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Genetic Comparison of a Croatian Isolate and CEPH European Founders Edinburgh Research Explorer Genetic comparison of a Croatian isolate and CEPH European founders Citation for published version: Navarro, P, Vitart, V, Hayward, C, Tenesa, A, Zgaga, L, Juricic, D, Polasek, O, Hastie, ND, Rudan, I, Campbell, H, Wright, AF, Haley, CS & Knott, SA 2010, 'Genetic comparison of a Croatian isolate and CEPH European founders', Genetic Epidemiology, vol. 34, no. 2, pp. 140-5. https://doi.org/10.1002/gepi.20443 Digital Object Identifier (DOI): 10.1002/gepi.20443 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Genetic Epidemiology General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 29. Sep. 2021 Genetic Epidemiology 34 : 140–145 (2010) Genetic Comparison of a Croatian Isolate and CEPH European Founders Pau Navarro,1Ã Ve´ronique Vitart,1 Caroline Hayward,1 Albert Tenesa,2 Lina Zgaga,3 Danica Juricic,4 Ozren Polasek,3,5 Nicholas D. Hastie,1 Igor Rudan,5,6 Harry Campbell,5 Alan F. Wright,1 Chris S. Haley,1 and Sara A. Knott7 1MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK 2Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK 3Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia 4Department of Internal Medicine, Zagreb University Hospital Center, Zagreb, Croatia 5Community Health Sciences, University of Edinburgh, Edinburgh, UK 6Croatian Centre for Global Health, University of Split, Split, Croatia 7Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, UK Human isolates have been postulated as a good resource for the identification of QTL due to reduced genetic diversity and a more homogeneous environment. Isolates may also have increased linkage disequilibrium (LD) due to small effective population size and, either loss or increase in frequency of alleles that are rare in the general population from which they originate. Here we investigate the difference in allele and genotype frequencies, LD and homozygous tracts between an isolate—several villages from the island of Vis in Croatia—and an outbred population of European origin: the Hapmap CEPH founders. Using the HumanHap300 v1 Genotyping BeadChip, we show that our population does not differ greatly from the reference CEU outbred population despite having a slightly higher proportion of monomorphic loci, a slightly higher long-range LD, and a greater proportion of individuals with long homozygous tracts. We conclude that genotyping arrays should perform equally well in our isolate as in outbred European populations for disease mapping studies and that SNP–trait associations discovered in our well-characterized Croatian isolate should be valid in the general European population from which they descend. Genet. Epidemiol. 34 : 140–145, 2010. r 2009 Wiley-Liss, Inc. Key words: linkage disequilibrium; mapping; population isolate Additional Supporting Information may be found in the online version of this article. Contract grant sponsors: Wellcome Trust; MRC; MRC Human Genetics Unit; RCUK; The National Foundation for Science, Higher Education and Technological Development of the Republic of Croatia. Ã Correspondence to: Pau Navarro, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. E-mail: [email protected] Received 26 January 2009; Revised 21 April 2009; Accepted 10 June 2009 Published online 20 August 2009 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/gepi.20443 INTRODUCTION MATERIAL AND METHODS Human isolates have been postulated as a good resource for the identification of QTL due to reduced POPULATION ISOLATE genetic diversity and a more homogeneous environment. Croatia has 15 Adriatic Sea islands with population Isolates may also have increased linkage disequilibrium greater than 1,000. The villages on the islands have unique (LD) due to small effective population size and, either loss population histories and preserved isolation from other or increase in frequency of alleles that are rare in the villages and outside world through centuries. The village general population from which they originate [Wright populations of these islands represent well-characterized et al., 1999]. genetic isolates [Bennett et al., 1983; Rudan et al., 1999; Here we investigate the difference in allele and Rudan et al., 1992]. Komiza and Vis, on the island of genotype frequencies, LD and homozygous tracts Vis, have excellent church and census records that between an isolate—several villages from the island show evidence of very limited immigration from other of Vis in Croatia—and an outbred