Skip to main content

Analytical Methods Applied to Psychiatric Genetics

  • Protocol

Part of the book series: Methods in Molecular Medicine™ ((MIMM,volume 77))

Abstract

The development of gene-mapping methodology has not been a linear process. Instead, this development has been multidimensional, culminating in the creation of a powerful and heterogeneous collection of tools. A description of the history of the development of this would include words such as “opportunistic” (i.e., capitalizing on the newest developments in computer technology and genomics) and “problem-solving oriented” (i.e., constantly addressing issues (such as the spotted nature of linkage disequilibrium) that arose during the development of the methodology). Therefore, the following presentation is method-oriented rather than problemoriented. In describing the modern methodology of gene mapping, attempts will be made to describe the origin of a given methodology, the problems it was designed to address, and its known strengths and weaknesses.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Morton N.E. (1955) Sequential tests for the detection of linkage. Am. J. Hum. Genet. 7, 277–318.

    CAS  PubMed  Google Scholar 

  2. Elston R.C. and Steward J. (1971) A general model for the analysis of pedigree data. Hum. Hered. 21, 523–542.

    Article  CAS  PubMed  Google Scholar 

  3. Ott J. (1974) Estimation of the recombination fraction in human pedigrees: Efficient computation of the likelihood for human linkage studies. Am. J. Hum. Genet. 26, 588–597.

    CAS  PubMed  Google Scholar 

  4. Lathrop G.M., Lalouel J.M., Julier C., and Ott J. (1984) Strategies for multilocus linkage analysis in humans. PNAS 81, 3443–3446.

    Article  CAS  PubMed  Google Scholar 

  5. Wijsman E.M. and Amos C. (1997) Genetic analysis of simulated oligogenic traits in nuclear and extended pedigrees: summary of GAW10 contributions. Genet. Epidemiol. 14, 719–735.

    Article  CAS  PubMed  Google Scholar 

  6. Yuan B., Vaske D., Weber J.L., Beck J., and Sheffield V.C. (1997) Improved set of short-tandem-repeat polymorphisms for screening the human genome. Am. J. Hum. Genet. 60, 459–460.

    CAS  PubMed  Google Scholar 

  7. Kruglyak L., Daly M.J., Reeve-Daly M.P., and Lander E.S. (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am. J. Hum. Genet. 58, 1347–1363.

    CAS  PubMed  Google Scholar 

  8. Daw E.W., Health S.C., and Wijsman E.M. (1999) Multipoint oligogenic analysis of age-at-onset data with applications to Alzheimer’s disease pedigrees. Am. J. Hum. Genet. 64, 839–851.

    Article  CAS  PubMed  Google Scholar 

  9. Heath S.C. (1997) Markov chain Monte Carlo segregatin and linkage analysis for oligogenic models. Am. J. Hum. Genet. 61, 748–760.

    Article  CAS  PubMed  Google Scholar 

  10. Health S.C., Snow G.L., Thompson E.A., Tseng C., and Wijsman E.M. (1997) MCMC segregation and linkage analysis. Genet. Epidemiol. 14, 1011–1016.

    Article  Google Scholar 

  11. Almasy L. and Blangero J. (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. Am. J. Hum. Genet. 62, 1198–1121.

    Article  CAS  PubMed  Google Scholar 

  12. Martinez M., Khlat M., Leboyer M., and Clerget-Darpoux F.(1989) Performance of linkage analysis under misclassification error when the genetic model is unknown. Genet. Epidemiol. 6, 253–258.

    Article  CAS  PubMed  Google Scholar 

  13. Risch N. and Giuffra L. (1992) Model misspecification and multipoint linkage analysis. Hum. Hered. 42, 77–92.

    Article  CAS  PubMed  Google Scholar 

  14. Schork N.J., Boehnke M., Terwilliger J.D., and Ott J. (1993) Twotrait-locus linkage analysis: a powerful strategy for mapping complex genetic traits. Am. J. Hum. Genet. 53, 1127–1136.

    CAS  PubMed  Google Scholar 

  15. Abreu P.C., Greenberg D.A., and Hodge S.E. (1999) Direct power comparisons between simple lod scores and NPL scores for linkage analysis in complex diseases. Am. J. Hum. Genet. 65, 847–857.

    Article  CAS  PubMed  Google Scholar 

  16. Göring H.H.H. and Terwilliger J.D. (2000) Linkage analysis in the presence of errors III: marker loci and their map as nuisance parameters. Am. J. Hum. Genet. 66, 1298–1309.

