Portal de Periódicos da CAPES

The Importance of Genealogy in Determining Genetic Associations with Complex Traits

2001; Elsevier BV; Volume: 69; Issue: 5 Linguagem: Inglês

10.1086/323659

1537-6605

Dina L. Newman, Mark Abney, Mary Sara McPeek, Carole Ober, Nancy J. Cox,

Nutrition, Genetics, and Disease

To the Editor: Most common diseases, such as asthma, type 2 diabetes, bipolar disorder, and cardiovascular disease, are known to have genetic components, but the susceptibility genes have been notoriously difficult to localize and to identify. These complex diseases likely have a large number of genetic and nongenetic risk factors that together have varying effects on phenotype. Many investigators have recommended founder populations for complex-trait mapping, with the expectation that fewer susceptibility alleles will be segregating in these restricted gene pools (Lander and Schork Lander and Schork, 1994Lander ES Schork NJ Genetic dissection of complex traits.Science. 1994; 265: 2037-2048Crossref PubMed Scopus (2763) Google Scholar; Wright et al. Wright et al., 1999Wright AF Carothers AD Pirastu M Population choice in mapping genes for complex diseases.Nat Genet. 1999; 23: 397-404Crossref PubMed Scopus (281) Google Scholar; Shifman and Darvasi Shifman and Darvasi, 2001Shifman S Darvasi A The value of isolated populations.Nat Genet. 2001; 28: 309-310Crossref PubMed Scopus (129) Google Scholar). Some or all individuals in these populations are inbred, but often the exact relationships between all members are either unknown or not taken into account. It is tempting to use such populations for their presumed homogeneity, even in the absence of accurate pedigree information. The failure to take full pedigree information into account can either reduce the power to detect linkage (Dyer et al., Dyer et al., in pressDyer TD, Williams JT, Goring, HHH Blangero J. The effect of pedigree complexity on quantitative trait linkage analysis. Genet Epidemiol Suppl (in press).Google Scholar) or inflate LOD scores (Miano et al. Miano et al., 2000Miano MG Jacobson SG Carothers A Hanson I Teague P Lovell J Cideciyan AV Haider N Stone EM Sheffield VC Wright AF Pitfalls in homozygosity mapping.Am J Hum Genet. 2000; 67: 1348-1351Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar). The failure to account for relatedness among individuals will also affect association studies. In particular, many statistical tests of association are not strictly valid, owing to the lack of true independence between individuals. Nonetheless, such populations have been used widely in association studies (e.g., de Silva et al. de Silva et al., 1999de Silva AM Walder KR Aitman TJ Gotoda T Goldstone AP Hodge AM de Courten MP Zimmet PZ Collier GR Combination of polymorphisms in OB-R and the OB gene associated with insulin resistance in Nauruan males.Intl J Obes Relat Metab Disord. 1999; 23: 816-822Crossref PubMed Scopus (33) Google Scholar; Laprise et al. Laprise et al., 2000Laprise C Boulet LP Morissette J Winstall E Raymond V Evidence for association and linkage between atopy, airway hyper-responsiveness, and the β subunit Glu237Gly variant of the high-affinity receptor for immunoglobulin E in the French-Canadian population.Immunogenetics. 2000; 51: 695-702Crossref PubMed Scopus (35) Google Scholar; Ospina-Duque et al. Ospina-Duque et al., 2000Ospina-Duque J Duque C Carvajal-Carmona L Ortiz-Barrientos D Soto I Pineda N Cuartas M et al.An association study of bipolar mood disorder (type I) with the 5-HTTLPR serotonin transporter polymorphism in a human population isolate from Colombia.Neurosci Lett. 2000; 292: 199-202Crossref PubMed Scopus (74) Google Scholar; Summerhill et al. Summerhill et al., 2000Summerhill E Leavitt SA Gidley H Parry R Solway J Ober C β2-Adrenergic receptor Arg16/Arg16 genotype is associated with reduced lung function, but not with asthma, in the Hutterites.Am J Respir Crit Care Med. 2000; 162: 599-602Crossref PubMed Scopus (82) Google Scholar; Bitti et al. Bitti et al., 2001Bitti PP Murgia BS Ticca A Ferrai R Musu L Piras ML Puledda E Campo S Durando S Montomoli C Clayton DG Mander AP Bernardinelli L Association between the ancestral haplotype HLA A30B18DR3 and multiple sclerosis in central Sardinia.Genet Epidemiol. 2001; 20: 271-283Crossref PubMed Scopus (36) Google Scholar; Hegele et al. Hegele et al., 2001Hegele RA Wang J Harris SB Brunt JH Young TK Hanley AJ Zinman B Connelly PW Anderson CM Variable association between genetic variation in the CYP7 gene promoter and plasma lipoproteins in three Canadian populations.Atherosclerosis. 2001; 154: 579-587Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar), and some authors have even recommended the inclusion of founder populations in case-control studies, owing to their decreased heterogeneity (Shifman and Darvasi Shifman and Darvasi, 2001Shifman S Darvasi A The value of isolated populations.Nat Genet. 