Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations

Forum Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations Igor Rudan1,2, Zrinka Biloglav2, Andrew D. Carothers3, Alan F. Wright3, Harry Campbell1 1Department of Public Health Aim. To present a novel strategy for mapping quantitative trait loci Sciences, Faculty of Medicine, (QTL), using human metapopulations. The strategy is based on the University of Edinburgh, Edinburgh, expectation that in geographic clusters of small and distinct human Scotland, UK 2Department of Medical Statistics, isolates, a combination of founder effect and genetic drift can dra- Epidemiology, and Medical matically increase population frequency of rare QTL variants with Informatics, Andrija Štampar large effect. In such cases, the distribution of QT measurements in an School of Public Health, Zagreb “affected” isolate is expected to deviate from that observed in neigh- University School of Medicine, boring isolates. Zagreb, Croatia 3MRC Human Genetics Unit, Methods. We tested this hypothesis in 9 villages from a larger Croa- Western General Hospital, tian isolate resource, where 7 Mendelian disorders have been previ- Edinburgh, Scotland, UK ously reported. The values of 10 physiological and biochemical QTs were measured in a random sample of 1001 individuals (100 inhabit- ants of each of 9 villages and 101 immigrant controls). > Correspondence to: Results. Significant over- or under- representation of individuals Igor Rudan from specific villages in extreme ends of standardized QT measure- Department of Medical Statistics, Epidemiology, ment distribution was found 10 times more frequently than expected and Medical Informatics by chance. The large majority of such clusters of individuals with ex- Andrija Štampar School of Public Health Zagreb University School of Medicine treme QT values (34/36, 94.4%) originated from the 6 villages with Rockefellerova 4 the most pronounced geographic isolation and endogamy. 10000 Zagreb, Croatia Conclusion. Early epidemiological assessment supports the feasibil- [email protected] ity of the proposed strategy. Clusters of individuals with extreme QT values responsible for over-representation of single villages can usually be linked to a larger pedigree and may be useful for further QTL mapping, using linkage analysis. > Received: October 4, 2006 > Accepted: May 20, 2006 > Croat Med J. 2006;47:532-42 532 www.cmj.hr Rudan et al: Mapping large effect QTL in metapopulation The common feature of Mendelian diseases is the World Health Organization as the main con- that their characteristic phenotype is caused by tributors to disease burden in developed coun- a rare mutation in a single gene in the genome. tries (8). An understanding of their genetic regu- Therefore, the segregation of affected individuals lation is therefore of great current interest (9,10). in families follows simple Mendelian predictions The genes underlying human quantitative traits (1). The catalogue of known Mendelian diseas- (QT) may actually be easier to detect than those es is regularly published, with some 8000 diseas- predisposing common complex diseases, as quan- es or syndromes listed and new ones continual- titative traits represent just a fraction of the many ly added to this number (2). The last decade saw recognized risk factors underlying common com- great successes in identifying genetic variants un- plex diseases of late onset (11). In this paper, we derlying several thousands of these diseases (3-5). present and test a novel strategy for finding very This success was facilitated by the fact that causal rare genetic variants with large effect on QTs in genetic mutation is both necessary and sufficient human populations, ie, genes underlying “invisi- for the development of the disease, which is the ble Mendelian diseases.” The proposed approach key property of Mendelian diseases. This ensures relies on specific population genetic proper- good correlation between disease phenotypes ties of geographically clustered and isolated hu- and underlying genotypes (high “penetrance” man populations, often referred to as metapop- and “detectance,” ie, the probabilities of observ- ulations, which allow for increased frequency of ing the disease phenotype given the disease gen- large effect genetic variants underlying quantita- otype, and vice versa), which is an important re- tive trait distributions that would have extremely quirement for the success of gene mapping using small frequencies in large outbred populations. pedigree-based approach (6,7). Croatia has 15 Adriatic Sea islands with a Most Mendelian diseases usually present at population greater than 1000. The villages on an early age and with a number of clinically ap- the islands have unique population histories and parent phenotypic changes. Such a spectrum