Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis

Human Heredity

Volumn 72, Issue 4, 2011, Pages 289-297

  Marchani, Elizabeth E ^a   Wijsman, Ellen M ^a,b  

^a Division of Medical Genetics   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Equivalence class; Genome scan; Haplotype; Inheritance vector; Segregation

Indexed keywords

ALZHEIMER DISEASE; ARTICLE; COMPUTER PROGRAM; GENE FREQUENCY; GENE SEQUENCE; GENETIC LINKAGE; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; PEDIGREE ANALYSIS;

ADULT; AGED; AGED, 80 AND OVER; ALZHEIMER DISEASE; COMPUTER SIMULATION; FEMALE; GENETIC LINKAGE; HUMANS; INHERITANCE PATTERNS; LOD SCORE; MALE; MIDDLE AGED; MODELS, GENETIC; MULTIFACTORIAL INHERITANCE; PEDIGREE;

EID: 84055199642     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000334083     Document Type: Article

References (66)

1. Morton NE: Sequential tests for the detection of linkage. Am J Hum Genet 1955; 7:277-318.
2. 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. (Pubitemid 26153846)
3. Terwilliger JD, Goring HH: Gene mapping in the 20th and 21st centuries: Statistical methods, data analysis, and experimental design. Human Biology 2000; 72:63-132. (Pubitemid 30132302)
4. Botstein D, Risch N: Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat Genet 2003; 33:228-237. (Pubitemid 36278833)
5. Almasy L, Blangero J: Human QTL linkage mapping. Genetica 2009; 136: 333-34 0.
6. Ng SB, Nickerson DA, Bamshad MJ, Shendure J: Massively parallel sequencing and rare disease. Hum Mol Genet 2010; 19:R119-R124.
7. Riazuddin S, Castelein CM, Ahmed ZM, Lalwani AK, Mastroianni MA, Naz S, Smith TN, Liburd NA, Friedman TB, Griffith AJ, Wilcox ER: Dominant modifier DFNM1 suppresses recessive deafness DFNB26. Nat Genet 2000; 26: 431-434.
8. Daw EW, Chen SN, Czernuszewicz G, Lom-bardi R, Lu Y, Ma J, Roberts R, Shete S, Marian AJ: Genome-wide mapping of modifier chromosomal loci for human hypertrophic cardiomyopathy. Hum Mol Genet 2007; 16: 2463-2471. (Pubitemid 47500632)
9. Rosenthal EA, Ronald J, Rothstein J, Rajago-palan R, Ranchalis J, Wolfbauer G, Albers JJ, Brunzell JD, Motulsky AG, Rieder MJ, Nick-erson DA, Wijsman EM, Jarvik GP: Linkage and association of phospholipid transfer protein activity to LASS4. J Lipid Res 2011; 52:1837-1846.
10. Guerreiro RJ, Baquero M, Blesa R, Boada M, Bras JM, Bullido MJ, Calado A, Crook R, Ferreira C, Frank A, Gomez-Isla T, Hernandez I, Lleo A, Machado A, Martinez-Lage P, Masdeu J, Molina-Porcel L, Molinuevo JL, Pastor P, Perez-Tur J, Relvas R, Oliveira CR, Ribeiro MH, Rogaeva E, Sa A, Samaranch L, Sanchez-Valle R, Santana I, Tarraga L, Va ldivieso F, Singleton A, Hardy J, Clarimon J: Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP. Neurobiol Aging 2010; 31:725-731.
11. Campion D, Dumanchin C, Hannequin D, Dubois B, Belliard S, Puel M, Thomas-An-terion C, Michon A, Martin C, Charbonnier F, Raux G, Camuzat A, Penet C, Mesnage V, Martinez M, Clerget-Darpoux F, Brice A, Frebourg T: Early-onset autosomal dominant Alzheimer disease: prevalence, genetic heterogeneity, and mutation spectrum. Am J Hum Genet 1999; 65:664-670. (Pubitemid 30468710)
12. Bernardi L, Tomaino C, Anfossi M, Gallo M, Geracitano S, Puccio G, Colao R, Frangipane F, Mirabelli M, Smirne N, Maletta RG, Bruni AC: Late onset familial Alzheimer's disease: novel presenilin 2 mutation and PS1 E318G polymorphism. J Neurol 2008; 255:604-606.
