IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0237721.html

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. 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.
    2. 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.
    3. 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.
    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. 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.
    2. 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.
    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. Junyang Qian & Yosuke Tanigawa & Wenfei Du & Matthew Aguirre & Chris Chang & Robert Tibshirani & Manuel A Rivas & Trevor Hastie, 2020. "A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank," PLOS Genetics, Public Library of Science, vol. 16(10), pages 1-30, October.
    5. 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.
    6. Yuk Yee Leung & Adam C. Naj & Yi-Fan Chou & Otto Valladares & Michael Schmidt & Kara Hamilton-Nelson & Nicholas Wheeler & Honghuang Lin & Prabhakaran Gangadharan & Liming Qu & Kaylyn Clark & Amanda B., 2024. "Human whole-exome genotype data for Alzheimer’s disease," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    7. Jose Blanca & Joaquín Cañizares & Laura Cordero & Laura Pascual & María José Diez & Fernando Nuez, 2012. "Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-17, October.
    8. Poojitha Balakrishnan & Miranda R. Jones & Dhananjay Vaidya & Maria Tellez-Plaza & Wendy S. Post & Joel D. Kaufman & Suzette J. Bielinski & Kent Taylor & Kevin Francesconi & Walter Goessler & Ana Nava, 2018. "Ethnic, Geographic, and Genetic Differences in Arsenic Metabolism at Low Arsenic Exposure: A Preliminary Analysis in the Multi-Ethnic Study of Atherosclerosis (MESA)," IJERPH, MDPI, vol. 15(6), pages 1-11, June.
    9. 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.
    10. Wei-Yu Lin & Ian W Brock & Dan Connley & Helen Cramp & Rachel Tucker & Jon Slate & Malcolm W R Reed & Sabapathy P Balasubramanian & Lisa A Cannon-Albright & Nicola J Camp & Angela Cox, 2013. "Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-1, July.
    11. Felsenstein, Joseph, 2015. "Covariation of gene frequencies in a stepping-stone lattice of populations," Theoretical Population Biology, Elsevier, vol. 100(C), pages 88-97.
    12. Craig, Sarah J.C. & Kenney, Ana M. & Lin, Junli & Paul, Ian M. & Birch, Leann L. & Savage, Jennifer S. & Marini, Michele E. & Chiaromonte, Francesca & Reimherr, Matthew L. & Makova, Kateryna D., 2023. "Constructing a polygenic risk score for childhood obesity using functional data analysis," Econometrics and Statistics, Elsevier, vol. 25(C), pages 66-86.
    13. Marie-Claude Babron & Marie de Tayrac & Douglas N Rutledge & Eleftheria Zeggini & Emmanuelle Génin, 2012. "Rare and Low Frequency Variant Stratification in the UK Population: Description and Impact on Association Tests," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-9, October.
    14. Anshuman Sewda & A J Agopian & Elizabeth Goldmuntz & Hakon Hakonarson & Bernice E Morrow & Deanne Taylor & Laura E Mitchell & on behalf of the Pediatric Cardiac Genomics Consortium, 2019. "Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
    15. Harriëtte Riese & Loretto M Muñoz & Catharina A Hartman & Xiuhua Ding & Shaoyong Su & Albertine J Oldehinkel & Arie M van Roon & Peter J van der Most & Joop Lefrandt & Ron T Gansevoort & Pim van der H, 2014. "Identifying Genetic Variants for Heart Rate Variability in the Acetylcholine Pathway," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
    16. Franz Förster & David Emmert & Katrin Horn & Janne Pott & Johannes Frasnelli & Mohammed Aslam Imtiaz & Konstantinos Melas & Valentina Talevi & Honglei Chen & Christoph Engel & Michele Filosi & Myriam , 2025. "Genome-wide association meta-analysis of human olfactory identification discovers sex-specific and sex-differential genetic variants," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    17. Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    18. Indra Adrianto & Chee Paul Lin & Jessica J Hale & Albert M Levin & Indrani Datta & Ryan Parker & Adam Adler & Jennifer A Kelly & Kenneth M Kaufman & Christopher J Lessard & Kathy L Moser & Robert P Ki, 2012. "Genome-Wide Association Study of African and European Americans Implicates Multiple Shared and Ethnic Specific Loci in Sarcoidosis Susceptibility," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-10, August.
    19. Seyoun Byun & Jacqueline Shine & Philip Coryell & Nicole E. Kramer & Susan D’Costa & Eliza Thulson & Sylvie M. Parkus & Susan Chubinskaya & Richard F. Loeser & Brian O. Diekman & Douglas H. Phanstiel, 2025. "Response splicing quantitative trait loci in primary human chondrocytes identify putative osteoarthritis risk genes," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    20. 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.

    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.