Cargando…
A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences
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 nat...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485808/ https://www.ncbi.nlm.nih.gov/pubmed/32915809 http://dx.doi.org/10.1371/journal.pone.0237721 |
_version_ | 1783581220210212864 |
---|---|
author | Svensson, Daniel Rentoft, Matilda Dahlin, Anna M. Lundholm, Emma Olason, Pall I. Sjödin, Andreas Nylander, Carin Melin, Beatrice S. Trygg, Johan Johansson, Erik |
author_facet | Svensson, Daniel Rentoft, Matilda Dahlin, Anna M. Lundholm, Emma Olason, Pall I. Sjödin, Andreas Nylander, Carin Melin, Beatrice S. Trygg, Johan Johansson, Erik |
author_sort | Svensson, Daniel |
collection | PubMed |
description | 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 < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden. |
format | Online Article Text |
id | pubmed-7485808 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-74858082020-09-21 A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences Svensson, Daniel Rentoft, Matilda Dahlin, Anna M. Lundholm, Emma Olason, Pall I. Sjödin, Andreas Nylander, Carin Melin, Beatrice S. Trygg, Johan Johansson, Erik PLoS One Research Article 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 < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden. Public Library of Science 2020-09-11 /pmc/articles/PMC7485808/ /pubmed/32915809 http://dx.doi.org/10.1371/journal.pone.0237721 Text en © 2020 Svensson et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Svensson, Daniel Rentoft, Matilda Dahlin, Anna M. Lundholm, Emma Olason, Pall I. Sjödin, Andreas Nylander, Carin Melin, Beatrice S. Trygg, Johan Johansson, Erik A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title | A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title_full | A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title_fullStr | A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title_full_unstemmed | A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title_short | A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences |
title_sort | whole-genome sequenced control population in northern sweden reveals subregional genetic differences |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485808/ https://www.ncbi.nlm.nih.gov/pubmed/32915809 http://dx.doi.org/10.1371/journal.pone.0237721 |
work_keys_str_mv | AT svenssondaniel awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT rentoftmatilda awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT dahlinannam awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT lundholmemma awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT olasonpalli awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT sjodinandreas awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT nylandercarin awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT melinbeatrices awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT tryggjohan awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT johanssonerik awholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT svenssondaniel wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT rentoftmatilda wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT dahlinannam wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT lundholmemma wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT olasonpalli wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT sjodinandreas wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT nylandercarin wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT melinbeatrices wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT tryggjohan wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences AT johanssonerik wholegenomesequencedcontrolpopulationinnorthernswedenrevealssubregionalgeneticdifferences |