    Article  PubMed  Google Scholar 

  17. Göring H.H.H. and Terwilliger J.D. (2000) 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.

    Article  PubMed  Google Scholar 

  18. Whittemore A.S. (1996) Genome scanning for linkage: an overview. Am. J. Hum. Genet. 59, 704–716.

    CAS  PubMed  Google Scholar 

  19. Fimmers R., Seuchter S.A., Neugebauer M., Knapp M., and Baur M.P. (1989) Identity-by-descent analysis using all genotype solutions, in Multipoint mapping and linkage based on affected pedigree members: Genetic Analysis Workshop 6, (Elston R.C., Spence M.A., Hodge S.E., and MacCluer J. W., eds.), Alan R. Liss, New York, NY, pp. 123–128.

    Google Scholar 

  20. Kruglyak L. and Lander E.S. (1995) Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am. J. Hum. Genet. 57, 439–454.

    CAS  PubMed  Google Scholar 

  21. Whittemore A.S. and Halpern J. (1994) A class of tests for linkage using affected pedigree members. Biometrics 50, 117–127.

    Google Scholar 

  22. Irwin M., Cox N., and Kong A. (1994) Sequential imputation for multilocus linkage analysis. Proc. Natl. Acad. Sci. USA 91, 11,684–11,688.

    Article  CAS  PubMed  Google Scholar 

  23. O’Connell J.R. and Weeks D.E. (1995) The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat. Genet. 11, 402–408.

    Article  PubMed  Google Scholar 

  24. Schwab S.G., Albus M., Hallmayer J., Honig S., Borrmann M., Lichtermann D., et al. (1995) Evaluation of a susceptibility gene for schizophrenia on chromosome 6p by multipoint affected sib-pair linkage analysis. Nat. Genet. 11, 325–327.

    Article  CAS  PubMed  Google Scholar 

  25. Friddle C., Koskela R., Ranade K., Hebert J., Cargill M., Clark C.D., et al. (2000) Full-genome scan for linkage in 50 families segregating the bipolar affective disease phenotype. Am. J. Hum. Genet. 66, 205–215.

    Article  CAS  PubMed  Google Scholar 

  26. Gudbjartsoon D.F., Jonasson K., Frigge M.L., and Kong C.A. (2000) Allegro, a new computer program for multipoint linkage analysis. Nat. Genet. 25, 12–13.

    Article  CAS  Google Scholar 

  27. Hyer R.N., Julier C., Buckley J.D., Trucco M., Rotter J., Spielman R., et al. (1991) High-resolution linkage mapping for susceptibility genes in human polygenic disease: insulin-dependent diabetes mellitus and chromosome 11q. Am. J. Hum. Genet. 48, 243–257.

    CAS  PubMed  Google Scholar 

  28. Knapp M., Seuchter S.A., and Baur M.P. (1994) Two-locus disease models with two marker loci: the power of affected-sib-pair tests. Am. J. Hum. Genet. 55, 1030–1041.

    CAS  PubMed  Google Scholar 

  29. Lander E.S. and Green P. (1987) Construction of multilocus genetic maps in humans. Proc. Natl. Acad. Sci. USA 84, 2363–2367.

    Article  CAS  PubMed  Google Scholar 

  30. Guo S.W. and Thompson E.A. (1992) A Monte Carlo method for combined segregation and linkage analysis. Am. J. Hum. Genet. 51, 1111–1126.

    CAS  PubMed  Google Scholar 

  31. Borewinkle E., Chakraborty R., and Sing C. (1986) The use of measured genotype information in the analysis of quantitative phenotypes in man. Ann. Hum. Genet. 50, 181–194.

    Article  Google Scholar 

  32. Boerwinkle E.R.C. and Sing C.F. (1986) Bias of the contribution of single-locus effects to the variance of a quantitative trait. Am. J. Hum. Genet. 39, 663–676.

    Google Scholar 

  33. Wijsman E.M. and Nur N. (2000) On estimating the proportion of variance in a phenotypic trait attributable to a measured locus. Hum. Hered. 51, 145–149.

    Article  Google Scholar 

  34. Haseman J.K. and Elston R.C. (1972) The investigation of linkage between a quantitative trait and a marker locus. Behav. Genet. 2, 3–19.

    Article  CAS  PubMed  Google Scholar 

  35. Lange K., Westlake J., and Spence M.A. (1976) Extensions to pedigree analysis. III. Variance components by the scoring method. Ann. Hum. Genet. 39, 485–491.

    Article  CAS  PubMed  Google Scholar 

  36. Hopper J.L. and Matthews J.D. (1982) Extensions to multivariate normal models for pedigree analysis. Ann. Hum. Genet. 46, 373–383.

    Article  CAS  PubMed  Google Scholar 

  37. Amos C.I. (1994) Robust variance-components approach for assessing genetic linkage in pedigrees. Am. J. Hum. Genet. 54, 535–543.