13. Gomez-Isla T, Growdon WB, McNamara MJ, Nochlin D, Bird TD, Arango JC, Lopera F, Kosik KS, Lantos PL, Cairns NJ, Hyman BT: The impact of different presenilin 1 and presenilin 2 mutations on amyloid deposition, neurofibrillary changes and neuronal loss in the familial Alzheimer's disease brain-evidence for other phenotype-modifying factors. Brain 1999; 122:1709-1719. (Pubitemid 29425674)
14. McClellan J, King MC: Genetic heterogeneity in human disease. Cell 2010; 141:210-217.
15. Hobbs HH, Russell DW, Brown MS, Goldstein JL: The LDL receptor locus in familial hypercholesterolemia-mutational analysis of a membrane-protein. Annu Rev Genet 199 0; 24: 133-170. (Pubitemid 120011544)
16. Wilund KR, Yi M, Campagna F, Arca M, Zu-liani G, Fellin R, Ho YK, Garcia JV, Hobbs HH, Cohen JC: Molecular mechanisms of autosomal recessive hypercholesterolemia. Hu m Mol Genet 20 02; 11: 3019-3030. (Pubitemid 35414815)
17. Wijsman EM, Amos CI: Genetic analysis of simulated oligogenic traits in nuclear and extended pedigrees: Summary of GAW10 contributions. Genet Epidemiol 1997; 14: 719-735. (Pubitemid 28027478)
18. Wright AF, Carothers AD, Pirastu M: Population choice in mapping genes for complex diseases. Nat Genet 1999; 23: 397-404.
19. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TFC, McCarroll SA, Visscher PM: Finding the missing heritability of complex diseases. Nature 2009; 461:747-753.
20. Marchani EE, Bird TD, Steinbart EJ, Rosen-thal E, Yu CE, Schellenberg GD, Wijsman EM: Evidence for three loci modifying age-at-onset of Alzheimer's disease in early-onset PSEN2 families. Am J Med Genet B 2010; 153B:1031-1041.
21. Hasstedt SJ, Scott BT, Callas PW, Vossen CY, Rosendaal FR, Long GL, Bovill EG: Genome scan of venous thrombosis in a pedigree with protein c deficiency. J Thromb Haemost 2004; 2:868-873. (Pubitemid 40185730)
22. Thompson EA: The structure of genetic linkage data: from LIPED to 1M SNPs. Hum Hered 2011; 71: 86-96.
23. Thomas A, Camp NJ, Farnham JM, Allen-Brady K, Cannon-Albright LA: Shared ge-nomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays. Ann Hum Genet 2008; 72: 279-287. (Pubitemid 351228466)
24. Sobel E, Lange K: Descent graphs in pedigree analysis: Applications to haplotyping, location scores, and marker-sharing statistics. A m J Hum Genet 1996; 58: 1323-1337 (Pubitemid 26153844)
25. MORGAN: A package for Markov chain Monte Carlo in genetic analysis (version 3.0), 2009. http://www.stat.washington.edu/thompson/Genepi/MORGAN/ Morgan.shtml.
26. Lander ES, Green P: Construction of multi-locus genetic maps in humans. P Natl Acad Sci USA 1987; 84:2363-2367. (Pubitemid 17075870)
27. Donnelly KP: The probability that related individuals share some section of genome identical by descent. Theor Popul Biol 1983; 23: 34-63.
28. Elston RC, Stewart J: A general model for the genetic analysis of pedigree data. Hum Hered 1971; 21:523-542.
29. Gao GM, Allison DB, Hoeschele I: Haplotyp-ing methods for pedigrees. Hum Hered 2009; 67: 248-266.
30. Lange K, Sobel E: A random walk method for computing genetic location scores. Am J Hum Genet 1991; 49: 1320-1334. (Pubitemid 21891777)
31. Sobel E, Sengul H, Weeks DE: Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees. Hum Hered 2001; 52:121-131. (Pubitemid 34701496)
