Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals

Ulykbek Kairov; Askhat Molkenov; Aigul Sharip; Saule Rakhimova; Madina Seidualy; Arang Rhie; Ulan Kozhamkulov; Maxat Zhabagin; Jong-Il Kim; Joseph H Lee; Joseph D Terwilliger; Jeong-Sun Seo; Zhaxybay Zhumadilov; Ainur Akilzhanova

doi:10.3389/fgene.2022.902804

Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals

Front Genet. 2022 Jul 11:13:902804. doi: 10.3389/fgene.2022.902804. eCollection 2022.

Authors

Affiliations

¹ Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
² Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
³ Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea.
⁴ Sergievsky Center, Departments of Neurology and Epidemiology, Taub Institute, Columbia University, New York City, NY, United States.
⁵ Departments of Genetics and Development and Psychiatry, Sergievsky Center, Columbia University, New York City, NY, United States.
⁶ School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan.

Abstract

Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype-phenotype relations at the population level.

Keywords: Kazakh whole genomes; Kazakhstan; genome analysis; human genetics; next-generation sequencing; whole-genome sequence (WGS); whole-genome sequence analysis.