Disease Associations and Family‐Based Tests

Warren J. Ewens1, Richard S. Spielman1, Norman L. Kaplan2, Xiaoyi Gao3, Richard W. Morris3, Eden R. Martin3

1 University of Pennsylvania, Philadelphia, Pennsylvania, 2 National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 3 Miami Institute for Human Genomics, Miami, Florida
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 1.12
DOI:  10.1002/0471142905.hg0112s58
Online Posting Date:  July, 2008
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Abstract

This unit describes the statistical techniques necessary for performing family‐based association studies (such as the TDT) for genetic polymorphisms. Such studies have become increasingly important in the identification of genes that confer an increased risk to disease, particularly for common diseases with a complex etiology. The family‐based approach avoids some of the problems often encountered when applying the traditional case‐control design to genetic studies. The unit includes the Sib TDT (S‐TDT) method, which allows application of the principle of the TDT to sibships without parental data, and several related tests. Curr. Protoc. Hum. Genet. 58:1.12.1‐1.12.24. © 2008 by John Wiley & Sons, Inc.

Keywords: genetic association; genetic linkage; linkage disequilibrium; TDT

     
 
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Table of Contents

  • Introduction
  • Key Concepts
  • Case‐Control Design: Disease Association in Population‐Based Samples
  • Population Structure
  • Family‐Based Tests of Association and the Haplotype Relative Risk
  • Family‐Based Tests of Linkage: The TDT
  • Family‐Based Tests of Association: The TDT and other Tests
  • Generalizing the TDT: More than Two Marker Alleles
  • Tests of Association Using Marker Haplotypes
  • The Sib TDT (S‐TDT)
  • Pedigrees
  • Family‐Based Tests of Association for Continuous Traits
  • Family‐Based Tests for Gene‐Gene and Gene‐Environment Interactions
  • Family‐Based Tests for Genome‐Wide Association
  • Literature Cited
  • Tables
     