    CAS  PubMed  Google Scholar 

  38. Goldgar D.E. (1990) Multipoint analysis of human quantitative genetic variation. Am. J. Hum. Genet. 47, 957–967.

    CAS  PubMed  Google Scholar 

  39. Schork N.J. (1993) Extended multipoint identity-by-descent analysis of human quantitative traits: efficiency, power, and modeling considerations. Am. J. Hum. Genet. 53, 1306–1319.

    CAS  PubMed  Google Scholar 

  40. Pratt S.C., Daly M.J., and Kruglyak L. (2000) Exact multipoint quantitative-trait linkage analysis in pedigrees by variance components. Am. J. Hum. Genet. 66, 1153–1157.

    Article  CAS  PubMed  Google Scholar 

  41. Amos C.I., Zhu D.K., and Boerwinkle E. (1996) Assessing genetic linkage and association with robust components of variance approaches. Ann. Hum. Genet. 60, 143–160.

    Article  CAS  PubMed  Google Scholar 

  42. Amos C.I., Krushkal J., Thiel T.J., Young A., Zhu D.K., Boerwinkle E., et al. (1997) Comparison of model-free linkage mapping strategies for the study of a complex trait. Genet. Epidemiol. 14, 743–748.

    Article  CAS  PubMed  Google Scholar 

  43. Pugh E.W., Jaquish C.E., Sorant A.J.M., Doetsch J.P., Bailey-Wilson J.E., and Wilson A.F. (1997) Comparison of sib-pair and variance components methods for genomic screening. Genet. Epidemiol. 14, 867–872.

    Article  CAS  PubMed  Google Scholar 

  44. Williams J.T., Duggirala R., and Blangero J. (1997) Statistical properties of a variance components method for quantitative trait linkage analysis in nuclear families and extended pedigrees. Genet. Epidemiol. 14, 1065–1070.

    Article  CAS  PubMed  Google Scholar 

  45. Boehnke M. (1994) Limits of resolution of genetic linkage studies: implications for the positional cloning of human genetic disease. Am. J. Hum. Genet. 55, 379–390.

    CAS  PubMed  Google Scholar 

  46. Hästbacka J., de la Chapelle A., Kaitila I., Sistonen P., Weaver A., and Lander E. (1992) Linkage disequilibrium mapping in isolated founder populations: diastrophis dysphasia in Finland. Nat. Genet. 2, 204–211.

    Article  PubMed  Google Scholar 

  47. Hästbacka J.K., de la Chapelle A., Mahanti M. M., Clines G., Reeve-Daly M.P., Daly M., et al. (1994) The diastrophic dysphasia gene encodes a novel sulfate transporter: positional cloning by finestructure linkage disequilibrium mapping. Cell 78, 1073–1087.

    Article  PubMed  Google Scholar 

  48. Kerem B., Rommens J.M., Buchanan J.A., Markiewicz D., Cox T.K., Chakravarti A., et al. (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245, 1073–1080.

    Article  CAS  PubMed  Google Scholar 

  49. Altshuler D., Pollara V.J., Cowles C.R., Van Etten W.J., Baldwin J., Linton L., et al. (2000a) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516.

    Article  CAS  PubMed  Google Scholar 

  50. Mullikin J.C., Hunt S.E., Cole C.G., Mortimore B.J., Rice C.M., Burton J., et al. (2000) An SNP map of human chromosome 22. Nature 407, 516–520.

    Article  CAS  PubMed  Google Scholar 

  51. Devlin B. and Risch N. (1995) A comparison of linkage disequilibrium measures for fine scale mapping. Genomics 29, 311–322.

    Article  CAS  PubMed  Google Scholar 

  52. Feder J.N., Gnirke A., Thomas W., Tsuchihashi Z., Ruddy D.A., Basava A., et al. (1996) A novel MHC class I-like gene is mutation in patients with hereditary haemochromatosis. Nat. Genet. 13, 399–408.

    Article  CAS  PubMed  Google Scholar 

  53. Kaplan N., Hill W.G., and Weir B.S. (1995) Likelihood methods for locating disease genes in nonequilibrium populations. Am. J. Hum. Genet. 56, 18–32.

    CAS  PubMed  Google Scholar 

  54. Devlin B., Risch N., and Roeder K. (1996) Disequilibrium mapping: composite likelihood for pairwise disequilibrium. Genomics 36, 1–16.

    Article  CAS  PubMed  Google Scholar 

  55. Lam J.C., Roeder K., and Devlin B. (2000) Haplotype fine mapping by evolutionary trees. Am. J. Hum. Genet. 66, 659–673.

    Article  CAS  PubMed  Google Scholar 

  56. Riordan J.R., Rommens J.M., Kerem B., Alon N., Rozmahel R., Grzelczak Z., et al. (1989) Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245, 1066–1073.

    Article  CAS  PubMed  Google Scholar 

  57. Rommens J.M., Iannuzzi M.C., Kerem B., Drumm M.L., Melmer G., Dean M., et al. (1989) Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245, 1059–1065.

