On computation of p-values in parametric linkage analysis

Human Heredity

Volumn 57, Issue 4, 2004, Pages 207-219

  Kurbasic, Azra ^a   Hössjer, Ola ^b  

^a LUND UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Linkage analysis; Lod score distribution; Pointwise genomewide p value

Indexed keywords

ARTICLE; CALCULATION; CHROMOSOME; GENETIC LINKAGE; GENETIC MODEL; LINKAGE ANALYSIS; MATHEMATICAL MODEL; PARAMETRIC TEST;

CHROMOSOME MAPPING; DATA INTERPRETATION, STATISTICAL; FEMALE; HUMANS; LINKAGE (GENETICS); LOD SCORE; MALE; PEDIGREE;

EID: 10844237959     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000081448     Document Type: Article

References (24)

1. Sham P: Statistics in Human Genetics. New York, Arnold applications of Statistics, 1998.
2. Ott J: Analysis of Human Genetic linkage, ed 3. Baltimore, Johns Hopkins University Press, 1999.
3. Weeks DE, Lange K: The affected-pedigree-member method of linkage analysis. Am J Hum Genet 1988;42:315-326.
4. Fimmers R, Seuchter SA, Neugebauer M, Knapp M, Baur MP: Identity by descent analysis using all genotype solutions; in Elston RC, Spence MA, Hodge SE, MacCluer JW (eds): Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop 6. New York, Alan R. Liss, 1989.
5. Whittemore A, Halpern J: A class of tests for linkage using affected pedigree members. Biometrics 1994;50:118-127.
6. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES: Parametric and nonparametric linkage analysis: A unified multipoint approach. Am J Hum Genet 1996;58:1347-1363.
7. Risch N: Segregation analysis incorporating genetic markers. I. Single-locus models with an application to type I diabetes. Am J Hum Genet 1984;36:363-386.
8. Clerget-Darpoux F, Bonaïti-Pellié C, Hoches J: Effects of misspecifying genetic parameters in lod score analysis. Biometrics 1986;42:393-399.
9. Whittemore AC: Genome scanning for linkage: An overview. Am J Hum Genet 1996;59:704-716.
10. Self SG, Liang KY: Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Am Stat Assoc 1987;82:605-610.
11. Dudoit S, Speed TP: A score test for linkage using identity by descent data from sibships. Ann Stat 1999;27:943-986.
12. Williamson JA, Amos CI: On the asymptotic behaviour of the estimate of the recombination fraction under the null hypotesis of no linkage, when the model is misspecified. Genet Epidemiol 1990;7:309-318.
13. Morton NE: Seqential tests for the detection of linkage. Am J Hum Genet 1995;7:277-318.
14. Royden HL: Real Analysis, ed 2. New York, Macmillan Publishing, 1968.
15. Lander E, Kruglyak L: Genetic dissection of complex traits: Guidelines for interpreting and reporting linkage results. Nat Genet 1995;11:241-247.
16. Ängquist L, Hössjer O: Improving the Calculation of Statistical Significance in Genome-Wide Scans. To appear in Biostatistics.
17. Feingold E, Brown PO, Siegmund D: Gaussian models for genetic linkage analysis using complete high resolution maps of identity by descent. Am J Hum Genet 1993;53:234-251.
18. Gundmundsson J, Johanesdottir G, Arason A, Bergthorasson JT, Ingvarsson S, Egilsson V, Barkardottir RB: Frequent occurance of BRCA2 linkage in Icelandic breast cancer families and segregation of a common BRCA2 haplotype. Am J Hum Genet 1996;58:749-756.
19. Rotnitzky A, Cox DR, Bottai M, Robins J: Likelihood-based inference with singular information matrix. Bernoulli 2000;6:243-284.
20. Hössjer O: Conditional likelihood score function in linkage analysis. To appear in Biostatistics.
21. McPeek MS: Optimal allele-sharing statistics for genetic mapping using affected relatives. Genet Epidemiol 1999;16:225-249.
22. Hössjer O: Determining inheritance distributions via stochastic penetrances. Preprints in mathematical sciences, Centre for Mathematical Sciences, Lund University, 2001. J Am Stat Assoc 2003;98:1035-1051.
23. Kong A, Cox NJ: Allele-sharing models: LOD scores and accurate linkage tests. Am J Hum Genet 1997;61:1179-1188.
24. Claus EB, Rish NJ, Thompson WD: Age at onset of familial risk of breast cancer. Am J Epidemiol 1990;131:961-967.