Linkage analysis in the presenoe of errors III: Marker loci and their map nuisance parameters

American Journal of Human Genetics

Volumn 66, Issue 4, 2000, Pages 1298-1309

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

^a NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^b Howard Hughes Medical Institute   (United States)

^c SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENETIC LINKAGE; GENETIC RECOMBINATION; HAPLOTYPE; HUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; FEMALE; GENE FREQUENCY; GENETIC DISORDER; GENETIC MARKER; GENETICS; GENOTYPE; LABORATORY DIAGNOSIS; MALE; METHODOLOGY; PEDIGREE; REPRODUCIBILITY; STATISTICAL MODEL; STATISTICS;

ALLELES; CHROMOSOME MAPPING; COMPUTER SIMULATION; FALSE POSITIVE REACTIONS; FEMALE; GENE FREQUENCY; GENETIC DISEASES, INBORN; GENETIC MARKERS; GENOTYPE; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE (GENETICS); LOD SCORE; MALE; MICROSATELLITE REPEATS; MODELS, GENETIC; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SOFTWARE;

EID: 0034164617     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/302846     Document Type: Article

References (67)

1. Agarwala R, Biesecker LG, Schäffer AA. Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations. Discrete Appl Math (in press)
2. Ajioka R, Jorde LB, Gruen JR, Yu P, Dimitrova D, Barrow J, Radisky E, et al (1997) Haplotype analysis of hemochromatosis: evaluation of different linkage-disequilibrium approaches and evolution of disease chromosomes. Am J Hum Genet 60:1439-1447
3. Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62: 1198-1211
4. Boehnke M (1991) Allele frequency estimation from data on relatives. Am J Hum Genet 48:22-25
5. Botstein D, White RL, Skolnick MH, Davies RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331
6. Broman KW, Murray JC, Sheffield VS, White RL, Weber JL (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet 63:861-869
7. Buetow KH (1991) Influence of aberrant observations on high-resolution linkage analysis outcomes. Am J Hum Genet 49: 985-994
8. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton
9. Chakravarti A (1991) A graphical representation of genetic and physical maps: the Marey map. Genomics 11:219-222
10. Chase GA (1977) Genetic linkage, gene-locus assignment, and the association of alleles with diseases. Transplant Proc 9: 167-171
11. Chin DC (1992) On the connection between maximum likelihood sensitivity analysis and nuisance parameter analysis. IEEE Transact Aerosp Electron Syst 28:884-886
12. Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengård J, Salomaa V et al (1998) Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 63: 595-612
13. Clerget-Darpoux F, Bonaïti-Peilié C, Hochez J (1986) Effects of misspecifying genetic parameters in lod score analysis. Biometrics 42:393-399
14. Collins FS, Guyer MS, Chakravarti A (1997) Variations on a theme: cataloging human DNA sequence variation. Science 278:1580-1581
15. Cottingham RW Jr, Idury RM, Schaffer AA (1993) Faster sequential genetic linkage computations. Am J Hum Genet 53: 252-263
16. Dausset J, Cann H, Cohen D, Lathrop GM, Lalouel JM, White R (1990) Centre d'Étude du Polymorphisme Humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6:575-577
17. Daw EW, Thompson EA, Wijsman EM (1998) Bias in multipoint linkage analysis arising from map misspecification. Am J Hum Genet Suppl 63:A17
18. Dib C, Fauré S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, et al (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152-154
19. Dupuis J, Brown PO, Siegmund D (1995) Statistical methods for linkage analysis of complex traits from high-resolution maps of identity by descent. Genetics 140:843-856
20. Eguchi S (1991) A geometric look at nuisance parameter effect of local powers in testing hypotheses. Ann Inst Statist Math 43:245-260
21. Falk CT, Rubinstein P (1987) Haplotype relative risks: an easy reliable way to construct a proper control sample for risk calculations. Ann Hum Genet 51:227-233
22. 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
23. -(2000b) Linkage analysis in the presence of errors II: marker-locus genotyping errors modeled with hypercomplex recombination fractions. Am J Hum Genet 66:1107-1118
24. -(2000c) Linkage analysis in the presence of errors IV: joint pseudomarker analysis of linkage and/or linkage disequilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified. Am J Hum Genet 66:1310-1327 (in this issue)
25. Göring HHH, Terwilliger JD, Ott J (1997) A likelihood-based approach to extended haplotype analysis of shared segments using a Markovian branching process. Am J Hum Genet Suppl 61:A277
26. Haldane JBS (1922) Sex ratio and unisexual sterility in hybrid animals. J Genet 12:101-109
27. Hardy GH (1908) Mendelian proportions in a mixed population. Science 28:49-50
28. Hellsten E, Vesa J, Speer MC, Mäkelä TP, Järvelä I, Alitalo K, Ott J et al (1993) Refined assignment of the infantile neuronal ceroid lipofuscinosis (INCL, CLN1) locus at 1p32: incorporation of linkage disequilibrium in multipoint analysis. Genomics 16:720-725