    Article  CAS  PubMed  Google Scholar 

  58. Abecasis G.R., Nogushi E., Heinzmann A., Traherne J.A., Bhattacharyya S., Leaves N.I., et al. (2001) Extent and distortion of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68, 191–197.

    Article  CAS  PubMed  Google Scholar 

  59. Cardon L.R. and Bell J.I. (2001) Association study designs for complexd iseases. Nature Reviews, Genetics 2, 91–99.

    Article  CAS  Google Scholar 

  60. Devlin B. and Roeder K. (1999) Genomic control for association studies. Biometrics 55, 997–1004.

    Article  CAS  PubMed  Google Scholar 

  61. Cambien F., Poirier O., Lecerf L., Eans A., Cambou J.P., Arveiler D., et al. (1992) Deletion polymorphism in the gene for angiotensin-converting enzyme is a potent risk factor for myocardial infarction. Nature 359, 641–644.

    Article  CAS  PubMed  Google Scholar 

  62. Jeron A., Hengstenberg C., Engel S., Lowel H., Riegger G.A., Schunkert H., et al. (2001) The D-allele of the ACE polymorphism is related to increased QT dispersion in 609 patients after myocardial infarction. Eur. Heart J. 22, 663–668.

    Article  CAS  PubMed  Google Scholar 

  63. Keavney B., McKenzie C., Parish S., Palmer A., Clark S., Youngman L., et al. (2000) Large-scale test of hypothesized associations between the angiotensin-converting-enzyme insertion/deletion polymorphism and myocardial infarction in about 5000 cases and 6000 controls. International Studies of Infarct Survival (ISIS) Collaborators. Lancet 355, 434–442.

    CAS  PubMed  Google Scholar 

  64. Altshuler D., Hirschhorn J.N., Klannemark M., Lindgren C.M., Vohl M.C., Nemesh J., et al. (2000b) The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet. 26, 76–80.

    Article  CAS  PubMed  Google Scholar 

  65. Barcellos L.F., Klitz W., Field L.L., Tobias R., Bowcock A.M., Wilson R., et al. (1997) Associating mapping of disease loci by use of a pooled DNA genomic screen. Am. J. Hum. Genet. 61, 734–747.

    Article  CAS  PubMed  Google Scholar 

  66. Daniels J., Holmans P., Williams N., Turic D., McGuffin P., Plomin R., et al. (1998) A simple method for analyzing microsatellite allele image patterns generated from DNA pools and its application to allelic association studies. Am. J. Hum. Genet. 62, 1189–1197.

    Article  CAS  PubMed  Google Scholar 

  67. Shaw S.H., Carrasquillo M.M., Kashuk C., Puffenberger E.G., and Chakravarti A. (1998) Allele frequency distributions in poled DNA samples: applications to mapping complex disease gene. Genome Res. 8, 111–123.

    CAS  PubMed  Google Scholar 

  68. Emahazion T., Feuk L., Jobs M., Sawyer S.L., Fredman D., St. Clair D., et al. (2001) SNP association studies in Alzheimer’s disease highlight problems for complex disease analysis. Trends Genet. 17, 401–407.

    Article  Google Scholar 

  69. Jorde L.B., Watkins W.S., Carlson M., Groden J., Albertson H., Thliveris A., et al. (1994) Linkage disequilibrium predicts physical distance in the adenomatous polyposis coli region. Am. J. Hum. Genet. 54, 884–898.

    CAS  PubMed  Google Scholar 

  70. Hill W.G. and Weis B.S. (1994) Maximum-likelihood estimation of gene location by linkage disequilibrium. Am. J. Hum. Genet. 54, 705–714.

    CAS  PubMed  Google Scholar 

  71. Rubinstein P., Walker M., Carpenter C., Carrier C., Krassner J., Falk C., et al. (1981) Genetics of HLA disease association: the use of the haplotype relative risk (HRR) and the “Haplo-Delta” (Dh) estimates in juvenile diabetes from three racial groups. Hum. Immunol. 3, 384.

    Article  Google Scholar 

  72. Field L.L., Fothrgill-Payne C., Bertrams J., and Baur M.P. (1986) HLD-DR effects in a large German IDDM data set. Genet. Epidemiol. (suppl.) 1, 323–328.

    Article  CAS  Google Scholar 

  73. Falk C.T. and 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.

    Article  CAS  PubMed  Google Scholar 

  74. Khoury M.J. (1994) Case-parental control method in the search for disease-susceptibility genes. Am. J. Hum. Genet. 55, 414–415.

    CAS  PubMed  Google Scholar 

  75. Schaid D.J. and Sommer S.S. (1994) Comparison of statistics for candidate-gene association studies using cases and parents. Am. J. Hum. Genet. 55, 402–409.

