Genetics in an isolated population like Finland: a different basis for genomic medicine?

Kääriäinen, Helena; Muilu, Juha; Perola, Markus; Kristiansson, Kati

doi:10.1007/s12687-017-0318-4

Cited by 45 publications

(42 citation statements)

References 45 publications

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“…unsuitable genetic composition relative to the new environment because of a founder effect. For example, in the Finnish human population, a founder effect due to geographic and cultural isolation has caused enrichment of diseasecausing gene variants and losses of others (Kääriäinen et al 2017). Genetic diversity is a particularly critical determinant of the viability and conservation of rare or endangered species.…”

Section: Introductionmentioning

confidence: 99%

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

et al. 2020

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Background Reduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was hunted to extinction from Finland and many other countries in Europe in the nineteenth century. In Finland, the species was reintroduced in the 1930s with only a few individuals from Norway. Re-introductions were performed also in other countries of northern Europe and as a result, Eurasian beaver populations have undergone population bottlenecks leading to low levels of genetic diversity. Materials and Methods Here, 200 Eurasian beaver samples from Finland, Estonia, Lithuania, and Russian Karelia were investigated using 12 microsatellite markers to examine the level of genetic diversity and relationship between the populations. Results While Russian and Estonian populations were genetically the closest, the Finnish population was clearly distinct from all others and had the lowest genetic variability among the study populations. This may be deleterious to the population especially in a changing environment. Conclusions Genetic rescue could be the best solution to increase the genetic diversity and improve the future prospects of the population, although more studies are required to resolve the optimal source population.

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Section: Introductionmentioning

confidence: 99%

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

et al. 2020

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“…These findings, alongside high mortality rate, make this network an area of interest to further investigate treatments for Spanish and Italian COVID-19 patients with current medications for liver disease as an option for those who develop liver malfunction during the infection while those with a pre-existing liver condition may need to go through a more thorough follow up after the recovery period. As mentioned previously, Finland has a unique genetic background originated from geographic and cultural isolation and its population has been the focus of heritable diseases studies and precision medicine treatments [91]. Interestingly, as mentioned above liver cancer is the main cause of liver disease deaths in Spain and Italy while it is alcohol consumption in Finland.…”

Section: Discussionmentioning

confidence: 99%

Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations

Moya

Farashi

Suravajhala

et al. 2020

Preprint

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AbstractAimThe novel SARS-CoV-2 virus, which causes the COVID-19 disease, has infected more than 10 million people and caused 500K deaths worldwide. In Europe, over 2 million confirmed cases have been reported, while nearly 200K people have died from the disease. Despite strict containment measures in Spain and Italy after the first reported COVID-19 patient, these two countries have remained in the top five European nations with the highest mortality rate for over two months. We hypothesised that a genetic mechanism could partially explain the poor survival outcome observed in these two countries.MethodsAn extensive literature search to identify human candidate genes linked to SARS-CoV infection, host immune evasion and disease aggressiveness was carried out. Pathway analysis (IPA) was performed to select the most significantly associated canonical signalling pathways with the genes of interest. The genetic variants’ at these genes with ±1Mb flanking region was extracted (GRCh37/hg19 built). Over 80 million single nucleotide polymorphisms (SNPs) were analysed in genome-wide data of 2,504 individuals (1000 genomes, phase III, https://www.internationalgenome.org/). Principal component (PC) analysis was performed, ancestry by the whole genome was inferred and subsets of the regions of interest were extracted (PLINK v1.9b, http://pngu.mgh.harvard.edu/purcell/plink/). PC1 to PC20 values from five European ancestries, including the Spanish and Italian populations, were used for PC analysis. Gene function predictions were run with our genes of interest as a query to the GeneMANIA Cytoscape plugin (https://genemania.org/).ResultsA total of 437 candidate genes associated with SARS were identified, including 21 correlated with COVID-19 aggressiveness. The two most significant pathways associated with all 437 genes (Caveolar-mediated Endocytosis and MSP-RON Signalling) did not show any segregation at the population level. However, the most significant canonical pathway associated with genes linked to COVID-19 aggressiveness, the Hepatic Fibrosis and Hepatic Stellate Cell Activation, showed population-specific segregation. Both the Spanish and Italian populations clustered together from the rest of Europe. This was also observed for the Finnish population but in the opposite direction. These results suggest some of the severe COVID-19 cases reported in Spain and Italy could be partially explained by a pre-existing liver condition (especially liver cancer) and/or may lead to further COVID-19 related liver complications.

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“…We performed the analysis on the two levels: with the Finnish (FIN) population for population genetic analysis (PCA, ADMIXTURE, Fst) and without FIN population to test the allele frequency differences for clinically and pharmacogenetically important variants. The FIN population was excluded from the second analysis as the most divergent European population with unique history [12]. To reduce the influence of the tightly linked loci on the patterns of population structure we applied the linkage-disequilibrium pruning using PLINK V1.93 software (Table 1).…”

Section: Methodsmentioning

confidence: 99%

Exome-wide survey of the Siberian Caucasian population

2019

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Background Population structure is an important factor in the genetic association studies but often remains underexplored for many human populations. We identified exome variants in 39 Siberian Caucasian individuals from Novosibirsk, Russia and compared their genetic allele frequencies with European populations from 1000 Genomes Project. Methods The study participants were from Novosibirsk and represented people with monogenic diabetes, healthy individuals and a cohort from the tick-borne encephalitis study. Isolated DNA was enriched using Agilent SureSelect V5 kit and sequenced on Illumina HiSeq 4000 and genetic variants were identified using GATK pipeline. To estimate the patterns of the population structure we used PCA and ADMIXTURE analysis. Pharmocogenetically and medically important variants were annotated based on PharmGKB and ClinVar databases. Results The analysis identified low, but highly significant population differentiation attributed to numerous loci between the Siberian Caucasian population and other European population samples as well as a higher proportion of the Finnish genetic component in the studied sample. The medical and pharmacogenetic annotation of highly significantly differentiated variants between the Novosibirsk and the combined European populations revealed a number of important genetic polymorphisms located in such genes as FCGR3B , TYR , OCA2 , FABP1 , CHEK2 and SLC4A1 . Conclusions The study reports for the first time an exome-wide comparison of a population from Russia with European samples and emphasizes the importance of population studies with medical annotation of variants.

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Genetics in an isolated population like Finland: a different basis for genomic medicine?

Cited by 45 publications

References 45 publications

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations

Exome-wide survey of the Siberian Caucasian population

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