 
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Materials

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Literature Cited

   Abecasis, G.R., Cookson, W.O.C., and Cardon, L.R. 2000. Pedigree tests of transmission disequilibrium. Eur. J. Hum. Genet. 8:545‐551.
   Allison, D.B. 1997. Transmission‐disequilibrium tests for quantitative traits. Am. J. Hum. Genet. 60:676‐690.
   Allison, D.B., Heo, M., Kaplan, N., and Martin, E.R. 1999. Sibling‐based tests of linkage and association for quantitative trials. Am. J. Hum. Genet. 64:1754‐1764.
   Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289‐300.
   Boehnke, M. and Langefeld, C.D. 1998. Genetic association mapping based on discordant sib pairs: The discordant‐alleles test. Am. J. Hum. Genet. 62:950‐961.
   Camp, N.J. 1997. Genome‐wide transmission/disequilibrium testing: Consideration of the genotypic relative risks at disease loci. Am. J. Hum. Genet. 61:1424‐1430.
   Camp, N.J. 1999. Genome‐wide transmission/disequilibrium testing: A correction. Am. J. Hum. Genet. 64:1485‐1487.
   Chen, W.M. and Deng, H.W. 2001. A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes. Genet. Epidemiol 21:53‐67.
   Chen W.M. and Abecasis, G.R. 2007. Family‐based association tests for genomewide association scans. Am. J Hum. Genet. 81:913‐926.
   Chung, R.H., Hauser, E.R., and Martin, E.R. 2006. The APL test: Extension to general nuclear families and haplotypes and examination of its robustness. Hum. Hered. 61:189‐199.
   Clayton, D. 1999. A generalization of the transmission/disequilibrium test for uncertain‐haplotype transmission. Am. J. Hum. Genet. 65:1170‐1177.
   Cleves, M.A., Olson, J.M., and Jacobs, K.B. 1997. Exact transmission‐disequilibrium tests with multiallelic markers. Genet. Epidemiol. 14:337‐348.
   Collins, F.S., Guyer M.S., and Chakravarti, A. 1997. Variations on a theme: Cataloging human DNA‐sequence variation. Science 258:1580‐1581.
   Croiseau, P., Genin, E., Gordell, H.J. 2007. Dealing with missing data in family‐based association studies: A multiple imputation approach. Hum. Hered. 63:229‐238.
   Culverhouse, R., Klein, T., and Shannon, W. 2004. Detecting epistatic interactions contributing to quantitative traits. Genet. Epidemiol. 27:141‐152.
   Curtis, D.R. 1997. Use of siblings as controls in case‐control association studies. Ann. Hum. Genet. 61:319‐333.
   Curtis, D. and Sham, P.C. 1995. A note on the application of the transmission disequilibrium test when a parent is missing. Am. J. Hum. Genet. 56:811‐812.
   Dempster, A.P., Laird, N.M., and Rubin, D.B. 1977. Maximum likelihood from incomplete data via the EM algorithm (with discussion). J. R. Stat. Soc. B. B39:1‐38.
   Devlin, B. and Roeder, K. 1999. Genomic control for association studies. Biometrics 55:997‐1004.
   Devlin, B., Roeder, K., and Bacanu, S.A. 2001. Unbiased methods for population‐based association studies. Genet. Epidemiol. 21:273‐284.
   Duffy, D.L. 1995. Screening a 2 cM genetic map for allelic association: A simulated oligogenic trait. Genet. Epidemiol. 12:595‐600.
   Ewens, W.J. and Spielman, R.S. 1995. The transmission/disequilibrium test: History, subdivision and admixture. Am. J. Hum. Genet. 57:455‐464.
   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.
   Fallin, D., Cohen, A., Essioux, L., Chumakov, I., Blumenfeld, M., Cohen, D., and Schork, N.J. 2001. Genetic analysis of case/control data using estimated haplotype frequencies: Application to APOE locus variation and Alzheimer′s disease. Genome Res. 11:143‐151.
   Feng, T., Zhang, S.L., and Sha, Q. 2007. Two‐stage association tests for genome‐wide association studies based on family data with arbitrary family structure. Eur. J. Hum. Genet. 15:1169‐1175.
   Guo, C.Y., Lunetta, K.L., DeStefano, A.L., Ordovas, J.M., and Cupples, L.A. 2007. Informative‐transmission disequilibrium test (i‐TDT): Combined linkage and association mapping that includes unaffected offspring as well as affected offspring. Genet. Epidemiol. 31:115‐133.
   Harley, J.B., Moser, K.L., and Neas, B.R. 1995. Logistic transmission modeling of simulated data. Genet. Epidemiol. 12:607‐612.
