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Mapping Genes for Common Diseases: Statistical Planning, Power, Efficiency and Informatics

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Molecular Genetic Epidemiology — A Laboratory Perspective

Part of the book series: Principles and Practice ((PRINCIPLES))

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Abstract

After a decade or so of progress with the identification of major genes, the emphasis has shifted towards genes for common diseases (complex traits). Real successes have been few so far. There has been a gradual appreciation of the difficulties presented by genes that have a relatively small individual phenotypic effect and which may show complex interactions. Furthermore, there may be different genetic determinants of the disease in different populations together with environmental effects and practical difficulties in obtaining sufficiently large samples of suitable material for analysis. At the same time, analytical methods have been in flux with many new tests and variations on existing methods appearing in the literature. The choice of analytical strategy is determined to a large extent by the nature of the disease and the DNA resources that can be obtained. Some assessment of power to detect a genetic locus can be useful; however, this may be of limited value given the ignorance of the nature of the genetic basis of the disease. Consideration of the efficiency of different approaches is also important and careful statistical planning should be undertaken.

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References

  • Allison DB (1997) Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet 60:676–690

    PubMed  CAS  Google Scholar 

  • Chakravarti A (1999) Population genetics — making sense out of sequence. Nat Genet Suppl 21:56–60

    Article  CAS  Google Scholar 

  • Collins A (1999) Mapping in the sequencing era. Hum Hered 50:76–84

    Article  Google Scholar 

  • Collins A, Morton NE (1995) Nonparametric tests for linkage with dependent sib-pairs. Hum Hered 45:311–318

    Article  PubMed  CAS  Google Scholar 

  • Collins A, MacLean CJ, Morton NE (1996) Trials of the ß model for complex inheritance. Proc Natl Acad Sci USA 93:9177–9181

    Article  PubMed  CAS  Google Scholar 

  • Collins A, Ennis S, Tapper W, Morton NE (2000) Mapping oligogenes for atopy and asthma by meta-analysis. Genet Mol Biol 23:1–10

    Article  CAS  Google Scholar 

  • Collins A, Morton NE (1998) Mapping a disease locus by allelic association. Proc Natl Acad Sci USA 95:1741–1745

    Article  PubMed  CAS  Google Scholar 

  • Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L, Fearon E, Hartwelt L, Langley CH, Mathies RA, Olson M, Pawson AJ, Pollard T, Williamson A, Wold B, Buetow K, Branscomb E, Capecchi M, Church G, Garner J, Gibbs RA, Hawkins T, Hodgson K, Knotek M, Meisler M, Rubin GM, Smith LM, Smith RF, Westerfield M, Clayton EW, Fisher NL, Lerman CE, Mclnerney JD, Nebo W, Press N, Valle D (1998) New goals for the US Human Genome Project. Science 282:682–689

    Article  PubMed  CAS  Google Scholar 

  • Cox NJ, Spielman R (1989) The insulin gene and susceptibility to IDDM. Genet Epidemiol 6:65–69

    Article  PubMed  CAS  Google Scholar 

  • Davies JL, Kamaguchi Y, Bennett ST, Copeman JB, Cordell HJ, Pritchard LE, Reed PW, Gough SCL, Jenkins SC, Palmer SM, Balfour KM, Rowe BR, Farrall M, Barnett AH, Bain SC, Todd JA (1994) A genome-wide search for human type-1 diabetes susceptibility genes. Nature 371:130–136

    Article  PubMed  CAS  Google Scholar 

  • Gusella JF, Wexler NS, Conneally PM, Naylor SL, Anderson MA, Tanzi RE, Watkins PC, Ottina K, Wallace MR, Sakaguchi AY, Young AB, Shoulson I, Bonilla E, Martin JB (1983) A polymorphic DNA marker genetically linked to Huntington’s disease. Nature 306:234–238

    Article  PubMed  CAS  Google Scholar 

  • Holmans P (1993) Asymptotic properties of affected sib-pair linkage analysis. Am J Hum Genet 12:362–374

    Google Scholar 

  • Kerem BS, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui L-C (1989) Identification of the cystic fibrosis gene — genetic analysis. Science 245:1073–1080

    Article  PubMed  CAS  Google Scholar 

  • Kruglyak L, Daly MJ, Lander ES (1995) Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping. Am J Hum Genet 56:519–527

    PubMed  CAS  Google Scholar 

  • Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES (1996) Parametric and non-parametric linkage analysis: a unified approach. Am J Hum Genet 58:1347–1363

    PubMed  CAS  Google Scholar 

  • Lander ES, Kryglyak L (1995) Genetic dissection of complex traits. Guidelines for interpreting and reporting linkage results. Nat Genet 11:241

    Article  PubMed  CAS  Google Scholar 

  • Lathrop GM, Lalouel JM, Julier C, Ott J (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 81:3443–3446

    Article  PubMed  CAS  Google Scholar 

  • Lio P, Morton NE (I997) Comparison of parametric and nonparametric methods to map oligogenes by linkage. Proc Natl Acad Sci USA 94:5344–5348

    Article  Google Scholar 

  • Lonjou C, Collins A, Ajioka RS, Jorde LB, Kushner JP, Morton NE (1998) Allelic association under map error and recombinational heterogeneity: a tale of two sites. Proc Natl Acad Sci USA 95:11366–11370