32. Tong LP, Thompson E: Multilocus lod scores in large pedigrees: Combination of exact and approximate calculations. Hum Hered 2008; 65:142-153. (Pubitemid 350253954)
33. Thompson EA, Lin S, Olshen AB, Wijsman EM: Monte Carlo segregation and linkage analysis of a large hypercholesterolemia pedigree. Genet Epidemiol 1993; 10:677-682.
34. Thompson EA: Monte Carlo likelihood in genetic mapping. Stat Sci 1994; 9: 355-366.
35. Thompson EA, Heath SC: Estimation of conditional multilocus gene identity among relatives; in Seillier-Moseiwitch F, D on n e l l y P, Wat er ma n M (e d s): S t at i s t ic s i n Molecular Biology and Genetics: Selected Proceedings of the 1997 Joint AMS-IMS-SIAM Summer Conference on Statistics in Molecular Biology. Hayward, CA, Institute of Mathematical Statistics, 1999, vol 33, pp 93-113.
36. Thompson EA: MCMC estimation of multi-locus genome sharing and multipoint gene location scores. Int Stat Rev 2000; 68:53-73.
37. Heath SC: Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am J Hum Genet 1997; 61:748-760. (Pubitemid 27418415)
38. Daw EW, Heath SC, Wijsman EM: Multipoint oligogenic analysis of age-at-onset data with applications to Alzheimer's disease pedigrees. Am J Hum Genet 1999; 64: 839-851. (Pubitemid 30460427)
39. Thompson EA: Statistical inferences from genet ic data on pedigrees. Beachwood, Ohio, IMS, 2000.
40. Thompson EA: MCMC in the analysis of genetic data on pedigrees; in Kendall WS, Wang JS, Liang F (eds): Markov Chain Monte Carlo: Innovations and Applications. Singapore, World Scientific Publishing Company, 2005.
41. Wijsman EM, Rothstein JH, Thompson EA: Multipoint linkage analysis with many mul-tiallelic or dense diallelic markers: MCMC provides practical approaches for genome scans on general pedigrees. Am J Hum Ge-net 2006; 79: 846-858. (Pubitemid 44763399)
42. Wilcox MA, Pugh EW, Zhang H, Zhong X, Levinson DF, Kennedy GC, Wijsman EM: Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14:Pre-sentation groups 1, 2, and 3. Genet Epidemiol 2005; 29 (suppl 1):S7-S28. (Pubitemid 43062722)
43. Baum LE: An inequality and associated maximization technique in statistical estimation for probabilistic functions on Markov processes; in Shisha O (ed): Inequalities-iii; Proceedings of the Third Symposium on Inequalities University of California Los Angeles, 1969. New York, Academic Press, 1972, pp 1-8.
44. Koepke HA, Thompson EA: Efficient testing operations on dynamic graph structures using strong hash functions: Technical report #567, Department of Statistics, University of Washington, available at http://www.stat. washington.edu/research/reports/2010/tr567.pdf, 2010.
45. Lautenschlager NT, Cupples LA, Rao VS, Auerbach SA, Becker R, Burke J, Chui H, Du-ara R, Foley EJ, Glatt SL, Green RC, Jones R, Karlinsky H, Kukull WA, Kurz A, Larson EB, Martelli K, Sadovnick AD, Volicer L, Waring SC, Growdon JH, Farrer LA: Risk of dementia among relatives of Alzheimer's disease patients in the MIRAGE study: What is in store for the oldest old? Neurology 1996; 46: 641-650. (Pubitemid 26099626)
46. Mayeux R, Sano M, Chen J, Tatemichi T, Stern Y: Risk of dementia in 1st-degree relatives of patients with Alzheimers-disease and related disorders. Arch Neurol 1991; 48: 269-273.
47. Cruts M: Alzheimer disease & frontotempo-ral dementia mutation database, 2010. http://www.molgen.ua.ac.be/ADMutations and http://www.molgen.ua. ac.be/FTDMutations.
