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This journal is published by the University Library System of the University of Pittsburgh as part  

of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. 

 

 

 

 

 

 

 

 

 

The First Kazakh Whole Genomes:  
The First Report of NGS Data 

 

Ainur Akilzhanova1, Ulykbek 

Kairov1, Saule Rakhimova1, 

Askhat Molkenov1, Arang Rhie2, 

Jong-Il Kim2, Jeong-Sun Seo2, 

Zhaxybay Zhumadilov1  
 
1Center for Life Sciences, Nazarbayev 
University, Astana, Kazakhstan; 
2Department of Biochemistry and 
Molecular Biology, Genomic Medicine 
Institute, Seoul National University 
College of Medicine, South Korea 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Vol. 3, Suppl. (2014)   |   ISSN 2166-7403 (online)    

DOI 10.5195/cajgh.2014.146   |   http://cajgh.pitt.edu 

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AKILZHANOVA 

 

 

This work is licensed under a Creative Commons Attribution 4.0 United States License. 

 

This journal is published by the University Library System of the University of Pittsburgh as part  

of its D-Scribe Digital Publishing Program and is cosponsored by the University of Pittsburgh Press. 

 

Central Asian Journal of Global Health 

Volume 3, Suppl. (2014)  |  ISSN 2166-7403 (online)  |  DOI 10.5195/cajgh.2014.146  |  http://cajgh.pitt.edu 

  

 

Abstract 

Introduction: The human genome sequence will underpin human biology and medicine in the next century, providing a single, 

essential reference to all genetic information. Extraordinary technological advances and decreases in the cost of DNA sequencing 

have made the possibility of whole genome sequencing (WGS) feasible as a highly accessible test for numerous indications. The 

international project “Genetic architecture of Kazakh population” is well underway to determine the complete DNA. Next 

generation sequencing is a powerful tool for genetic analysis, which will enable us to uncover the association of loci at specific 

sites in the genome associated with disease. The aim of this study was to introduce first data on WGS of 6 Kazakh individuals. 

Methods: This pilot study is among the first WGS performed on 6 healthy Kazakh individuals, using next generation sequencing 

platform HiSeq2000, Illumina by manufacturer’s protocols. All generated *.bcl files were simultaneously converted and 

demultiplexed using bcl2fasta application. Alignment of sequence reads performed using bwa-mem against human b19 reference 

genome. Sorting, removing of intermediate files, *.bam files assembling, and marking duplicates were performed using PicardTools 

package. GATK haplotype caller tool was used for variant calling. ClinVar, SNPedia, and Cosmic databases were processed to 

identify clinical genomic variants in 6 Kazakh whole genomes. Java Runtime Environment and R. Bioconductor packages were 

installed to perform raw data processing and run program scripts. 

Results: The sequence alignment and mapping procedures on reference genome hg19 of each 6 healthy Kazakh individual were 

completed. Between 87,308,581,400 and 107,526,741,301 total base pairs were sequenced with average coverage x29.85. Between 

98.85% and 99.58% base pairs were totally mapped and on average 96.07% were properly paired. Het/Hom and Ti/Tv ratios for 

each whole genome ranged from 1.35 to 1.52 and from 2.07 to 2.08, respectively. We compared and analyzed each genome with 

on existing clinical databases ClinVar, SNPedia, Cosmic and found from 20 to 25, from 269 to 288, from 7 to 12 SNP records, 

respectively. The availability of a reference Kazakh genome sequences provides the basis for studying the nature of sequence 

variation, particularly single nucleotide polymorphisms.  

Conclusion: The first whole genome sequencing of Kazakhs were performed. In this pilot study, we identified SNPs associated 

with different conditions. Further studies of WGS on Kazakh population are needed to identify possible unique genetic variants in 

Kazakhs. 

Keywords: whole genome sequencing, Kazakh population 

 

 

 

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