of have preserved their isolation from other villag- phenotypes, initially described as a distinct clin- es and outside world through many centuries. ical syndrome, reflects the multiple roles the af- The history, demography, and genetic structure fected gene products have in human develop- of these villages have been investigated for more ment and metabolism. As the human genome than 50 years. The research, mainly carried out harbors some 25 000 predicted genes and an un- by the Institute for Anthropological Research known number of conserved functional elements in Zagreb, Croatia, resulted in over 100 publica- and regulatory regions, perhaps many more than tions in international journals (12-14). On some 8000 Mendelian diseases should be expected. of the islands, monogenic (Mendelian) diseases Many genes, however, may interact with each and rare genetic variants were found in unexpect- other within common biochemical pathways, edly high frequencies (Table 1) (15-27). thus limiting the number of possible phenotypic The studies of population genetic structure, outcomes of their mutations. However, the diag- along with reports of at least seven autochtho- nosis of Mendelian diseases is typically based on nous Mendelian diseases and four highly unusu- noticing visually apparent disease phenotypes. al rare genetic variants, represent strong evidence These phenotypes all have in common that that each small human isolate may harbor ex- they represent measurable human biological tremely rare variant(s) that were brought to com- quantitative traits. Some of them (eg, blood pres- mon frequencies by genetic drift. Some of these sure, body mass index, cholesterol levels, and variants cause the reported Mendelian diseases, blood glucose) have recently been identified by especially if causal mutations are recessive and ex- 533 Croat Med J 2006;47:532-542 Table 1. Overview of the evidence of extremely rare mutations present in unusually high frequencies in specific Croatian island isolates Type of research Island Reference Reports on autochthonous Mendelian diseases: dwarfism Krk 15-17 albinism Krk 17 progressive spastic quadriplegia Krk 17 familial cognitive dysfunction Susak 18,19 familial congenital hip dislocation Lastovo 20 familial ovarian cancer Lastovo 21,22 keratoderma palmoplantaris transgrediens Mljet 23 Reports of high population frequencies of extremely rare genetic variants: deleted/triplicated alpha-globin gene Silba 24 PGM1*W3 phosphoglucomutase-1 variant Olib 25 mtDNA haplogroup F Hvar 26 Y-chromosome haplogroup P* Hvar 27 cessively “exposed” by inbreeding, while others Figure 1. Geographic location of the investigated islands of Rab, Vis, may have large effects on quantitative traits. Re- Lastovo, and Mljet. Villages from 1 to 9 (V1-V9) are study populations. Immigrants into the islands originate from mainland Croatia (V10). cent studies in these populations showed a significant positive effect of inbreeding on a quantitative trait (hypertension) and on the prevalence of villages on an island) (Figure 2). The founder ef- a number of late-onset complex diseases (28,29), fect would probably not have the power to sig- suggestive of the presence of a major class of rare nificantly change the distribution of QT values recessive variants underlying those phenotypes in in any individual village from the one expected these Croatian isolates. in the general population of their origin (Fig- ure 2). However, over the course of time, genet- Population and Methods ic drift would randomly increase the population frequencies of some of those variants of interest, Study design as long as they do not substantially affect individual fitness. This would provide an opportuni- Figure 1 shows the geographic location of the ty for genetic variants of large effect on QT (eg, main inhabited islands and the villages chosen blood pressure, cholesterol, and glucose levels) to for this study. become very common in particular isolates. They Assuming a polygenic nature of QTs and ex- would not be removed from the gene pool by se- ponential distribution of effect size (30,31), the lection, as the resulting chronic late-onset diseas- limited number of founders would initially in- es (eg, stroke, coronary heart disease, cancer, or troduce an unknown number of rare mutations type 2 diabetes mellitus) would develop during (variants specific for their individual genomes) the post-reproductive period, although perhaps into the gene pool of the isolate they had estab- at an earlier age than expected in the majority of lished. Through such a “founder effect,” the fre- affected cases in the population. quency of those variants would thus increase When an introduced variant with large ef- from extremely rare in the general population

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