Faster linkage analysis computations for pedigrees with loops or unused alleles

Human Heredity

Volumn 46, Issue 4, 1996, Pages 226-235

  Schäffer, Alejandro A ^a,b  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b Rice University   (United States)

Author keywords

Algorithms; Genetic linkage analysis; Loops; Unknown genotypes

Indexed keywords

ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; DOCUMENTATION; GENETIC LINKAGE; GENOTYPE; PEDIGREE;

EID: 0029946879     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000154358     Document Type: Article

References (26)

1. Lathrop GM, Lalouel JM, Julicr C, Ott J: Strategies for multilocus linkage analysis in humans, Proc Nat Acad Sci USA 1984;81:3443-3446.
2. Lathrop GM, Lalouel JM: Easy calculations of lod scores and genetic risks on small computers, Am J Hum Genet 1984:36:460-465.
3. Lathrop GM, Lalouel JM, Julicr C, Ott, J: Multilocus linkage analysis in humans: Detection of linkage and estimation of recombination, Am J Hum Genet 1985:37:482-498.
4. Lange K, Weeks D, Boehnke M: Programs for pedigree analysis: MENDEL, FISHER, and dGenc, Genet Epidem 1988:5:471-473.
5. Hasstcdt SJ: PAP - Pedigree Analysis Package, Revision 3. Department of Human Genetics, University of Utah, Sail Lake City, Utah, 1989.
6. Cottingham RW Jr., Idury RM, Schaffer AA: Faster sequential genetic linkage computations Am J Hum Genet 1993:53:252-263.
7. Schafler AA, Gupta SK, Shr ram K, Cottingham RW Jr.: Avoiding recomputation in linkage analysis, Hum Hercd 1994:44:225-237.
8. Dwarkadas S, Schaffer AA, Cottingham RW Jr., Cox AL, Keleher P, Zwaenepocl W: Parallel izat ion of general linkage analysis problems, Hum Hercd 1994:44:127-141.
9. Gupta SK, Schaffer AA, Cox AL, Dwarkadas S, Zwaenepocl W: Integrating parallelization strategies for linkage analysis, Cornput Biomed Res 1995:28:116-139.
10. Schaffer AA: Pedigree traversal in FASTLINK, One file in the FAST-LINK documentation, 1993.
11. Schaffer AA: Loops in FASTLINK, One file in the FASTLINK documentation, 1993.
12. SchäfTer AA: The mystery of (the) Unknown, One file in the FAST-L1NK documentation, 1994.
13. Elston RC, Stewart J: A general model for the analysis of pedigree data, Hum Hered 1971:21:523-542.
14. Lange K, Elston RC: Extensions to pedigree analysis, I Likelihood calculation for simple and complex pedigrees, Hum Hered 1975:25:95-105.
15. Tcrwilliger JD, Ott J: Handbook of Human Genetic Linkage, Baltimore, Johns Hopkins University Press, 1994.
16. Diehl SR, Lange KL, MacLean C: Personal communication, 1995.
17. Blanton SH, Hcckcnlivcly JR, Cot-tingham AW, Friedman J, Sadler LA, Wagner M, Friedman LH, Daiger SP: Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8. Genomics 1991;11:857-869.
18. Law A, Richard CW III, Cotting-ham RW Jr, Lathrop GM, Cox DR, Myers RM: Genetic linkage analysis of bipolar affective disorder in an Old Order Amish pedigree, Hum Genet 1992;88:562-568.
19. Berettini WB, Ferraro TN, Weeks D, Goldin LR, Detcra-Wadeigh S, Nürnberger JI Jr., Gershon ES: Pericentric chromosome 18 DNA markers and manic-depressive illness: Evidence for a susceptibility gene, Proc Natl Acad Sei USA 1994: 91:5918-5921.
20. Hecht JT, Wang Y, Connor B, Blanton SH, Daiger SP: Non-syndromic cleft lip and palate: No evidence of linkage to HLA or factor 13a, Am J Hum Genet 1993:52:1230-1233.
21. Passos-Bueno MR, Richard I, Vain-zof M, Fougerousse F, Weissenbach J, Broux O, Cohen D, Akiyama J, Marie SKN, Carvalho AA, Guil-herme L, Kalil J, Tsanaclis AM, Zatz M, Beckmann JS: Evidence of genetic heterogeneity in the autosomal recessive adult forms of lirnb-girdle muscular dystrophy following linkage analysis with 15q probes in Brazilian families, J Med Genet 1993:30:385-387.
22. Ben Othmanc K, Ben Hamida M, Pericak-Vance MA, Ben Hamida C, Biel S, Carter SC, Bowcock AM, Pe-trukhin K, Gilliam TC, Roses AD, Hentati F, Vance JM: Linkage of Tunisian autosomal recessive Du-chenne-like muscular dystrophy to the pericentromeric region of chromosome IJq, Nature Genet 1992:2: 315-317.
23. Pericak-Vance MA, Johnson CC, Rimmler JB, Saunders AM, Robinson LC, Hondl EG, Jackson CE, Haines JL: Alzheimer dementia and APOE-4 in an Amish population, Arch Neurol, in press
24. Nakura J, Wijsman EM, Miki T, Ramino K, Yu CE, Oshima J, Fuku-chi KI, Weber JL, Piussan C, Mcla-ragno ML, Epstein CJ, Scappaiicci S, Fraccaro M, Matshumara T, Murano S, Yoshida S, Fujiwara Y, Saida T, Ogihara T, Martin GM, Schcllcn-bcrg GD: Homozygosity mapping of the Werner syndrome locus (WRN), Genomics 1994:23:600-608.
25. Thompson EA: Monte Carlo estimation of multilocus autozvgosity probabilities: in Proc of the 1994 Interface Conference, Interface Foundation of North America, 1994. pp 498-506.
26. O'Connell JR, Weeks DE: The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype sel-rccoding and fuzzy inheritance, Nature Genet 1995:11:402-408.