population of populations and this is supported by the very high European origin: the Hapmap CEPH founders (Utah endogamy (calculated as the percentage of grandparents residents with ancestry from northern and western born in the same village as the participant) estimated for Europe, CEU). the villages: 91% for Komiza and 85% for Vis. Several rare r 2009 Wiley-Liss, Inc. Comparison of a Croatian Isolate and CEPH Europeans 141 autochthonous Mendelian diseases occur in these Adriatic the positions of the start and end SNP for each tract. Tracts islands [Bakija-Konsuo et al., 2002; Saftic et al., 2006] where with an average density of less than one SNP per 50 kb or at least four highly unusual rare genetic variants segregate with less than 10 SNPs in total were excluded to avoid [Barac et al., 2003; Borot et al., 1991; Tolk et al., 2001; regions of low SNP coverage such as the centromeric Turcinov et al., 2000]. Each one of these findings is regions. This analysis was implemented in PLINK 1.04, generally consistent with the hypothesis that all affected using a sliding window of 200 kb. (carrier of a particular variant) chromosomes descend from a single founder. RESULTS HUMAN SUBJECTS The average inter-marker distance for adjacent marker 60 founders from the CEPH European sample have been pairs was 9,285 bp (range 1–22072916) (Figure S1). Table I genotyped by the HapMap project. summarizes the results on allele frequency in each For comparison we selected 60 unrelated (based upon population. In total 170 SNPs were monomorphic in both their pedigrees obtained from church/parish records) and populations. The average MAF was similar at 0.25 for healthy individuals from our study population from the CROATIA and 0.26 for CEU; however, the distributions of island of Vis, Croatia (CROATIA, for description see Vitart allele frequencies differed. CROATIA exhibited an excess et al. [2008]). of loci in the 0–0.05 MAF range compared to CEU, but the trend was the opposite for loci with MAFs of 0.05–0.15. For MAFs of 0.15–0.5 the populations were very similar GENOTYPING (Figure S2). Mean heterozygosity was also similar for the The Croatian samples were genotyped using the populations (34.17% (range 0–78.33%) for CROATIA and Illumina’s Sentrix HumanHap300 Genotyping BeadChip 34.98% (0–71.67%) for CEU). CROATIA had an excess of (v1) comprising 317,503 SNPs. Genotypes for these same loci with lower heterozygosity (range 0–10%) compared to SNPs for the 60 CEPH founders were obtained from CEU but CEU had an excess of loci in the range 10–20%, Illumina Inc.1 with the rest of the distribution being similar (Figure S3). We used the exact test for HWE described in Wigginton et al. [2005]. 3.41% of loci showed P-values o0.05 in STATISTICAL METHODS CROATIA and 2.77% in CEU when only loci with MAFs In both populations, we excluded markers with less than 40.05 in both populations were used (for all loci, these 90% call rate in each population (9,075 in CROATIA, 71 in figures were 3.25 and 2.64%, respectively), so no more loci CEU, 9,088 in total) and markers on the sex chromosomes were found to be out of HWE in either population than (9,173), leaving 299,242 SNPs. This set of SNPs was used to expected by chance. produce the results presented except when otherwise stated. We estimated the proportion of loci segregating in GENETIC DISTANCE BETWEEN POPULATIONS each population, the allele and genotype frequencies and the proportion of loci out of Hardy-Weinberg equilibrium Average Fst for these populations was 0.014 both when (HWE). Data were analyzed using PLINK 1.04 [Purcell loci polymorphic in both populations were tested and et al., 2007], R [R Development Core Team, 2008] and when only loci with MAF 40.05 in both populations were custom-made software. used, indicating very little differentiation [S. Wright, 1978]. Overall the populations are quite similar, but several loci Genetic distance between populations. Pairwise show high Fst values (Figure S4). A group of markers with Fst statistics were calculated for all SNP markers segregat- Fst 40.25 is located on chromosome 2; it spans around ing in both populations. A mean Fst was calculated for all 1.8 Mb and includes SNPs in the Lactase (LCT) gene. markers and for the subset with minor allele frequency Results were similar when using all polymorphic loci or (MAF) 40.05 in both populations. We studied the using only loci with MAF 40.05 in both populations sampling properties of Fst estimates by bootstrapping as (Figure S5).
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