48. Tanzi RE, Bertram L: Twenty years of the Alzheimer's disease amyloid hypothesis: A genetic perspective. Cell 2005; 120: 545-555. (Pubitemid 40269768)
49. Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW, Roses AD, Haines JL, Pericak-Vance MA: Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 1993; 261: 921-923. (Pubitemid 23275809)
50. Pastor P, Roe C, Villegas A, Bedoya G, Chakraverty S, Garcia G, Tirado V, Norton J, Rios S, Martinez M, Kosik K, Lopera F, Goate A: Apolipoprotei n E e4 mod if ies A l zhei mer's disease onset in an E280A PS1 kindred. Ann Neurol 2003; 54:163-169. (Pubitemid 36909615)
51. Wijsman EM, Daw EW, Yu X, Steinbart EJ, Nochlin D, Bird TD, Schellenberg G: APOE and other loci affect age-at-onset in Alzheimer's disease families with PS2 mutation. Am J Med Genet B 2005; 132B:14-20. (Pubitemid 40066188)
52. Risch N, Giuffra L: Model misspecification and multipoint linkage analysis. Hum Hered 1992; 42:77-92.
53. Göring HHH, Terwilliger JD: Linkage analysis in the presence of errors I V: 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 2000; 66: 1310-1327. (Pubitemid 30468787)
54. Levy-Lahad E, Wasco W, Poorkaj P, Romano DM, Oshima J, Pettingell WH, Yu CE, Jon-dro PD, Schmidt SD, Wang K, Crowley AC, Fu YH, Guenette SY, Galas D, Nemens E, Wijsman EM, Bird TD, Schellenberg GD, Tanzi RE: Candidate gene for the chromosome 1 familial Alzheimer's disease locus. Science 1995; 269: 973-977.
55. Ott J: Estimation of the recombination fraction in human pedigrees: Efficient computation of the likelihood for human linkage studies. Am J Hum Genet 1974; 26: 588-597.
56. Clerget-Da r poux F, Bonaiti-Pel lie C, Hochez J: Effects of misspecifying genetic parameters in lod score analysis. Biometrics 1986; 42: 393-399.
57. Williamson JA, Amos CI: On the asymptotic-behavior of the estimate of the recombination fraction under the null hypothesis of no linkage when the model is misspecified. Genet Epidemiol 1990; 7:309-318. (Pubitemid 20376034)
58. Hamshere ML, Holmans PA, Avramopoulos D, Bassett SS, Blacker D, Bertram L, Wiener H, Rochberg N, Tanzi RE, Myers A, Vrieze FWD, Go R, Fallin D, Lovestone S, Hardy J
59. Goate A, O'Donovan M, Williams J, Owen MJ: Genome-wide linkage analysis of 723 affected relative pairs with late-onset Alzheimer's disease. Hum Mol Genet 2007; 16: 2703-2712 (Pubitemid 350018512)
60. plotIBD.pl: http://faculty.washington.edu/wijsman/software.shtml, 2011
61. Gnuplot: http://gnuplot.Info/, 2009.
62. Leykin I, Hao K, Cheng JS, Meyer N, Pollak MR, Smith RJ, Wong WH, Rosenow C, Li C: Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genet 2005; 6:7.
63. Ploughman LM, Boehnke M: Estimating the power of a proposed linkage study for a complex genetic trait. Am J Hum Genet 1989; 44: 543-551. (Pubitemid 19095400)
64. Logue MW, Vieland VJ: A new method for computing the multipoint posterior probability of linkage. Hum Hered 2004; 57:90-99. (Pubitemid 38798151)
65. Marchani EE, Di Y, Choi Y, Cheung C, Su M, Boehm F, Thompson EA, Wijsman EM: Contrasting IBD estimators, association studies, and linkage analysis using the Fram-ingham Heart Study. BMC Proceedings 2009; 3:S102.
66. Cheung CY, Thompson EA, Wijsman EM: In silico genotype imputation on large pedigrees. Genet Epidemiol 2010; 34: 919.