Browsing by Subject "ANCESTRY"

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  • Khrunin, Andrey V.; Khokhrin, Denis V.; Filippova, Irina N.; Esko, Tonu; Nelis, Mari; Bebyakova, Natalia A.; Bolotova, Natalia L.; Klovins, Janis; Nikitina-Zake, Liene; Rehnström, Karola Hannele; Ripatti, Samuli; Schreiber, Stefan; Franke, Andre; Macek, Milan; Krulisova, Veronika; Lubinski, Jan; Metspalu, Andres; Limborska, Svetlana A. (2013)
  • Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Haggstrom, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A. (2013)
  • Tonkin-Hill, Gerry; Lees, John A.; Bentley, Stephen D.; Frost, Simon D. W.; Corander, Jukka (2019)
    We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10-100 times larger than the existing model-based methods, which we demonstrate by analyzing an alignment of over 110 000 sequences of HIV-1 pol genes. We also provide a method for rapidly partitioning an existing hierarchy in order to maximize the DPM model marginal likelihood, allowing us to split phylogenetic trees into clades and sub-clades using a population genomic model. Extensive tests on simulated data as well as a diverse set of real bacterial and viral datasets show that fastbaps provides comparable or improved solutions to previous model-based methods, while being significantly faster. The method is made freely available under an open source MIT licence as an easy to use R package at https://github.com/gtonkinhill/fastbaps.
  • Stronen, Astrid V.; Salmela, Elina; Baldursdottir, Birna K.; Berg, Peer; Espelien, Ingvild S.; Järvi, Kirsi; Jensen, Henrik; Kristensen, Torsten N.; Melis, Claudia; Manenti, Tommaso; Lohi, Hannes; Pertoldi, Cino (2017)
    Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (H-E 0.035) than for other breeds (H-E 0.209-0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise F-ST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project.
  • Liu, Mengling; Rogers, Linda; Cheng, Qinyi; Shao, Yongzhao; Fernandez-Beros, Maria Elena; Hirschhorn, Joel N.; Lyon, Helen N.; Gajdos, Zofia K. Z.; Vedantam, Sailaja; Gregersen, Peter; Seldin, Michael F.; Bleck, Bertram; Ramasamy, Adaikalavan; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Kuokkanen, Mikko; Laitinen, Tarja; Eriksson, Johan; Lehtimaki, Terho; Raitakari, Olli T.; Reibman, Joan (2011)
  • Tarkkala, Heta; Tupasela, Aaro (2018)
    Since the sequencing of the human genome, as well as the completion of the first Human Genome Diversity Project, the benefits of studying one human population over another has been an ongoing debate relating to the replicability of findings in other populations. The leveraging of specific populations into research markets has made headlines in cases such as deCode in Iceland, Quebec Founder Population, and Generation Scotland. In such cases, researchers and policy makers have used the genetic and historical uniqueness of their populations to attract scientific, commercial and political interest. In this article, we explore how in countries with population isolates, such as Finland, the researchers balance considerations relating to the generalization and replicability of findings in small yet unique research populations to global biomedical research interests. This highlights challenges related to forms of competition associated with genetics research markets, as well as what counts as the right' population for genetic research.