SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands

Abstract Background The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was impleme...

Full description

Bibliographic Details
Main Author: Hannes Gislason
Format: Article
Language:English
Published: BMC 2023-11-01
Series:BMC Genomics
Subjects:
Online Access:https://doi.org/10.1186/s12864-023-09763-x
_version_ 1827635465174384640
author Hannes Gislason
author_facet Hannes Gislason
author_sort Hannes Gislason
collection DOAJ
description Abstract Background The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals. Results We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years $$\sim 50-300$$ ∼ 50 - 300 with a maximum consanguineous population in year $$\sim 600$$ ∼ 600 and similarly consanguineous between years $$500-700$$ 500 - 700 . The ancestry analysis shows the population descends from founders of $$>99\%$$ > 99 % European and $$<1\%$$ < 1 % Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants. Conclusions The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.
first_indexed 2024-03-09T15:27:04Z
format Article
id doaj.art-378e0a9af902489a9607c91f09d1a1ee
institution Directory Open Access Journal
issn 1471-2164
language English
last_indexed 2024-03-09T15:27:04Z
publishDate 2023-11-01
publisher BMC
record_format Article
series BMC Genomics
spelling doaj.art-378e0a9af902489a9607c91f09d1a1ee2023-11-26T12:26:05ZengBMCBMC Genomics1471-21642023-11-0124111410.1186/s12864-023-09763-xSNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe IslandsHannes Gislason0Faculty of Science and Technology, University of the Faroe IslandsAbstract Background The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals. Results We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years $$\sim 50-300$$ ∼ 50 - 300 with a maximum consanguineous population in year $$\sim 600$$ ∼ 600 and similarly consanguineous between years $$500-700$$ 500 - 700 . The ancestry analysis shows the population descends from founders of $$>99\%$$ > 99 % European and $$<1\%$$ < 1 % Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants. Conclusions The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.https://doi.org/10.1186/s12864-023-09763-xWG SNPsHeterozygosityRelatednessROHInbreedingmaf
spellingShingle Hannes Gislason
SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
BMC Genomics
WG SNPs
Heterozygosity
Relatedness
ROH
Inbreeding
maf
title SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
title_full SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
title_fullStr SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
title_full_unstemmed SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
title_short SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands
title_sort snp heterozygosity relatedness and inbreeding of whole genomes from the isolated population of the faroe islands
topic WG SNPs
Heterozygosity
Relatedness
ROH
Inbreeding
maf
url https://doi.org/10.1186/s12864-023-09763-x
work_keys_str_mv AT hannesgislason snpheterozygosityrelatednessandinbreedingofwholegenomesfromtheisolatedpopulationofthefaroeislands