   Hartl, D.L. and Clark, A.G. 1997. Principles of Population Genetics, 3rd ed. Sinauer Associates, Inc. Sunderland, Mass.
   Hill, W.G. and Robertson, A. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38:226‐231.
   Horne, B.D. 2007. Genetic association studies and false discoveries. J. Am. Med. Assoc. 297:2477‐2478.
   Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W., and Lee, C. 2004. Detection of large‐scale variation in the human genome. Nat. Genet. 36:949‐951.
   Kaplan, N.L., Martin, E.R., and Weir, B.S. 1997. Power studies for the transmission/disequilibrium test with multiple alleles. Am. J. Hum. Genet. 60:691‐702.
   Kaplan, N.L. and Martin, E.R. 2001. Power calculations for a general class of tests of linkage and association that use nuclear families with affected and unaffected sibs. Theor. Popul. Biol. 60:193‐201.
   Kimmel, G., Jordan, M.I., Halperin, E., Shamir, R., and Karp, R.M. 2007. A randomization test for controlling population stratification in whole‐genome association studies. Am. J. Hum. Genet. 81:895‐905.
   Knapp, M. 1999. The transmission/disequilibrium test and parental‐genotype reconstruction: The reconstruction‐combined transmission/disequilibrium test. Am. J. Hum. Genet. 64:861‐870.
   Laird, N.M. and Lange, C. 2006. Family‐based designs in the age of large‐scale gene‐association studies. Nat. Rev. Genet. 7:385‐94.
   Lake, S.L., Blacker, D., and Laird, N.M. 2000. Family‐based tests of association in the presence of linkage. Am. J. Hum. Genet. 67:1515‐1525.
   Lander, E.S. and Kruglyak, L. 1995. Genetic dissection of complex traits: Guidelines for interpreting linkage results. Nature Genet. 11:241‐247.
   Lange, C., DeMeo, D.L., and Laird, N.M. 2002. Power and design considerations for a general class of family‐based association tests: Quantitative traits. Am. J. Hum. Genet. 71:1330‐1341.
   Lazzeroni, L.C. and Lange, K. 1998. A conditional inference framework for extending the transmission/disequilibrium test. Hum. Hered. 48:67‐81.
   Lewontin, R.C. 1964. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49‐67.
   Lou, X.Y., Chen, G.B., Yan, L., Ma, J.Z., Zhu, J., Elston, R.C., and Li, M.D. 2007. A generalized combinational approach for detecting gene‐by‐gene and gene‐by‐environment interactions with application to nicotine dependence. Am. J. Hum. Genet. 80:1125‐1137.
   Marchini, J., Cardon, L.R., Phillips, M.S., and Donnelly, P. 2004. The effects of human population structure on large genetic association studies. Nat. Genet. 36:512‐517.
   Martin, E.R., Kaplan N.L., and Weir, B.S. 1997. Tests for linkage and association in nuclear families. Am. J. Hum. Genet. 61:439‐448.
   Martin, E.R., Monks S.A., Warren L.L., and Kaplan, N.L. 2000. A test for linkage and association in general pedigrees: The pedigree disequilibrium test. Am. J. Hum. Gen. 67:146‐154.
   Martin, E,R., Bass, M.P., and Kaplan, N.L. 2001. Correcting for a potential bias in the pedigree disequilibrium test. Am. J. Hum. Gen. 68:1065‐1067.
   Martin, E.R., Bass, M.P., Hauser, E.R., and Kaplan, N.L. 2003. Accounting for linkage in family‐based tests of association with missing parental genotypes. Am. J. Hum. Genet. 73:1016‐1026.
   Martin, E.R., Ritchie, M.D., Hahn, L., Kang, S., and Moore, J.H. 2006. A novel method to identify gene‐gene effects in nuclear families: The MDR‐PDT. Genet. Epidemiol. 30:111‐123.
   Martin, L.J., Woo, J.G., Avery, C.L., Chen, H.S., and North, K.E. 2007. Multiple testing in the genomics era: Findings from Genetic Analysis Workshop 15, Group 15 (p S124‐S131). Genet. Epidemiol. 31:S124‐S131.
   McCarroll, S.A. and Altshuler, D.M. 2007. Copy‐number variation and association studies of human disease. Nat Genet. 39:S37‐42.
   McIntyre, L.M., Martin, E.R., Simonsen, K., and Kaplan, N.L. 2000. Circumventing the multiple testing problem: A multilocus transmission/disequilibrium test. Genet. Epidemiol. 19:18‐29.
   Mei, H., Cuccaro, M.L., Martin, E.R. 2007. Multifactor dimensionality reduction‐phenomics: A novel method to capture genetic heterogeneity with use of phenotypic variables. Am. J. Hum. Genet. 81:1251‐1261.