2001; 28: 309-310Crossref PubMed Scopus (129) Google Scholar). However, the impact that ignoring pedigree relationships has on tests of association has not been evaluated. The Hutterites are an extreme example of a large, complex pedigree with multiple inbreeding loops. We are in the unique position of having complete genealogical information on this 12,903-person, 13-generation pedigree (Abney et al. Abney et al., 2000Abney MA McPeek MS Ober C Estimation of variance components of quantitative traits in inbred populations.Am J Hum Genet. 2000; 66: 629-650Abstract Full Text Full Text PDF PubMed Scopus (119) Google Scholar). Additionally, we have extensive phenotype characterization and a dense microsatellite map (of 568 short-tandem-repeat–polymorphism markers) of ∼750 members of this population, who are descendants of just 64 Hutterite founders (Ober et al. Ober et al., 2000Ober C Tsalenko A Parry R Cox NJ A second-generation genomewide screen for asthma-susceptibility alleles in a founder population.Am J Hum Genet. 2000; 67: 1154-1162Abstract Full Text Full Text PDF PubMed Scopus (323) Google Scholar). Thus, we were able to assess the effect that ignoring pedigree information has on statistical tests of association. We performed two separate genomewide scans of association on each of three quantitative phenotypes: serum immunoglobulin E (IgE), serum LDL, and body-mass index (BMI). These phenotypes were chosen to represent quantitative traits associated with diverse complex diseases (asthma, cardiovascular disease, and diabetes, respectively). All phenotypes were adjusted for age and sex and were transformed so that the residuals were approximately normally distributed (Abney et al. Abney et al., 2001Abney MA McPeek MS Ober C Narrow and broad heritabilities of quantitative traits in a founder population.Am J Hum Genet. 2001; 68: 1302-1307Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar). The heritabilities of IgE and BMI were completely accounted for by additive genetic variance, with heritabilities of .63 and .54, respectively; the heritability of LDL had a strong dominance component in addition to additive genetic variance, with a broad heritability of .96 (discussed in detail by Abney et al. [Abney et al., 2001Abney MA McPeek MS Ober C Narrow and broad heritabilities of quantitative traits in a founder population.Am J Hum Genet. 2001; 68: 1302-1307Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar]). To estimate the effect that each allele at each locus has on the trait values, we used a statistical test of association, developed specifically for use in large, inbred pedigrees (Ober et al. Ober et al., 2001Ober C Abney M McPeek MS The genetic dissection of traits in a founder population.Am J Hum Genet. 2001; 69 (in this issue): 1068-1079Abstract Full Text Full Text PDF PubMed Scopus (160) Google Scholar [in this issue]). Pedigree structure is taken into account by the use of variance components to model the polygenic background (Abney et al. Abney et al., 2000Abney MA McPeek MS Ober C Estimation of variance components of quantitative traits in inbred populations.Am J Hum Genet. 2000; 66: 629-650Abstract Full Text Full Text PDF PubMed Scopus (119) Google Scholar, Abney et al., 2001Abney MA McPeek MS Ober C Narrow and broad heritabilities of quantitative traits in a founder population.Am J Hum Genet. 2001; 68: 1302-1307Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar). When pedigree structure is ignored, the method is equivalent to a linear regression of the trait on age, sex, and genotype, with a Bonferroni correction applied to the P value for the t test for significance of genotype. In the first scan, we included the variance components and therefore took into account the relatedness between individuals. In the second scan, we did not include any pedigree information (additive and dominance variances were 0). In both scans, the observed P values were adjusted for multiple comparisons, by use of a Bonferroni correction. The two methods yielded dramatically different results. In general, the significance of association with a given marker was considerably inflated when pedigree structure was not included, although in some cases the reverse was true (see fig. 1). Only two loci were among the five most significant results, by both methods, for the three traits (the same marker at 7p21 was associated with IgE, by both methods, and the same marker at 8q12 was associated with LDL, by both methods). In addition, many more loci showed evidence of association when the pedigree structure was not included (see fig. 2). In fact, 10%–22% of all markers appeared to have a strong association (P<.01) with the phenotype, when pedigree structure was not included. Results for 58 single-nucleotide polymorphisms showed similar trends (data not shown).Figure 2Number of significantly associated (P<.01) loci when pedigree structure is included (lighter bars) and when pedigree structure is not included (darker bars).View Large Image Figure ViewerDownload Hi-res image Download (PPT) Although the Hutterites are an extreme example of a complex pedigree, there are several other populations known to have similar structures (Badner et al. Badner et al., 1990Badner JA Sieber WK Garver KL Chakravarti A A genetic study of Hirschsprung disease.Am J Hum Genet. 