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Volume 17   Issue 2   Year 2022
Linkage Disequilibrium in Targeted Sequencing

Dmitriy Romanov1,2, Nikolai Skoblikow1,3,4

1Medical laboratory CL, Krasnodar, Russia
2Southern Federal University, Rostov-on-Don, Russia
3Kuban State Medical University, Krasnodar, Russia
4Krasnodar Research Center for Animal Husbandry and Veterinary Medicine, Krasnodar, Russia

Abstract. We propose an approach for optimizing the development of gene diagnostic panels, which is based on the construction of non-equilibrium linkage maps. In the process of gene selection we essentially use  genome-wide association analysis (GWAS). Whole-genome analysis of associations makes it possible to reveal the relationship of genomic variants with the studied phenotype. However, the nucleotide variants that showed the highest degree of association can only be statistically associated with the phenotype, not being the true cause of the phenotype. In this case, they may be in the block of linked inheritance with nucleotide variants that really affect the manifestation of the phenotype. The construction of maps of non-equilibrium linkage of nucleotides makes it possible to optimally determine the boundaries of linkage blocks, in which the desired variants fall. The aim of this study was to optimize the demarcation of genomic loci to create targeted panels aimed at predicting susceptibility to SARS-CoV-2 and the severity of COVID-19. The proposed method for selecting loci for a target panel, taking into account nonequilibrium linkage, makes it possible to use the phenomenon of nonequilibrium linkage in order to maximally cover the regions involved in the development of the phenotype, while simultaneously minimizing the length of these regions, and, at the same time, the cost of sequencing.

Key words: COVID-19, linkage disequilibrium, targeted sequencing.


Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2022.17.325
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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