TY - JOUR

T1 - Exome-wide survey of the Siberian Caucasian population

AU - Yurchenko, Andrey A.

AU - Yudin, Nikolai S.

AU - Voevoda, Mikhail I.

N1 - Publisher Copyright: © 2019 The Author(s).

PY - 2019/4/9

Y1 - 2019/4/9

N2 - 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.

AB - 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.

KW - Associations

KW - Exome sequencing

KW - Population structure

KW - Russia

KW - Siberia

KW - GENE

KW - ASSOCIATION

KW - GENOME

UR - http://www.scopus.com/inward/record.url?scp=85064130796&partnerID=8YFLogxK

U2 - 10.1186/s12881-019-0772-4

DO - 10.1186/s12881-019-0772-4

M3 - Article

C2 - 30967127

AN - SCOPUS:85064130796

VL - 20

SP - 51

JO - BMC Medical Genetics

JF - BMC Medical Genetics

SN - 1471-2350

IS - Suppl 1

M1 - 51

ER -