29. Hovatta IM, Varilo T, Suvisaari J, Terwilliger JD, Ollikainen V, Arajärvi R, Juovinen H, et al (1999) A genomewide screen for schizophrenia genes in an isolated Finnish subpopulation suggesting multiple susceptibility loci. Am J Hum Genet 65: 1114-1124
30. Jorde LB, Watkins WS, Carlson M, Groden J, Albertsen H, Thliveris A, Leppert M (1994) Linkage disequilibrium predicts physical distance in the adenomatous polyposis coli region. Am J Hum Genet 54:884-898
31. Kalbfleisch JD, Sprott DA (1970) Application of likelihood methods to models involving large numbers of parameters (with discussion). J R Stat Soc (B) 32:175-208
32. Kruglyak L (1997) The use of a genetic map of biallelic markers in linkage studies. Nat Genet 17:21-24
33. Lalouel J-M (1979) GEMINI - a computer program for optimization of general nonlinear functions. Tech rep 14, University of Hawaii, Honolulu
34. Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84: 2363-2367
35. 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
36. Lathrop GM, Lalouel JM, Julier C, Ott J (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 81:3443-3446
37. Lichten M, Goldman AS (1995) Meiotic recombination hotspots. Annu Rev Genet 29:423-444
38. Mohrenweiser HW, Tsujimoto S, Gordon L, Olsen AS (1998) Regions of sex-specific hypo-and hyper-recombination identified through integration of 180 genetic markers into the metric physical map of human chromosome 19. Genomics 47:153-162
39. Morton NE, Collins A (1990) Standard maps of chromosome 10. Ann Hum Genet 54:235-251
40. Murray JC, Buetow KH, Weber JL, Ludwigsen S, Scherpbier Heddema T, Manion F, Quillen J, et al (1994) A comprehensive human linkage map with centimorgan density. Cooperative Human Linkage Center (CHLC). Science 265: 2049-2054
41. Nordheim EV, O'Malley DM, Chow SC (1984) On the performance of a likelihood ratio test for genetic linkage. Biometrics 40:785-790
42. Ott J (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. Am J Hum Genet 51: 283-290
43. Ott J (1999) Analysis of human genetic linkage. 3d ed. Johns Hopkins University Press, Baltimore
44. Pennisi E (1998) A closer look at SNPs suggests difficulties. Science 281: 1787-1789
45. Risch N, Giuffra L (1992) Model misspecification and multipoint linkage analysis. Hum Hered 42:77-92
46. Royall RM (1997) Statistical evidence: a likelihood paradigm. Chapman & Hall, London
47. Sall T, Bengtsson BO (1989) Apparent negative interference due to variation in recombination frequencies. Genetics 122: 935-942
48. Smith HF (1937) Test of significance for Mendelian ratios when classification is uncertain. Ann Eugen 8:94-95
49. Smith CAB (1953) The detection of linkage in human genetics. J R Stat Soc 15B:153-184
50. -(1957) Counting methods in genetical statistics. Ann Hum Genet 21:254-276
51. Tai JJ, Chen CL (1989) Asymptotic distribution of the lod score for familial data. Proc Natl Sci Counc Repub China [B] 13: 38-41
52. Tanzi RE, Watkins PC, Stewart GD, Wexler NS, Gusella JF, Haines JL (1992) A genetic linkage map of human chromosome 21: analysis of recombination as a function of sex and age. Am J Hum Genet 50:551-558
53. Terwilliger JD (1994) The available possibilities to analyse data of polygenic disease statistically. Paper presented at the IVth workshop of the Nordic Genome Initiative, Helsinki, September 3-5
54. Terwilliger JD (1995) A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. Am J Hum Genet 56: 777-787
55. -(1996) Likelihood ratio tests for linkage and linkage disequilibrium: Asymptotic distribution and power - reply. Am J Hum Genet 58:1095-1096
56. -. A likelihood-based admixture model of oligogenic inheritance in "model-based" or "model-free," two-point or multi-point, linkage and/or LD analysis. Eur J Hum Genet (in press)
57. Terwilliger JD, Ding Y, Ott J (1992) On the relative importance of heterozygosity and intermarker distance in gene mapping. Genomics 13:951-956
58. Terwilliger JD, Göring HHH (2000) Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design. Hum Biol 72:63-132
59. Terwilliger JD, Ott J (1992) A haplotype-based "haplotype relative risk" approach to detecting allelic associations. Hum Hered 42:337-346
60. -(1994) Handbook of human genetic linkage. Johns Hopkins University Press, Baltimore
61. 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
62. Terwilliger JD, Weiss KM (1998) Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotechnol 9:578-594
63. Terwilliger JD, Zöllner S, Laan M, Pääbo S (1998) Mapping genes through the use of linkage disequilibrium generated by genetic drift: "drift mapping" in small populations with no demographic expansion. Hum Hered 48:138-154
64. Tienari PJ, Terwilliger JD, Ott J, Palo J, Peltonen L (1994) Two-locus linkage analysis in multiple sclerosis. Genomics 19:320-325
65. Weeks DE, Ott J, Lathrop GM (1991) Multipoint mapping under different models of interference using the LINKAGE programs. Am J Hum Genet Suppl 49:A372
66. Weinberg W (1908) Über den Nachweis der Vererbung beim Menschen. Jahreshefte des Vereins für vaterländische Naturkunde in Württemberg 64:368-382
67. Wright SE (1922) Coefficients of inbreeding and relationship. Am Nat 56:330-338