    CAS  PubMed  Google Scholar 

  76. Thomson G. (1995) Mapping disease genes: family-based association studies. Am. J. Hum. Genet. 57, 487–498.

    CAS  PubMed  Google Scholar 

  77. Knapp M., Seuchter S.A., and Baur M.P. (1993) The haplotyperelative risk (HRR) method for analysis of association in nuclear families. Am. J. Hum. Genet. 52, 1085–1093.

    CAS  PubMed  Google Scholar 

  78. Ott J. (1989) Statistical properties of the haplotype relative risk. Genet. Epidemiol. 6, 127–130.

    Article  CAS  PubMed  Google Scholar 

  79. Terwilliger J.D. and Ott J. (1992) A haplotype based ‘haplotype relative risk’ approach to detecting allelic associations. Hum. Hered. 42, 337–346.

    Article  CAS  PubMed  Google Scholar 

  80. Schaid D.J. and Sommer S.S. (1993) Genotype relative risks: methods for design and analysis of candidate-gene association studies. Am. J. Hum. Genet. 53, 1114–1126.

    CAS  PubMed  Google Scholar 

  81. Spielman R.S. and Ewens W.J. (1993) Transmission/disequilibrium test (TDT) for linkage and linkage disequilibrium between disease and marker. Am. J. Hum. Genet. (suppl.) 53, 863.

    Google Scholar 

  82. Spielman R.S., McGinnis R.E., and Ewens W.J. (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52, 506–516.

    CAS  PubMed  Google Scholar 

  83. Tiret L., Nicaud V., Ehnholm C., Havekes L., Menzel H.J., Ducimetiere P., et al. (1993) Inference of the strength of genotypedisease association from studies comparing off-spring with and without parental history of disease. Ann. Hum. Genet. 57, 141–149.

    Article  CAS  PubMed  Google Scholar 

  84. Hodge S.E. (1993) Linkage analysis versus association analysis: distinguishing between two models that explain disease-marker associations. Am. J. Hum. Genet. 53, 367–384.

    CAS  PubMed  Google Scholar 

  85. Hodge S.E. (1994) Reply to Suarez and Hampe and Spielman et al.: cosegregation, association, and linkage. Am. J. Hum. Genet. 54, 560–563.

    Google Scholar 

  86. Suarez B.K. and Hampe C.L. (1994) Linkage and association. Am. J. Hum. Genet. 54, 554–559.

    CAS  PubMed  Google Scholar 

  87. Klitz W., Thomson G., Borot N., and Cambon-Thomsen A. (1992) Evolutionary and population perspective of the human HLA complex, in Evolutionary Biology (vol. 26), (Hecht M. K., ed.), Plenum, New York, NY, pp., 35–72.

    Google Scholar 

  88. Field L.L. (1989) Genes predisposing to IDDM in multiplex families. Genet. Epidemiol. 6, 101–106.

    Article  CAS  PubMed  Google Scholar 

  89. Thomson G., Robinson W.P., Kuhner M.K., Joe S., and Klitz W. (1989) HLA and insulin gene associations with IDDM. Genet. Epidemiol. 6, 155–160.

    Article  CAS  PubMed  Google Scholar 

  90. Spielman R.S., Baur M.P., and Clerget-Darpoux F. (1989) Genetic analysis of IDDM: summary of GAW 5 IDDM results. Genet. Epidemiol. 6, 43–58.

    Article  CAS  PubMed  Google Scholar 

  91. Bennet S.T., Lucassen A.M., Gough S. C., Powell E.E., Undlien D.E., Pritchard L.E., et al. (1995) Susceptibility to human type diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nat. Genet. 9, 284–292.

    Article  Google Scholar 

  92. Merriman T., Twells R., Merriman M., Eaves I., Cox R., Cucca F., et al. (1997) Evidence by allelic association-dependent methods for a type I diabetes polygene (IDDM6) on chromosome 18q21. Hum. Mol. Genet. 6, 1003–1010.

    Article  CAS  PubMed  Google Scholar 

  93. Boehnke M. and Langefeld C.D. (1998) Genetic association mapping based on discordant sib pairs: the discordant-alleles test. Am. J. Hum. Genet. 61, 319–333.

    Google Scholar 

  94. Curtis D. (1997) Use of siblings as controls in case-control association studies. Ann. Hum. Genet. 61, 319–333.

    Article  CAS  PubMed  Google Scholar 

  95. Martin E.R., Kaplan N.I., and Weir B.S. (1997) Tests for linkage and association in nuclear families. Am. J. Hum. Genet. 61, 439–448.

    Article  CAS  PubMed  Google Scholar 

  96. Sham P.C. and Curtis D. (1995) An extended transmission/disequilibrium test (TDT) for multiallelic marker loci. Ann. Hum. Genet. 59, 323–336.

