Linkage analysis in the presence of errors II: Marker-locus genotyping errors modeled with hypercomplex recombination fractions

American Journal of Human Genetics

Volumn 66, Issue 3, 2000, Pages 1107-1118

  Göring, Harald H H ^a,d   Terwilliger, Joseph D ^a,b,c  

^a Columbia University ^*  (United States)

^b New York Presbyterian Columbia University Medical Center   (United States)

^c NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^d SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; ERROR; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENETIC LINKAGE; GENETIC MODEL; GENETIC PREDISPOSITION; GENETIC RECOMBINATION; GENOME; GENOTYPE; HUMAN; MARKER GENE; MEIOSIS; MULTIFACTORIAL INHERITANCE; PRIORITY JOURNAL; PROBABILITY; STATISTICAL ANALYSIS;

EID: 0033942718     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/302798     Document Type: Article

References (34)

1. Brzustowicz LM, Mérette C, Xie X, Townsend L, Gilliam TC, Ott J (1993) Molecular and statistical approaches to the detection and correction of errors in genotype databases. Am J Hum Genet 53:1137-1145
2. Buetow KH (1991) Influence of aberrant observations on high-resolution linkage analysis outcomes. Am J Hum Genet 49: 985-994
3. Daw EW, Thompson EA, Wijsman EM (1998) Bias in multipoint linkage analysis arising from map misspecification. Am J Hum Genet Suppl 63:A17
4. de la Chapelle A, Wright FA (1998) Linkage disequilibrium mapping in isolated populations: the example of Finland revisited. Proc Natl Acad Sci USA 95:12416-12423
5. Ehm MG, Kimmel M, Cottingham RW (1996) Error detection for genetic data using likelihood methods. Am J Hum Genet 58:225-234
6. Goldstein DR, Zhao H, Speed TP (1997) The effects of genotyping errors and interference on estimation of genetic distance. Hum Hered 47:86-100
7. Göring HHH, Terwilliger JD (2000a) Linkage analysis in the presence of errors I. complex-valued recombination fractions and complex phenotypes. Am J Hum Genet 66; 1095-1106 (in this issue)
8. _ (2000b) Linkage analysis in the presence of errors III. marker loci and their map as nuisance parameters. Am J Hum Genet (in press)
9. _ (2000c) Linkage analysis in the presence of errors IV. joint pseudomarker analysis of linkage and/or linkage dis-equilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified. Am J Hum Genet (in press)
10. Göring HHH, Terwilliger JD, Ott J. (1997) A likelihood-based approach to extended haplotype analysis of shared segments using a Markov branching process. Am J Hum Genet 61: 1614
11. Haldane JBS (1919) The combination of linkage values and the calculation of distances between the loci of linked factors. J Genet 8:299-309
12. Holmans P, Craddock N (1997) Efficient strategies for genome-scanning using maximum-likelihood affected-sib-pair analysis. Am J Hum Genet 60:657-666
13. Jaynes ET (1996) Probability theory: the logic of science. http://bayes.wustl.edu/etj/prob.html
14. Krause EF (1975) Taxicab geometry - an adventure in non-Euclidean geometry. Addison-Wesley, Menlo Park, NJ
15. Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363-2367
16. Lathrop GM, Hooper AB, Huntsman JW, Ward RH (1983) Evaluating pedigree data. I. The estimation of pedigree error in the presence of marker mistyping. Am J Hum Genet 35: 241-262
17. Lathrop, GM, Lalouel JM, Julier C, Ott J (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 81:3443-3446
18. Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610
19. Lindqvist AK, Magnusson PK, Balciuniene J, Wadelius C, Lindholm E, Alarcón-Riquelme ME, Gyllensten UB (1996) Chromosome-specific panels of tri- and tetra-nucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics. Genome Res 6:1170-1176
20. Morton NE (1988) Multipoint mapping and the emperor's clothes. Ann Hum Genet 52:309-318
21. Morton NE, Andrews V (1989) MAP, an expert system for multiple pairwise linkage analysis. Ann Hum Genet 53:263-269
22. Nordheim EV (1984) On the performance of a likelihood ratio test for genetic linkage. Biometrics 40:785-790
23. Ott, J (1977) Linkage analysis with misclassification at one locus. Clin Genet 12:119-124
24. _ (1985) Analysis of human genetic linkage, 1st ed. Baltimore, Johns Hopkins University Press
25. _ (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. Am J Hum Genet 51: 283-290
26. Shields DC, Collins A, Buetow KH, Morton NE (1991) Error filtration, interference, and the human linkage map. Proc Natl Acad Sci USA 88:6501-6505
27. Smith HF (1937) Test of significance for Mendelian ratios when classification is uncertain. Ann Eugen 8:94-95
28. Tai JJ, Chen CL (1989) Asymptotic distribution of the LOD score for familial data. Proc Natl Sci Counc Repub China B 13:38-41
29. Terwilliger JD. On the resolution and feasibility of genome scanning approaches to unraveling the genetic components of multifactorial phenotypes. In: Rao DC, Province MA (eds) Genetic dissection of complex phenotypes: challenges for the new millennium. Academic Press, San Diego (in press)
30. Terwilliger JD, Göring HHH. A review of gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design. Hum Biol 72:63-132
31. Terwilliger JD, Ott J (1994) Handbook of human genetic linkage. The Johns Hopkins University Press, Baltimore
32. Terwilliger JD, Shannon WD, Lathrop GM, Nolan JP, Goldin LR, Chase GA, Weeks DE (1997) True and false positive peaks in genomewide scans: applications of length-biased sampling to linkage mapping. Am J Hum Genet 61:430-438
33. Terwilliger JD, Weeks DE, Ott J (1990) Laboratory errors in the reading of marker alleles cause massive reductions in LOD score and lead to gross overestimation of the recombination fraction. Am J Hum Genet Suppl 47:A201
34. Walley P (1991) Statistical reasoning with imprecise probabilities. Chapman and Hall, London