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Leif Groop

Leif Groop

Principal investigator

Leif Groop

Haplotype Sharing Provides Insights into Fine-Scale Population History and Disease in Finland


  • Alicia R Martin
  • Konrad J Karczewski
  • Sini Kerminen
  • Mitja I Kurki
  • Antti-Pekka Sarin
  • Mykyta Artomov
  • Johan G Eriksson
  • Tõnu Esko
  • Giulio Genovese
  • Aki S Havulinna
  • Jaakko Kaprio
  • Alexandra Konradi
  • László Korányi
  • Anna Kostareva
  • Minna Männikkö
  • Andres Metspalu
  • Markus Perola
  • Rashmi B Prasad
  • Olli Raitakari
  • Oxana Rotar
  • Veikko Salomaa
  • Leif Groop
  • Aarno Palotie
  • Benjamin M Neale
  • Samuli Ripatti
  • Matti Pirinen
  • Mark J Daly

Summary, in English

Finland provides unique opportunities to investigate population and medical genomics because of its adoption of unified national electronic health records, detailed historical and birth records, and serial population bottlenecks. We assembled a comprehensive view of recent population history (≤100 generations), the timespan during which most rare-disease-causing alleles arose, by comparing pairwise haplotype sharing from 43,254 Finns to that of 16,060 Swedes, Estonians, Russians, and Hungarians from geographically and linguistically adjacent countries with different population histories. We find much more extensive sharing in Finns, with at least one ≥ 5 cM tract on average between pairs of unrelated individuals. By coupling haplotype sharing with fine-scale birth records from more than 25,000 individuals, we find that although haplotype sharing broadly decays with geographical distance, there are pockets of excess haplotype sharing; individuals from northeast Finland typically share several-fold more of their genome in identity-by-descent segments than individuals from southwest regions. We estimate recent effective population-size changes through time across regions of Finland, and we find that there was more continuous gene flow as Finns migrated from southwest to northeast between the early- and late-settlement regions than was dichotomously described previously. Lastly, we show that haplotype sharing is locally enriched by an order of magnitude among pairs of individuals sharing rare alleles and especially among pairs sharing rare disease-causing variants. Our work provides a general framework for using haplotype sharing to reconstruct an integrative view of recent population history and gain insight into the evolutionary origins of rare variants contributing to disease.


  • Genomics, Diabetes and Endocrinology

Publishing year







American Journal of Human Genetics





Document type

Journal article


Cell Press


  • Medical Genetics
  • Endocrinology and Diabetes


  • Journal Article



Research group

  • Genomics, Diabetes and Endocrinology


  • ISSN: 0002-9297