   Monks, S.A. and Kaplan, N.L. 2000. Removing the sampling restrictions from family‐based tests of association for a quantitative‐trait locus. Am. J. Hum. Genet. 66:576‐592.
   Monks, S.A., Kaplan, N.L., and Weir, B.S. 1998. A comparative study of sibship tests of linkage and/or association. Am. J. Hum. Genet. 63:1507‐1516.
   Morton, N.E. 1955. Sequential tests for the detection of linkage. Am. J. Hum. Genet. 7:277‐318.
   Nelson, M.R., Kardia, S.L.R., Ferrell, R.E., and Sing, C.F. 2001. A combinatorial partitioning method (CPM) to identify multi‐locus genotypic partitions that predict quantitative trait variations. Genome. Res. 11:458‐470.
   Nguyen, D.Q., Webber, C., and Ponting, C.P. 2006. Bias of selection on human copy‐number variants. PLoS Genet. 2:e20.
   Ott, J. 1989. Statistical properties of the haplotype relative risk. Genet. Epidemiol. 6:127‐130.
   Parsian, A., Todd, R.D., Devor, E.J., O'Malley, K.L., Suarez, B.K., Reich, T., and Cloninger, C.R. 1991. Alcoholism and alleles of the human D2 dopamine receptor locus. Arch. Gen. Psychiatry 48:655‐663.
   Patterson, N., Price, A.L., and Reich, D. 2006. Population structure and eigenanalysis. PLoS Genet. 2006 2:e190.
   Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., and Reich, D. 2006. Principal components analysis corrects for stratification in genome‐wide association studies. Nat. Genet. 38:904‐909.
   Pritchard, J.K. and Rosenberg, N.A. 1999. Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65:220‐228.
   Pritchard, J.K., Stephens, M., Rosenberg, N.A., and Donnelly, P. 2000. Association mapping in structured populations. Am. J. Hum. Genet. 67:170‐181.
   Rabinowitz, D. 1997. A transmission disequilibrium test for quantitative trait loci. Hum. Hered. 47:342‐350.
   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.
   Reich, D.E., Cargill, M., Stacey, B., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R., and Lander, E.S. 2001. Linkage disequilibrium in the human genome. Nature 411:199‐204.
   Risch, N. and Merikangas, K. 1996. The future of genetic studies of complex human diseases. Science 273:1516‐1517.
   Risch, N. and Merikangas, K. 1997. Genetic analysis of complex diseases. Science 275:1329‐1330.
   Ritchie, M.D., Hahn, L.W., Roodi, N., Bailey, L.R., Dupont, W.D., Parl, F.F., and Moore, J.H. 2001. Multifactor‐dimensionality reduction reveals high‐order interactions among estrogen‐metabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69:138‐147.
   Satten, G.A., Flanders, W.D., and Yang, Q. 2001. Accounting for unmeasured population substructure in case‐control studies of genetic association using a novel latent‐class model. Am. J. Hum. Genet. 68:466‐477.
   Schaid, D.J. 1996. General score tests for associations of genetic markers with disease using cases and their parents. Genet. Epidemiol. 13:423‐450.
   Schaid, D.J. 1999. Case‐parents design for gene‐environment interaction. Genet. Epidemiol. 16:261‐273.
   Schaid, D.J. and Li, H. 1997. Genotype relative‐risks and association tests for nuclear families with missing parental data. Genet. Epidemiol. 14:1113‐1118.
   Schaid, D.J. and Rowland, C. 1998. Use of parents, sibs, and unrelated controls for detection of associations between genetic markers and disease. Am. J. Hum. Genet. 63:1492‐1506.
   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.
   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.
   Schaid, D.J., Rowland, C.M., Tines, D.E., Jacobson, R.M., and Poland, G.A. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet. 70:425‐434.
   Schneiter, K., Laird, N., and Corcoran, C. 2005. Exact family‐based association tests for biallelic data. Genet. Epidemiol. 29:185‐194.
   Schneiter, K., Degnan, J.H., Corcoran, C., Xu, X., and Laird, N. 2007. EFBAT: Exact family‐based association tests. BMC Genet. 8:86.
   Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T.C., Trask, B., Patterson, N., Zetterberg, A., and Wigler, M. 2004. Large‐scale copy number polymorphism in the human genome. Science 305:525‐528.
