IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0237721.html
   My bibliography  Save this article

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

Author

Listed:
  • Daniel Svensson
  • Matilda Rentoft
  • Anna M Dahlin
  • Emma Lundholm
  • Pall I Olason
  • Andreas Sjödin
  • Carin Nylander
  • Beatrice S Melin
  • Johan Trygg
  • Erik Johansson

Abstract

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency

Suggested Citation

  • Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
    • Handle: RePEc:plo:pone00:0237721
    DOI: 10.1371/journal.pone.0237721
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237721
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0237721&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0237721?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    2. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    3. Keith Humphreys & Alexander Grankvist & Monica Leu & Per Hall & Jianjun Liu & Samuli Ripatti & Karola Rehnström & Leif Groop & Lars Klareskog & Bo Ding & Henrik Grönberg & Jianfeng Xu & Nancy L Peders, 2011. "The Genetic Structure of the Swedish Population," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-11, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Morten Dybdahl Krebs & Gonçalo Espregueira Themudo & Michael Eriksen Benros & Ole Mors & Anders D. Børglum & David Hougaard & Preben Bo Mortensen & Merete Nordentoft & Michael J. Gandal & Chun Chieh F, 2021. "Associations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Diana Chang & Feng Gao & Andrea Slavney & Li Ma & Yedael Y Waldman & Aaron J Sams & Paul Billing-Ross & Aviv Madar & Richard Spritz & Alon Keinan, 2014. "Accounting for eXentricities: Analysis of the X Chromosome in GWAS Reveals X-Linked Genes Implicated in Autoimmune Diseases," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-31, December.
    3. Gyaneshwer Chaubey & Anurag Kadian & Saroj Bala & Vadlamudi Raghavendra Rao, 2015. "Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-11, June.
    4. Chuan Gao & Nan Wang & Xiuqing Guo & Julie T Ziegler & Kent D Taylor & Anny H Xiang & Yang Hai & Steven J Kridel & Jerry L Nadler & Fouad Kandeel & Leslie J Raffel & Yii-Der I Chen & Jill M Norris & J, 2015. "A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-17, November.
    5. Estavoyer, Maxime & François, Olivier, 2022. "Theoretical analysis of principal components in an umbrella model of intraspecific evolution," Theoretical Population Biology, Elsevier, vol. 148(C), pages 11-21.
    6. Felsenstein, Joseph, 2015. "Covariation of gene frequencies in a stepping-stone lattice of populations," Theoretical Population Biology, Elsevier, vol. 100(C), pages 88-97.
    7. Yaron Granot & Omri Tal & Saharon Rosset & Karl Skorecki, 2016. "On the Apportionment of Population Structure," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-24, August.
    8. Hyosik Jang & Ian M Ehrenreich, 2012. "Genome-Wide Characterization of Genetic Variation in the Unicellular, Green Alga Chlamydomonas reinhardtii," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-9, July.
    9. Mathieu Gautier & Denis Laloë & Katayoun Moazami-Goudarzi, 2010. "Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-11, September.
    10. Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.
    11. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    12. Bo Jiang & Jun S. Liu, 2015. "Bayesian Partition Models for Identifying Expression Quantitative Trait Loci," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(512), pages 1350-1361, December.
    13. Lee, Anthony J. & Hibbs, Courtney & Wright, Margaret J. & Martin, Nicholas G. & Keller, Matthew C. & Zietsch, Brendan P., 2017. "Assessing the accuracy of perceptions of intelligence based on heritable facial features," Intelligence, Elsevier, vol. 64(C), pages 1-8.
    14. Thompson Katherine L. & Linnen Catherine R. & Kubatko Laura, 2016. "Tree-based quantitative trait mapping in the presence of external covariates," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(6), pages 473-490, December.
    15. Rakesh Chettier & Lesa Nelson & James W Ogilvie & Hans M Albertsen & Kenneth Ward, 2015. "Haplotypes at LBX1 Have Distinct Inheritance Patterns with Opposite Effects in Adolescent Idiopathic Scoliosis," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-11, February.
    16. Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    17. Matthieu Bouaziz & Caroline Paccard & Mickael Guedj & Christophe Ambroise, 2012. "SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-17, October.
    18. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
    19. Jacobo Pardo-Seco & Alberto Gómez-Carballa & Jorge Amigo & Federico Martinón-Torres & Antonio Salas, 2014. "A Genome-Wide Study of Modern-Day Tuscans: Revisiting Herodotus's Theory on the Origin of the Etruscans," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
    20. Andrey V Khrunin & Denis V Khokhrin & Irina N Filippova & Tõnu Esko & Mari Nelis & Natalia A Bebyakova & Natalia L Bolotova & Janis Klovins & Liene Nikitina-Zake & Karola Rehnström & Samuli Ripatti & , 2013. "A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-9, March.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0237721. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.