WHOLE-GENOME SEQUENCING AND GENOMIC VARIANT ANALYSIS OF KAZAKH INDIVIDUALS
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Date
2020
Authors
Kairov, Ulykbek
Molkenov, Askhat
Rhie, Arang
Rakhimova, Saule
Yoo, Seong-Keun
Kozhamkulov, Ulan
Sharip, Aigul
Akhmetova, Ainur
Abilmazhinova, Aliya
Zhalbinova, Madina
Journal Title
Journal ISSN
Volume Title
Publisher
International conference "MODERN PERSPECTIVES FOR BIOMEDICAL SCIENCES: FROM BENCH TO BEDSIDEā; National Laboratory Astana
Abstract
Introduction: Kazakhstan is the multi-ethnic country with the dominant Kazakh ethnic group in the
middle of the Eurasian continent. All existing human genetic diversity datasets are only partial representations
of worldwide human diversity. The information about genetic diversity of Kazakh population is
lacking in these datasets. Our study aims to perform whole-genome sequencing of five healthy Kazakhs
to provide insights into genetic structure and diversity of Kazakh populations in Kazakhstan.
Materials and Methods: Genomic DNA of five healthy Kazakhs was isolated from peripheral blood and
sequenced with Illumina HiSeq2000 to target 30-fold coverage. Reads were aligned and assembly to the
human reference genome (NCBI GRCh37, hg19) and reference mitochondrial DNA rCRS (NC_012920) using
Burrows-Wheeler Aligner. GATK and haplotype caller procedure has been used for genomic variants
calling. All the found genomic variants were then further annotated by SIFT, PolyPhen2, SNPedia and
ClinVar using ANNOVAR.
Results: We sequenced and analysed the whole-genomes of ethnic Kazakh individuals with the coverage
(28X-32X). From 98.85 to 99.58 % base pairs were totally mapped with properly mapped 99.06 % in
average. Het/Hom and Ti/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to
2.08, respectively. We have identified the novel variants that previously not catalogued in 1000 Genomes
Project, ExAC or NCBI Reference Assembly dbSNP (snp138, avsnp138, avsnp150, hg19).
Conclusion: We showed high genetic admixture of Kazakh genomes on autosomal level and similar
complex heterogeneity of Central Asian populations. This whole-genome sequences information of
healthy Kazakh individuals may be an important reference for biomedical studies investigating disease
associations and population-wide genomic studies of ethnically diverse Central Asian region.
Acknowledgments: Work was supported by grant projects #AP05134722, #AP05135430 and
#AP05136106 from the Committee Science and Ministry of Education and Science at the Republic of
Kazakhstan.
Description
Keywords
Research Subject Categories::MEDICINE, genomics, DNA, dominant Kazakh ethnic group, whole-genome sequencing