   Sham, P.C. and Curtis, D. 1995. An extended transmission/disequilibrium test (TDT) for multi‐allelic marker loci. Ann. Hum. Genet. 59:323‐336.
   Shih, M.C. and Whittemore, A.S. 2002. Tests for genetic association using family data. Genet. Epidemiol. 22:128‐145.
   Siegmund, K.D., Langholz, B., Kraft, P., and Thomas, D.C. 2000. Testing linkage disequilibrium in sibships. Am. J. Hum. Genet. 67:244‐248.
   Smith, C.A.B. 1953. Detection of linkage in human genetics (with discussion). J. R. Stat. Soc. B 15:153‐192.
   Smith, N.L., Hindorff, L.A., Heckbert, S.R., Lemaitre, R.N., Marciante, K.D., Rice, K., Lumley, T., Bis, J.C., Wiggins, K.L., Rosendaal, F.R., and Psaty, B.M. 2007. Association of genetic variations with nonfatal venous thrombosis in postmenopausal women. J. Am. Med. Assoc. 297:489‐498.
   Spielman, R.S. and Ewens, W.J. 1996. The TDT and other family‐based tests for linkage disequilibrium and association. Am. J. Hum. Genet. 59:983‐989.
   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.
   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. Am. J. Hum. Genet. 52:506‐516.
   Storey, J.D. 2002. A direct approach to false discovery rates. J. R. Stat. Soc. B. 64:479‐498.
   Stranger, B.E., Forrest, M.S., Dunning, M., Ingle, C.E., Beazley, C., Thorne, N., Redon, R., Bird, C.P., de Grassi, A., Lee, C., Tyler‐Smith, C., Carter, N., Scherer, S.W., Tavaré, S., Deloukas, P., Hurles, M.E., and Dermitzakis, E.T. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848‐853.
   Teng, J. and Risch, N. 1999. The relative power of family‐based and case‐control designs for linkage disequilibrium studies of complex human diseases. II. Individual genotyping. Genome Res. 9:234‐241.
   Terwilliger, J.D. 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.
   Thomson, G.J. 1995. Mapping disease genes: Family‐based association studies. Am. J. Hum. Genet. 57:487‐498.
   Tu, I.P. and Whittemore, A.S. 1999. Power of association and linkage tests when the disease alleles are unobserved. Am. J. Hum. Genet. 64:641‐649.
   Umbach, D.M. and Weinberg, C. 2000. The use of case‐parent triads to study joint effects of genotype and exposure. Am. J. Hum. Genet. 66:251‐261.
   Van Steen, K., McQueen, M.B., Herbert, A., Raby, B., Lyon, H., DeMeo, D.L., Murphy, A., Su, J., Datta, S., Rosenow, C., Christman, M., Silverman, E.K., Laird, N.M., Weiss, S.T., and Lange, C. 2005. Genomic screening and replication using the same data set in family‐based association testing. Nat. Genet. 37:683‐691.
   Weinberg, C. 1999. Allowing for missing parents in genetic studies of case‐parent triads. Am. J. Hum. Genet. 64:1186‐1193.
   Weinberg, C.R., Wilcox, A.J., and Lie, R.T. 1998. A log‐linear approach to case‐parent‐triad data: Assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting. Am. J. Hum. Genet. 62:969‐978.
   Weller, J.I., Song, J.Z., Heyen, D.W., Lewin, H.A., and Ron, M. 1998. A new approach to the problem of multiple comparisons in the genetic dissection of complex traits. Genetics 150:1699‐1706.
   Whittaker, J.C. and Lewis, C.M. 1998. The effect of family structure on linkage tests using allelic association. Am. J. Hum. Genet. 63:889‐897.
   Witte, J.S., Gauderman, W.J., and Thomas, D.C. 1999. Asymptotic bias and efficiency in case‐control studies of candidate genes and gene‐environment interactions: Basic family designs. Am. J. Epidemiol. 149:693‐705.
   Zaykin, D.V., Young, S.S., and Westfall, P.H. 2000. Using the false discovery rate approach in the genetic dissection of complex traits: A response to Weller et al. Genetics 154:1917‐1918.
   Zhang, Z., Zhang, S., and Sha, Q. 2007. A multi‐marker test based on family data in genome‐wide association study. BMC Genetics 8:65.
   Zhao, J.H., Curtis, D., and Sham, P.C. 2000. Model‐free analysis and permutation tests for allelic associations. Hum. Hered. 50:133‐139.
Internet Resources
   http://www.mihg.org/
  Software for PDT, MDR‐PDT, and APL.
   http://www.biostat.harvard.edu/∼fbat/default.html
  FBAT software.
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