Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift

Urnikytė, Alina; Pranckėnienė, Laura; Domarkienė, Ingrida; Dauengauer-Kirlienė, Svetlana; Molytė, Alma; Matulevičienė, Aušra; Pilypienė, Ingrida; Kučinskas, Vaidutis

doi:10.3390/genes13040569

Cited by 3 publications

(3 citation statements)

References 50 publications

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“…during clean-up work in Chornobyl. We compared their whole-genome data with the WGS dataset of 25 men from LTU [ 30 ]. The LTU dataset was used as the control for common putative selection sweeps.…”

Section: Methodsmentioning

confidence: 99%

Identifying Genomic Signatures of Positive Selection to Predict Protective Genomic Loci in the Cohort of Lithuanian Clean-Up Workers of the Chornobyl Nuclear Disaster

Žukauskaitė

Domarkienė

Matulevičienė

et al. 2023

CIMB

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Some people resist or recover from health challenges better than others. We studied Lithuanian clean-up workers of the Chornobyl nuclear disaster (LCWC) who worked in the harshest conditions and, despite high ionising radiation doses as well as other factors, continue ageing relatively healthily. Thus, we hypothesised that there might be individual features encoded by the genome which act protectively for better adaptiveness and health that depend on unique positive selection signatures. Whole-genome sequencing was performed for 40 LCWC and a control group composed of 25 men from the general Lithuanian population (LTU). Selective sweep analysis was performed to identify genomic regions which may be under recent positive selection and determine better adaptiveness. Twenty-two autosomal loci with the highest positive selection signature values were identified. Most important, unique loci under positive selection have been identified in the genomes of the LCWC, which may influence the survival and adaptive qualities to extreme conditions, and the disaster itself. Characterising these loci provide a better understanding of the interaction between ongoing microevolutionary processes, multifactorial traits, and diseases. Studying unique groups of disease-resistant individuals could help create new insights for better, more individualised, disease diagnostics and prevention strategies.

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Section: Methodsmentioning

confidence: 99%

Identifying Genomic Signatures of Positive Selection to Predict Protective Genomic Loci in the Cohort of Lithuanian Clean-Up Workers of the Chornobyl Nuclear Disaster

Žukauskaitė

Domarkienė

Matulevičienė

et al. 2023

CIMB

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“…We applied the SNP data of 25 trios from Lithuania (25 newborns, 25 mothers, and 25 fathers) obtained by WGS. Inclusion criteria, DNA extraction, WGS data processing were described previously 20 . All participants and their LAR/ parents provided informed consent.…”

Section: Methodsmentioning

confidence: 99%

“…3 in this study (RIII). The second group was formed of adult individuals of Lithuanian origin (LTII) 20 . The first group of subjects are full-term healthy newborns from the general Lithuanian population, born in 2019–2020 (LTI).…”

Section: Methodsmentioning

confidence: 99%

Microevolutionary processes analysis in the Lithuanian genome

Pranckėnienė¹,

Urnikytė²,

Kučinskas³

2023

Sci Rep

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Differences in the relative fitness of genomic variants are foundational, without these, neither natural selection nor adaption can exist. This research analyzed two microevolutionary forces, mutations, and positive selection, using whole genome sequencing data from Lithuanians across three generations: newborns (generation I), their parents (generation II), 60 years old Lithuanians, and the root ancestors (generation III). The main objective was to determine the frequency of mutations under selection in modern humans and how allele frequencies change across generations. Our results show that going through all the landscapes of the relative fitness on each chromosome, the general relative fitness background pattern remains the same in analysed generations. However, the tendency of relative fitness to decrease, in general, is noted. We hypothesize that the de novo genome variants or genome variants with a very low frequency that formed in the previous generation did not have time to be as affected by natural selection, thus, in the following generation, the force of natural selection acting on them is greater and their cumulative relative fitness also decreases. The strong natural selection pressure on the genetic regions that encode the NEGR1 and PTPN1/PTNP21 genes were also identified, highlighting the evolution of the Lithuanian population’s genome over generations, and possible genomic “deficiencies” for better adaptation.

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Disentangling archaic introgression and genomic signatures of selection at human immunity genes

Urnikyte,

Masiulyte,

Pranckeniene

et al. 2023

Infection, Genetics and Evolution

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Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift

Cited by 3 publications

References 50 publications

Identifying Genomic Signatures of Positive Selection to Predict Protective Genomic Loci in the Cohort of Lithuanian Clean-Up Workers of the Chornobyl Nuclear Disaster

Identifying Genomic Signatures of Positive Selection to Predict Protective Genomic Loci in the Cohort of Lithuanian Clean-Up Workers of the Chornobyl Nuclear Disaster

Microevolutionary processes analysis in the Lithuanian genome

Disentangling archaic introgression and genomic signatures of selection at human immunity genes

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