    Article  PubMed  CAS  Google Scholar 

  • Lonjou C, Collins A, Ennis S, Tapper W, Morton NE (1999) Meta-analysis and retrospective collaboration: two methods to map oligogenes for atopy and asthma. Clin Exp Allergy 29 [suppl 4]:57–59

    PubMed  CAS  Google Scholar 

  • MacDonald ME, Novelletto A, Lin C, Tagle D, Barnes G, Bates G, Taylor S, Allitto B, Altherr M, Myers R, Lehrach J, Collins FS, Wasmuth JJ. Frontali M, Gusella JF (1992) The Huntingtonsdisease candidate region exhibits many different haplotypes. Nat Genet 1:99–103

    Article  PubMed  CAS  Google Scholar 

  • Malecot G (1948) Les mathérnatiques de l’heredité, Maison and Cie, Paris

    Google Scholar 

  • Marsh DG, Maestri NE, Freidhoff LR, Barnes KC, Togias A, Ehrlich E, Beaty T, Duffy D, Rosenthal R, Imani F, Dunston G, Furbert-Harris P, Malveaux F, Ober C, Cox NJ, Lester LA, Peterson R, Gidley H, Pluzhnikov A, Anderson J, Solway J, Leff A, Wolf R, Wylam M, Kurtz B, Richardson A, Parry R, Blumenthal MN, King RA, Oetting W, Drury D, Rosenberg A, Daniels L, McEvor C, Lou J, Hamra M, Brott M, Rich SS, Spray BJ, Weber JL, Yuan B, Wang ZY, Bleecker ER, Amelung P, Rechstiner B, Meyers DA, Samet J, Wiesch D, Xu JF, Murphy S, Banks-Schlegel S (1997) A genome-wide search for asthma susceptibility loci in ethnically diverse populations. Nat Genet 15:389–392

    Google Scholar 

  • Morton NE (1995) Sequential tests for the detection of linkage. Am J Hum Genet 7:277–318

    Google Scholar 

  • Morton NE (1996) Logar ithm of odds (lods) for linkage in complex inheritance. Proc Natl Acad Sci USA 93:3471–3476

    Article  PubMed  CAS  Google Scholar 

  • Morton NE (1998) Significance levels in complex inheritance. Am J Hum Genet 62:690–697

    Article  PubMed  CAS  Google Scholar 

  • Morton NE, Collins A (1998) Tests and est imates of allelic association in complex inheritance. Proc Natl Acad Sci USA 95:11389–11393

    Article  PubMed  CAS  Google Scholar 

  • Morton NE, Shields DC, Collins A (1991) Genetic epidemiology of complex phenotypes. Ann Hum Genet 55:301–314

    Article  PubMed  CAS  Google Scholar 

  • Ott J (1991) Analysis of human genetic linkage. John Hopkins University Press, Baltimore

    Google Scholar 

  • Risch N (1990) Linkage strategies for genetically complex traits. 1. Multilocus models. Am J Hum Genet 46:222–228

    PubMed  CAS  Google Scholar 

  • Risch N, Zhang HP (1995) Extreme discordant sib-pairs for mapping quantitative trait loci in humans. Science 268:1584–1589

    Article  PubMed  CAS  Google Scholar 

  • Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C, Farber CM, Saragosti S, Lapoumeroulie C, Cognaux T, Forceille C, Muyldermans G, Verhofstede C, Burtonboy G, Georges M, Imai T, Rana S, Yi YJ, Smyth RJ, Collman RG, Doms RW, Vassart G, Partmentier M (1996) Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chernokine receptor gene. Nature 382:722–725

    Article  PubMed  CAS  Google Scholar 

  • Spielman RS, Ewens WI (1996) The TDT and other family-based tests for linkage disequilibrium and association. Am I Hum Genet 59:983–989

    CAS  Google Scholar 

  • Spielman RS, Ewens WI (1998) A sibship test for linkage in the presence of association: the sib transmission-disequilibrium test. Am I Hum Genet 62:450–458

    Article  CAS  Google Scholar 

  • Suarez BH, Hodge SE (I979) A simple method to detect linkage for rare recessive diseases: an application to juvenile diabetes. Clin Genet 15:126–136

    Article  Google Scholar 

  • Wilkinson I, Grimley S, Collins A, Thomas NS, Holgate ST, Morton NE (1998) Linkage of asthma to markers on chromosome 12 in a sample of 240 families using quantitative phenotype scores. Genomics 53:251–259

    Article  PubMed  CAS  Google Scholar 

  • Williams JT, Blangero J (1999) Comparison of variance components with sib pair based approaches to quantitative trait linkage analysis in unselected samples. Genet Epiderniol 16:113–134

    Article  CAS  Google Scholar 

  • Wilson AF, Elston RC (1993) Statistical validity of the Haseman-Elston sib-pair test in small samples. Genet Epiderniol 10:593–598

    Article  CAS  Google Scholar 

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© 2002 Springer-Verlag Berlin Heidelberg

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Collins, A. (2002). Mapping Genes for Common Diseases: Statistical Planning, Power, Efficiency and Informatics. In: Day, I.N.M. (eds) Molecular Genetic Epidemiology — A Laboratory Perspective. Principles and Practice. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56207-5_1

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  • DOI: https://doi.org/10.1007/978-3-642-56207-5_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-41387-5

  • Online ISBN: 978-3-642-56207-5

  • eBook Packages: Springer Book Archive

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