1990; 46: 568-580PubMed Google Scholar; Slutsky et al. Slutsky et al., 1997Slutsky AS Zamel N University of Toronto Genetics of Asthma Research Group Genetics of asthma: the University of Toronto Program.Am J Respir Crit Care Med Suppl. 1997; 156: S130-S132Crossref PubMed Scopus (25) Google Scholar; Hsueh et al. Hsueh et al., 2000Hsueh WC Mitchell BD Aburomia R Pollin T Sakul H Gelder Ehm M Michelsen BK Wagner MJ St Jean PL Knowler WC Burns DK Bell CJ Shuldiner AR Diabetes in the Old Order Amish: characterization and heritability analysis of the Amish Family Diabetes Study.Diabetes Care. 2000; 23: 595-601Crossref PubMed Scopus (142) Google Scholar). Moreover, individuals from a variety of smaller, island populations who either have been or are currently being studied may be more related to each other than can be discerned from the recently collected pedigree data (de Silva et al. de Silva et al., 1999de Silva AM Walder KR Aitman TJ Gotoda T Goldstone AP Hodge AM de Courten MP Zimmet PZ Collier GR Combination of polymorphisms in OB-R and the OB gene associated with insulin resistance in Nauruan males.Intl J Obes Relat Metab Disord. 1999; 23: 816-822Crossref PubMed Scopus (33) Google Scholar; Mathias et al. Mathias et al., 2000Mathias RA Bickel CA Beaty TH Petersen GM Hetmanski JB Liang KY Barnes KC A study of contemporary levels and temporal trends in inbreeding in the Tangier Island, Virginia, population using pedigree data and isonymy.Am J Phys Anthropol. 2000; 112: 29-38Crossref PubMed Scopus (15) Google Scholar; Bitti et al. Bitti et al., 2001Bitti PP Murgia BS Ticca A Ferrai R Musu L Piras ML Puledda E Campo S Durando S Montomoli C Clayton DG Mander AP Bernardinelli L Association between the ancestral haplotype HLA A30B18DR3 and multiple sclerosis in central Sardinia.Genet Epidemiol. 2001; 20: 271-283Crossref PubMed Scopus (36) Google Scholar). In fact, even presumably outbred populations may contain hidden consanguinity (Broman and Weber Broman and Weber, 1999Broman KW Weber JL Long homozygous chromosomal segments in reference families from the Centre d'Etude du Polymorphisme Humain.Am J Hum Genet. 1999; 65: 1493-1500Abstract Full Text Full Text PDF PubMed Scopus (206) Google Scholar), and cryptic relatedness may be a problem in association studies of rare disorders (Bacanu et al. Bacanu et al., 2000Bacanu SA Devlin B Roeder K The power of genomic control.Am J Hum Genet. 2000; 66: 1933-1944Abstract Full Text Full Text PDF PubMed Scopus (275) Google Scholar). This problem may be avoided by the use of statistical tools designed to detect misspecified or cryptic relationships (McPeek and Sun McPeek and Sun, 2000McPeek MS Sun L Statistical tests for detection of misspecified relationships by use of genome-screen data.Am J Hum Genet. 2000; 66: 1076-1094Abstract Full Text Full Text PDF PubMed Scopus (286) Google Scholar; Sun et al., Sun et al., in pressSun L, Abney M, McPeek MS. Detection of misspecified relationships in inbred and outbred pedigrees. Genet Epidemiol Suppl (in press).Google Scholar). We cannot prove that the inclusion of the pedigree structure in the method results in true associations, until the alleles contributing to these quantitative traits are found; however, we believe that the number of associations found when structure is ignored is unrealistic. Presumably, a profound failure of the assumption of independence between individuals, in method 2, results in a dramatically increased number of type 1 errors. Overall, our data suggest that failing to take into account extended-familial relationships can result in a large number of false-positive results, and some “true” associations may be missed. In addition, the level of significance could be overestimated by several orders of magnitude. In an association study in which it is not possible to take into account all familial relationships, as we have done with the Hutterites, another option is to use genomic controls (Devlin and Roeder Devlin and Roeder, 1999Devlin B Roeder K Genomic control for association studies.Biometrics. 1999; 55: 997-1004Crossref PubMed Scopus (2289) Google Scholar). Otherwise, naïve approaches to genetic-association analysis could result in an enormous amount of time and of money spent in following up artifactual associations. We thank Harvey Dytch for assistance with computer programming and data management. This work was supported by National Institutes of Health grants DK55889, HD56399, and HG01645.