    Article  CAS  PubMed  Google Scholar 

  97. Spielman R.S. and Ewens W.J. (1996) The TDT and other familybased tests for linkage disequilibirum and association (Editorial). Am. J. Hum. Genet. 59, 983–989.

    CAS  PubMed  Google Scholar 

  98. Spielman R.S. and Ewens W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am. J. Hum. Genet. 62, 450–458.

    Article  CAS  PubMed  Google Scholar 

  99. Seltman H., Roeder K., and Devlin B. (2001) Transmission/Disequilibrium Test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes. Am. J. Hum. Genet. 68, 1250–1263.

    Article  CAS  PubMed  Google Scholar 

  100. Templeton A.R. (1995) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping of DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer’s disease and the apoprotein E locus. Genetics 140, 403–409.

    CAS  PubMed  Google Scholar 

  101. Gordon D., Heath S.C., Liu X., and Ott J. (2001) A transmission/ disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data. Am. J. Hum. Genet. 69, 371–780.

    Article  CAS  PubMed  Google Scholar 

  102. Bacanu S.-A., Devlin B., and Roeder K. (2000) The power of genomic control. Am. J. Hum. Genet. 66, 1933–1944.

    Article  CAS  PubMed  Google Scholar 

  103. Clayton D.G. and Jones H. (1999) Transmission/disequilibrium tests for extended marker haplotypes. Am. J. Hum. Genet. 65, 1161–1169.

    Article  CAS  PubMed  Google Scholar 

  104. Clayton D.G. (1999) A generalization of the transmission/disequilibrium tests for uncertain-haplotype transmission. Am. J. Hum. Genet. 65, 1170–1177.

    Article  CAS  PubMed  Google Scholar 

  105. Lazzeroni L.C. and Lange K. (1998) A conditional inference framework for extending the transmission/disequilibrium test. Hum. Hered. 48, 67–81.

    Article  CAS  PubMed  Google Scholar 

  106. Merriman T.R., Eaves I.A., Twells R.C., Merriman M.E., Danoy P.A., Muxworthy C.E., et al. (1998) Transmission of haplotypes of miscrosatellite markers rather than single marker alleles in the mapping of a putative type 1 diabetes susceptibility gene (IDDM6). Hum. Mol. Genet. 7, 517–524.

    Article  CAS  PubMed  Google Scholar 

  107. Rabinowitz D. and Laird N. (2000) A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum. Hered. 50, 211–223.

    Article  CAS  PubMed  Google Scholar 

  108. Zhao H., Zhang S., Merikangas K.R., Trixter M., Wildenauer D.B., Sun F., et al. (2000) Transmission/disequilibrium tests using multiple tightly linked markers. Am. J. Hum. Genet. 67, 936–946.

    Article  CAS  PubMed  Google Scholar 

  109. Jin K., Speed T., Klitz W., and Thomson G. (1994) A statistical test of segregation distortion. Biometrics 50, 1189–1198.

    Article  CAS  PubMed  Google Scholar 

  110. Maxwell A.E. (1970) Comparing the classification of subjects by two independent judges. Br. J. Psychiatry 116, 651–655.

    Article  CAS  PubMed  Google Scholar 

  111. Rothman K.J. (1986) Modern Epidemiology, Little & Brown, Boston, MA.

    Google Scholar 

  112. Trembath R.C., Clough R.L., Rosbotham J.L., Jones A.B., Camp R.D.R., Frodsham A., et al. (1997) Identification of a major susceptibility locus on chromosome 6p and evidence for further disease loci revealed by a two stage genome-wide search in psoriasis. Hum. Mol. Genet. 6, 813–820.

    Article  CAS  PubMed  Google Scholar 

  113. George V.T. and Elston R.C. (1987) Testing the association between polymorphic markers and quantitative traits in pedigrees. Genet. Epidemiol. 4, 193–201.

    Article  CAS  PubMed  Google Scholar 

  114. Allison D.D. (1997) Transmission-disequilibrium tests for quantitative traits. Am. J. Hum. Genet. 60, 676–690.

    CAS  PubMed  Google Scholar 

  115. Rabinowitz D. (1997) A transmission disequilibrium test for quantitative trait loci. Hum. Hered. 47, 342–350.

    Article  CAS  PubMed  Google Scholar 

  116. Fulker D.W., Cherny S.S., Sham P.C., and Hewitt J.K. (1999) Combined linkage and association sib-pair analysis for quantitative traits. Am. J. Hum. Genet. 64, 259–267.

    Article  CAS  PubMed  Google Scholar 

  117. Cardon L.R. (2000) A sib-pair regression model of linkage disequilibrium for quantitative traits. Hum. Hered. 50, 350–358.

