FarGen – participants in the genetic research infrastructure of the Faroe Islands

Apol, Katrin Didriksen; Lydersen, Leivur N.; Mortensen, Ólavur; Weihe, Pál; Steig, Bjarni á; Andorsdóttir, Guðrið; Gregersen, Noomi

doi:10.1177/14034948211046817

Cited by 3 publications

(3 citation statements)

References 25 publications

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“…The high incidence and prevalence of PBC and AIH in the Faroe Islands is an excellent opportunity to investigate familial aggregations and genetics using the Faroese national nationwide genealogy registry for data collection and whole-genome sequencing. The Faroese national nationwide genealogy registry is located at the Genetic Biobank and covers the Faroese population from approximately 1650 to date [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

A nationwide study of autoimmune liver diseases in the Faroe Islands: Incidence, prevalence, and causes of death 2004 - 2021

Nielsen

Midjord

Johannesen

et al. 2023

International Journal of Circumpolar Health

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Background and aims: Autoimmune liver diseases are rare diseases, and population-based studies on the epidemiology of autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC) are sparse. We aimed to assess the incidence of AIH, PBC, and PSC in the Faroe Islands. Methods: All cases of AIH, PBC, and PSC diagnosed in the Faroe Islands between January 1 st , 2004, and December 31 st , 2021, were included in this nationwide registry-based cohort study. In addition, we searched all medical records to assess diagnostic criteria and cause of death. Results: The incidences of AIH, PBC, and PSC in the Faroe Islands were 5.2, 2.5 and 0.7 per 100,000 population per year, respectively. Point prevalence per 100,000 population on December 31st 2021, was 71.8 for AIH, 38.5 for PBC, and 11.0 for PSC. Nine AIH patients died after a median of 3 years, three died of hepatocellular carcinoma (HCC), and two died of liver failure. Five PBC patients died after a median of 7 years, one of HCC and one of liver failure. One PSC patient died of cholangiocarcinoma. Conclusion: The incidence and prevalence of AIH, PBC and PSC in the Faroe Islands are among the highest reported in population-based settings.

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Section: Discussionmentioning

confidence: 99%

A nationwide study of autoimmune liver diseases in the Faroe Islands: Incidence, prevalence, and causes of death 2004 - 2021

Nielsen

Midjord

Johannesen

et al. 2023

International Journal of Circumpolar Health

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“…The FarGen cohort comprise 1541 individuals. The recruitment procedures, socio-demographics, availability of the bioresources, DNA extraction, DNA barcoding using the 10x Genomics-Chromium controller, library construction, and sequencing has been described previously [12,15,16]. In short, inclusion criteria were: 1) participants had to be 18 years or older, 2) had to live in the Faroe Islands or be of Faroese descent, and 3) had to join the project voluntarily.…”

Section: Subjects and Methods The Fargen Cohortmentioning

confidence: 99%

“…The Faroe Genome Project, FarGen, is an initiative to build cohorts and infrastructure for genetic research in the isolated population of the Faroe Islands. In the first phase of the project, we collected blood samples from 1541 Faroese individuals, corresponding to 3% of the total population [12]. The purpose of this cohort is to serve as controls for association studies, to build a catalog of genetic variants, and for population genetic studies in general.…”

Section: Introductionmentioning

confidence: 99%

FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands

Mortensen

Thomsen²,

Lydersen³

et al. 2022

Eur J Hum Genet

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Here we present results from FarGen Phase I exomes. This dataset is based on the FarGen cohort, which consists of 1,541 individuals from the isolated population of the Faroe Islands. The purpose of this cohort is to serve as a reference catalog of coding variants, and to conduct population genetic studies to better understand the genetic contribution to various diseases in the Faroese population. The first whole-exome data set comprise 465 individuals and a total of 148,267 genetic variants were discovered. Principle Component Analysis indicates that the population is isolated and weakly structured. The distribution of variants in various functional classes was compared with populations in the gnomAD dataset; the results indicated that the proportions were consistent across the cohorts, but probably due to a small sample size, the FarGen dataset contained relatively few rare variants. We identified 19 variants that are classified as pathogenic or likely pathogenic in ClinVar; several of these variants are associated with monogenetic diseases with increased prevalence in the Faroe Islands. The results support previous studies, which indicate that the Faroe Islands is an isolated and weakly structured population. Future studies may elucidate the significance of the 19 pathogenic variants that were identified. The FarGen Phase I dataset is an important step for genetic research in the Faroese population, and the next phase of FarGen will increase the sample size and broaden the scope.

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

Gislason

2023

BMC Genomics

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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.

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FarGen – participants in the genetic research infrastructure of the Faroe Islands

Cited by 3 publications

References 25 publications

A nationwide study of autoimmune liver diseases in the Faroe Islands: Incidence, prevalence, and causes of death 2004 - 2021

A nationwide study of autoimmune liver diseases in the Faroe Islands: Incidence, prevalence, and causes of death 2004 - 2021

FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands

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

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