Abstract
Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.
Highlights
Copy Number Variation (CNV) is defined here as DNA segments of 1 kb or longer in length and present at variable copy number in comparison with a reference genome [1]
The study samples were recruited from three populations across Europe, namely the Island of Vis, Croatia, Orkney Islands, Scotland and South Tyrol, Italy (Figure 1). 2789 individuals who passed quality control were included in the analysis
The combined analysis of CNV calling by QuantiSNP and cnvPartition software identified 4016 autosomal CNVs in 1964 individuals, out of the total 2789 samples, which makes 70.4% of them CNV carriers, with an average number of 2.05 detectable CNVs per carrier. 7.8% of the all autosomal single nucleotide polymorphism (SNP) were covered by CNVs
Summary
Copy Number Variation (CNV) is defined here as DNA segments of 1 kb or longer in length and present at variable copy number in comparison with a reference genome [1]. Several studies have reported evidence for a direct contribution of CNVs to complex disease phenotypes in human populations, such as Schizophrenia and Autism [7,8,9], and in other species [10,11,12,13,14,15,16]. As well as being applied to the search for genetic contribution to disease phenotypes, several studies have provided global estimates of CNV frequency and distribution in HapMap samples [1,6] and large population cohorts [22,25,26,27], but relatively little attention has been given to potential variation within major population groups. Comparisons of CNV frequency and distribution between independent studies have been hampered by discrepancies in study design, platform choice and analytical methods between studies
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