    Article  CAS  PubMed  Google Scholar 

  118. Abecasis G.R., Cardon L.R., and Cookson W.O.C. (2000) A general test of association for quantitative traits in nuclear families. Am. J. Hum. Genet. 66, 279–292.

    Article  CAS  PubMed  Google Scholar 

  119. Brookes A.J. (1999) The essence of SNPs. Gene 234, 177–186.

    Article  CAS  PubMed  Google Scholar 

  120. Kwok P.Y., Deng Q., Zakeri H., Taylor S.L., and Nickerson D.A. (1996) Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31, 123–126.

    Article  CAS  PubMed  Google Scholar 

  121. Wang D.G., Fan J.B., Siao C.J., Berno A., Young P., Sapolsky R., et al. (1988) Related articles, nucleotide large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280(5366), 1077–1082.

    Article  Google Scholar 

  122. Lander E.S. (1996) The new genomics: global views of biology. Science 274, 536–539.

    Article  CAS  PubMed  Google Scholar 

  123. Jorde L.B. (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res. 10, 1435–1444.

    Article  CAS  PubMed  Google Scholar 

  124. Kruglyak L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22, 139–144.

    Article  CAS  PubMed  Google Scholar 

  125. Risch N. and Merikangas K. (1996) Related Articles. The future of genetic studies of complex human diseases. Science 273(5281), 1516–1517.

    Article  CAS  PubMed  Google Scholar 

  126. Terwilliger J.D. and Weiss K.M. (1998) Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr. Opin. Biotechnol. 8, 578–594.

    Article  Google Scholar 

  127. Weiss K.M. and Tewilliger J.D. (2000) How many diseases does it take to map a gene with SNPs? Nat. Genet. 26, 151–157.

    Article  CAS  PubMed  Google Scholar 

  128. Bodmer W.F. (1986) Human genetics: the molecular challenge. Cold Spring Harbor Symp. Quant. Biol. 51, 1–13.

    CAS  PubMed  Google Scholar 

  129. Collins A., Lonjou C., and Morton N.E. (1999) Genetic epidemiology of single-nucleotide polymorphisms. PNAS 95, 15,173–15,177.

    Article  Google Scholar 

  130. Laan M. and Pääbo S. (1997) Demographic history and linkage disequilibrium in human populations. Nat. Genet. 17, 435–438.

    Article  CAS  PubMed  Google Scholar 

  131. Peltonen L. (2000) Positional cloning of disease genes: advantages of genetic isolates. Hum. Hered. 50, 66–75.

    Article  CAS  PubMed  Google Scholar 

  132. Jorde L.B., Watkins W.S., Kere J., Nyman D., and Eriksson A.W. (2000) Gene mapping in isolated populations: new roles for old friends? Hum. Hered. 50, 57–65.

    Article  CAS  PubMed  Google Scholar 

  133. Lonjou C., Collins A., and Morton N.E. (1999) Allelic association between marker loci. PNAS 96, 1621–1626.

    Article  CAS  PubMed  Google Scholar 

  134. Ott J. (2000) Predicting the range of linkage disequilibrium. PNAS 97, 2–3.

    Article  CAS  PubMed  Google Scholar 

  135. Brzustowicz L.M., Mérette C., Xie X., Townsend L., Gilliam T.C., and Ott J. (1993) Molecular and statistical approaches to the detection and correction of errors in genotype databases. Am. J. Hum. Genet. 53, 1137–1145.

    CAS  PubMed  Google Scholar 

  136. Ehm M.G., Kimmel M., and Cottingham R.W., Jr. (1996) Error detection for genetic data, using likelihood methods. Am. J. Hum. Genet. 58, 225–234.

    CAS  PubMed  Google Scholar 

  137. Lathrop G.M., Hooper A.B., Huntsman J.W., and Ward R.H. (1983) Evaluating pedigree data. 1. The estimation of pedigree error in the presence of marker mistyping. Am. J. Hum. Genet. 35, 241–262.

    CAS  PubMed  Google Scholar 

  138. Lincoln S.E. and Lander E.S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604–610.

    Article  CAS  PubMed  Google Scholar 

  139. Sasse G., Müller H., Chakraborty R., and Ott J. (1994) Estimating the frequency of nonpaternity in Switzerland. Hum. Hered. 44, 337–343.

    Article  CAS  PubMed  Google Scholar 

  140. Stringham H.M. and Boehnke M. (1996) Identifying marker typing incompatibilities in linkage analysis. Am. J. Hum. Genet. 59, 946–950.

    CAS  PubMed  Google Scholar 

  141. Gordon D., Heath S., and Ott J. (1999) True pedigree errors more frequent than apparent errors for single nucleotide polymorphisms. Hum. Hered. 49, 65–70.

