On the Significance of Linkage Studies of Complex Traits: Reply to Newton-Cheh et al.

To the Editor:Newton-Cheh et al. (2004xOn the significance of linkage studies of complex traits. Newton-Cheh, C, Larson, M, Kathiresan, S, and O'Donnell, C. Am J Hum Genet. 2004; 75: 151–152Abstract | Full Text | Full Text PDF | PubMedSee all References2004 [in this issue]) raise the issue of some methodological concerns in our genomewide-scan study that identified significant linkage on chromosome 1p34-36 for premature myocardial infarction (MI). We would like to systematically address their concerns. First, we do explicitly report that the genomewide significance for the chromosome 1p34-36 linkage as P<.05 (P=.030–.038), derived from Wiltshire et al. (2002xEvaluating the results of genomewide linkage scans of complex traits by locus counting. Wiltshire, S, Cardon, LR, and McCarthy, MI. Am J Hum Genet. 2002; 71: 1175–1182Abstract | Full Text | Full Text PDF | PubMed | Scopus (65)See all References2002). This point was duly emphasized in the abstract and the “Results” and “Discussion” sections (Wang et al. 2004xPremature myocardial infarction novel susceptibility locus on chromosome 1P34-36 identified by genomewide linkage analysis. Wang, Q, Rao, S, Shen, G-Q, Li, L, Moliterno, DJ, Newby, LK, Rogers, WJ, Cannata, R, Zirzow, E, Elston, RC, and Topol, EJ. Am J Hum Genet. 2004; 74: 262–271Abstract | Full Text | Full Text PDF | PubMed | Scopus (142)See all References2004). Second, with respect to the high number of loci with asymptotic P values (pP) that were suggestive of linkage, we performed permutation tests and reported empirical P values. As we reported, only the chromosome 1p34-36 locus fulfilled the criteria of genomewide significance. Third, MI is a dichotomous phenotype. Either patients have an MI or do not have this acute ischemic event. As reported by Altmuller et al. (2001xGenomewide scans of complex human diseases: true linkage is hard to find. Altmuller, J, Palmer, LJ, Fischer, G, Scherb, H, and Wjst, M. Am J Hum Genet. 2001; 69: 936–950Abstract | Full Text | Full Text PDF | PubMed | Scopus (378)See all References2001), studies of 101 genomewide scans in 31 different diseases revealed that quantitative “intermediate” traits did not have any advantages over dichotomous traits for linkage analysis. Furthermore, several methodological investigations indicated that, in practice, treatment of ordinal (or binary) data as continuous with standard linear models for genetic mapping of categorical traits is feasible, with marginal loss of statistical powers (Hackett and Weller 1995xGenetic mapping of quantitative trait loci for traits with ordinal distributions. Hackett, CA and Weller, JI. Biometrics. 1995; 51: 1252–1263Crossref | PubMed | Scopus (57)See all References1995; Rao and Xu 1998xMapping quantitative trait loci for ordered categorical traits in four-way crosses. Rao, S and Xu, S. Heredity. 1998; 81: 214–224Crossref | PubMedSee all References1998; Rao and Li 2000xStrategies for genetic mapping of categorical traits. Rao, S and Li, X. Genetica. 2000; 109: 183–197Crossref | PubMed | Scopus (13)See all References2000; Rebai 2000xComparison of methods for regression interval mapping in QTL analysis with non-normal traits. Rebai, A. Genet Res. 2000; 69: 69–74Crossref | Scopus (63)See all References2000). Fourth, we did indeed use permutation testing, and it was a significant computational burden. In addition, the results of genomewide significance fully incorporated the criteria as set forth by Wiltshire et al. (2002xEvaluating the results of genomewide linkage scans of complex traits by locus counting. Wiltshire, S, Cardon, LR, and McCarthy, MI. Am J Hum Genet. 2002; 71: 1175–1182Abstract | Full Text | Full Text PDF | PubMed | Scopus (65)See all References2002). Fifth, the fine-mapping study is ongoing; we agree that the 10-cM analysis will not maximally extract the identity-by-descent information. Since two markers at the chromosome 1p34-36 locus showed asymptotic multipoint P values of <10−12, it is unlikely that further fine mapping will be informative for confirming the finding of this positive linkage. Beyond fine mapping, the most convincing evidence of linkage will be the replication of our findings in an independent population. Sixth, our primary analysis was for both premature MI and coronary artery disease (CAD). No additional subgroups were analyzed by phenotype.Our population has the most restrictive demographic features of any cohort with CAD to date (Pajukanta et al. 2000xTwo loci on chromosomes 2 and X for premature coronary heart disease identified in early- and late-settlement populations of Finland. Pajukanta, P, Cargill, M, Viitanen, L, Nuotio, I, Kareinen, A, Perola, M, Terwilliger, JD, Kempas, E, Daly, M, Lilja, H, Rioux, JD, Brettin, T, Viikari, JSA, Ronnemaa, T, Laakso, M, Lander, ES, and Peltonen, L. Am J Hum Genet. 