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Whole genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom

By Himanshu Chheda, Priit Palta, Matti Pirinen, Shane McCarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark Daly, Richard Durbin, Aarno Palotie, Tero Aittokallio, Samuli Ripatti, Sequencing Initiative Suomi (SISu) Project

Posted 12 Jul 2016
bioRxiv DOI: 10.1101/063388 (published DOI: 10.1038/ejhg.2016.205)

Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared to Britons and 800,000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 - 5% (p < 2.2x10-16). When stratified by their functional annotations, loss-of-function (LoF) variants showed the highest proportional enrichment in Finns (p = 0.0291). In the non-coding part of the genome, variants in conserved regions (p = 0.002) and promoters (p = 0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using population isolates.

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