    Article  CAS  PubMed  Google Scholar 

  142. Gordon D., Leal S.M., Heath S.C., and Ott J. (2000) An analytic solution to single nucleotide polymorphism error-detection rates in nuclear families: implications for study design. Pacific Symposium on Biocomputing 1, 663–674.

    Google Scholar 

  143. Ott J. (2001) Major strengths and weaknesses of the lod score method. Adv. Genet. 42, 125–132.

    Article  CAS  PubMed  Google Scholar 

  144. Keats B.J., Sherman S.L., and Ott J. (1990) Human gene mapping 10.5—report of the Committee on Linkage and Gene Order. Cytogenet. Cell Genet. 55, 387–394.

    Article  CAS  PubMed  Google Scholar 

  145. Broman K.W., Murray J.C., Sheffield V.C., White R.L., and Weber R.L. (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63, 861–869.

    Article  CAS  PubMed  Google Scholar 

  146. Li W., Fann C., and Ott J. (1998) Low-order polynomial trends of female-to-male map distance ratios along human chromosomes. Hum. Hered. 48, 266–270.

    Article  CAS  PubMed  Google Scholar 

  147. Cleves M.A. and Elston R.C. (1997) Alternative test for linkage between two loci. Genet. Epidemiol. 14, 117–131.

    Article  CAS  PubMed  Google Scholar 

  148. Halpern J. and Whittemore A.S. (1999) Multipoint linkage analysis. A cautionary note. Hum. Hered. 49, 194–196.

    Article  CAS  PubMed  Google Scholar 

  149. Ott J., Lehner T., and Sandkuyl L.A. (1988) Fallacies of the technique of “ahplotyping” two apparently linked loci in multipoint linkage analysis. Am. J. Hum. Genet. 43, A154.

    Google Scholar 

  150. Daw E.W., Thompson E.A., and Wijsman E.M. (2000) Bias in multipoint linkage analysis arising from map misspecification. Genet. Epidemiol. 19, 336–380.

    Article  Google Scholar 

  151. Friemer N., Sandkuijl L., and Blower S. (1993) Incorrect specification of marker allele frequencies: effects on linkage analysis. Am. J. Hum. Genet. 52, 1102–1110.

    Google Scholar 

  152. Ott J. (1992) Strategies for characterizing highly polymorphic markers in human gene mapping. Am. J. Hum. Genet. 51, 293–290.

    Google Scholar 

  153. Devlin B., Risch N., and Roeder K. (1991) Estimation of allele frequencies for VNTR loci. Am. J. Hum. Genet. 48, 662–676.

    CAS  PubMed  Google Scholar 

  154. Lange K. (1995) Applications of the Dirichlet distribution to forensic match probabilities. Genetica 96, 107–117.

    Article  CAS  PubMed  Google Scholar 

  155. Lockwood J.R., Roder K., and Devlin B. (2001) A Bayesian hierarchical model for allele frequencies. Genet. Epidemiol. 20, 17–33.

    Article  CAS  PubMed  Google Scholar 

  156. Chapman N.H. and Wijsman E.M. (1998) Genome screen using linkage disequilibrium tests: optimal marker characteristics and feasibility. Am. J. Hum. Genet. 63, 1872–1885.

    Article  CAS  PubMed  Google Scholar 

  157. Rothman K. (1990) No adjustment are needed for multiple comparisons. Epidemiology 1, 43–46.

    Article  CAS  PubMed  Google Scholar 

  158. Lander E. and Kruglyak L. (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 11, 241–247.

    Article  CAS  PubMed  Google Scholar 

  159. Witte J.S., Elston R.C., and Schork N.S. (1996) Genetic dissection of complex traits (correspondence). Nat. Genet. 12, 355–356.

    Article  CAS  PubMed  Google Scholar 

  160. Witte J.S., Elston R.C., and Cardon L.R. (2000) On the relative sample size required for multiple comparisons. Stat. Med. 19, 369–372.

    Article  CAS  PubMed  Google Scholar 

  161. Lucek P., Hanke J., Reich J., Solla S., and Ott J. (1998) Multilocus nonparametric linkage analysis of complex trait loci with neural network. Hum. Hered. 48, 275–284.

    Article  CAS  PubMed  Google Scholar 

  162. Hoh J. and Ott J. (2000) Scan statistics to scan markers for susceptibility genes. PNAS 17, 9615–9617.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Humana Press Inc.

About this protocol

Cite this protocol

Grigorenko, E.L., Pauls, D.L. (2003). Analytical Methods Applied to Psychiatric Genetics. In: Leboyer, M., Bellivier, F. (eds) Psychiatric Genetics. Methods in Molecular Medicine™, vol 77. Humana Press. https://doi.org/10.1385/1-59259-348-8:23

Download citation

  • DOI: https://doi.org/10.1385/1-59259-348-8:23

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-037-3

  • Online ISBN: 978-1-59259-348-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics