
46. Terwilliger JD, Speer M, Ott J. Chromosome-based method for rapid computer simulation in human genetic linkage analysis. Genet Epidemiol. 1993;10:217-224.
47. Sturt E. A mapping function for human chromosomes. Ann Hum Genet. 1976;40:147-163.
48. Cottingham RW Jr, Idury RM, Schaffer AA. Faster sequential genetic linkage computations. Am J Hum Genet. 1993;53:252-263.
49. Lathrop GM, Lalouel JM, Julier C, Ott J. Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci U S A. 1984;81:3443-3446.
50. Weir BS. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, England: Sinauer Associates Inc Publishers; 1996.