2000; 67: 1481–1493Abstract | Full Text | Full Text PDF | PubMed | Scopus (126)See all References2000; Francke et al. 2001xA genome-wide scan for coronary heart disease suggests in Indo-Mauritians a susceptibility locus on chromosome 16p13 and replicates linkage with the metabolic syndrome on 3q27. Francke, S, Manraj, M, Lacquemant, C, Lecoeur, C, Lepretre, F, Passa, P, Hebe, A, Corset, L, Yan, SL, Lahmidi, S, Jankee, S, Gunness, TK, Ramjuttun, US, Balgobin, V, Dina, C, and Froguel, P. Hum Mol Genet. 2001; 10: 2751–2765Crossref | PubMedSee all References2001; Broeckel et al. 2002xA comprehensive linkage analysis for myocardial infarction and its related risk factors. Broeckel, U, Hengstenberg, C, Mayer, B, Holmer, S, Martin, LJ, Comuzzie, AG, Blangero, J, Nurnberg, P, Reis, A, Riegger, GA, Jacob, HJ, and Schunkert, H. Nat Genet. 2002; 30: 210–214Crossref | PubMed | Scopus (251)See all References2002; Harrap et al. 2002xGenome-wide linkage analysis of the acute coronary syndrome suggests a locus on chromosome 2. Harrap, SB, Zammit, KS, Wong, ZY, Williams, FM, Bahlo, M, Tonkin, AM, and Anderson, ST. Arterioscler Thromb Vasc Biol. 2002; 22: 874–878Crossref | PubMed | Scopus (101)See all References2002; Wang et al. 2004xPremature myocardial infarction novel susceptibility locus on chromosome 1P34-36 identified by genomewide linkage analysis. Wang, Q, Rao, S, Shen, G-Q, Li, L, Moliterno, DJ, Newby, LK, Rogers, WJ, Cannata, R, Zirzow, E, Elston, RC, and Topol, EJ. Am J Hum Genet. 2004; 74: 262–271Abstract | Full Text | Full Text PDF | PubMed | Scopus (142)See all References2004) (table 1table 1). (Not only were our patients the youngest, probably representing the most aggressive phenotype, but the exclusion of other important risk factors, such as insulin-dependent diabetes mellitus or significant hypercholesterolemia, also helped define a cohort with the highest likelihood of genetic underpinning.) Although it is true that our findings of a chromosome 1p locus are not concordant with those of the other four genomewide scans (table 1table 1), our population of young Americans is unique, and it is noteworthy that three of the other four studies (Pajukanta et al. 2000xTwo loci on chromosomes 2 and X for premature coronary heart disease identified in early- and late-settlement populations of Finland. Pajukanta, P, Cargill, M, Viitanen, L, Nuotio, I, Kareinen, A, Perola, M, Terwilliger, JD, Kempas, E, Daly, M, Lilja, H, Rioux, JD, Brettin, T, Viikari, JSA, Ronnemaa, T, Laakso, M, Lander, ES, and Peltonen, L. Am J Hum Genet. 2000; 67: 1481–1493Abstract | Full Text | Full Text PDF | PubMed | Scopus (126)See all References2000; Francke et al. 2001xA genome-wide scan for coronary heart disease suggests in Indo-Mauritians a susceptibility locus on chromosome 16p13 and replicates linkage with the metabolic syndrome on 3q27. Francke, S, Manraj, M, Lacquemant, C, Lecoeur, C, Lepretre, F, Passa, P, Hebe, A, Corset, L, Yan, SL, Lahmidi, S, Jankee, S, Gunness, TK, Ramjuttun, US, Balgobin, V, Dina, C, and Froguel, P. Hum Mol Genet. 2001; 10: 2751–2765Crossref | PubMedSee all References2001; Harrap et al. 2002xGenome-wide linkage analysis of the acute coronary syndrome suggests a locus on chromosome 2. Harrap, SB, Zammit, KS, Wong, ZY, Williams, FM, Bahlo, M, Tonkin, AM, and Anderson, ST. Arterioscler Thromb Vasc Biol. 2002; 22: 874–878Crossref | PubMed | Scopus (101)See all References2002) had a relatively small number of families. Furthermore, each of the studies used a different statistical method implemented in separate programs, and none of the loci recorded to date have been replicated by the other studies.Table 1Five Genomewide Scans for CADStudyPopulationNo. of FamiliesMean Age (years)Locus/LociAnalysis ProgramsPajukanta et al. 2000Finnish156<552q21 and Xq23MAPMAKER/SIBS, and SIBPAIR in the ANALYZER packageFrancke et al. 2001Mauritian994716p13Genehunter 2.1Broeckel et al. 2002European5135214q32SOLARHarrap et al. 2002Australian61622q36MAPMAKER/SIBSWang et al. 2004American428441p34-36SAGEIn summary, we reported a locus with high genomewide significance for linkage of premature MI through use of state-of-the-art analysis, including permutation testing. We look forward to identification of the specific gene(s) underlying this linkage peak and replication of this linkage in an independent population.