TY - JOUR

T1 - Genotype imputation in human genomic studies

AU - Berdnikova, A. A.

AU - Zorkoltseva, I. V.

AU - Tsepilov, Y. A.

AU - Elgaeva, E. E.

N1 - The work was supported by the Russian Science Foundation grant number 22-15-20037 and the Government of Novosibirsk Region.

PY - 2024/10

Y1 - 2024/10

N2 - Imputation is a method that supplies missing information about genetic variants that could not be directly genotyped with DNA microarrays or low-coverage sequencing. Imputation plays a critical role in genome-wide association studies (GWAS). It leads to a significant increase in the number of studied variants, which improves the resolution of the method and enhances the comparability of data obtained in different cohorts and/or by using different technologies, which is important for conducting meta-analyses. When performing imputation, genotype information from the study sample, in which only part of the genetic variants are known, is complemented using the standard (reference) sample, which has more complete genotype data (most often the results of whole-genome sequencing). Imputation has become an integral part of human genomic research due to the benefits it provides and the increasing availability of imputation tools and reference sample data. This review focuses on imputation in human genomic research. The first section of the review provides a description of technologies for obtaining information about human genotypes and characteristics of these types of data. The second section describes the imputation methodology, lists the stages of its implementation and the corresponding programs, provides a description of the most popular reference panels and methods for assessing the quality of imputation. The review concludes with examples of the use of imputation in genomic studies of samples from Russia. This review shows the importance of imputation, provides information on how to carry it out, and systematizes the results of its application using Russian samples.

AB - Imputation is a method that supplies missing information about genetic variants that could not be directly genotyped with DNA microarrays or low-coverage sequencing. Imputation plays a critical role in genome-wide association studies (GWAS). It leads to a significant increase in the number of studied variants, which improves the resolution of the method and enhances the comparability of data obtained in different cohorts and/or by using different technologies, which is important for conducting meta-analyses. When performing imputation, genotype information from the study sample, in which only part of the genetic variants are known, is complemented using the standard (reference) sample, which has more complete genotype data (most often the results of whole-genome sequencing). Imputation has become an integral part of human genomic research due to the benefits it provides and the increasing availability of imputation tools and reference sample data. This review focuses on imputation in human genomic research. The first section of the review provides a description of technologies for obtaining information about human genotypes and characteristics of these types of data. The second section describes the imputation methodology, lists the stages of its implementation and the corresponding programs, provides a description of the most popular reference panels and methods for assessing the quality of imputation. The review concludes with examples of the use of imputation in genomic studies of samples from Russia. This review shows the importance of imputation, provides information on how to carry it out, and systematizes the results of its application using Russian samples.

KW - DNA-microarray

KW - genome-wide association study

KW - genotyping

KW - human

KW - imputation

KW - sequencing

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85207878063&origin=inward&txGid=1e728886d790aef4af17deb531bcba3d

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001361444000006

UR - https://www.mendeley.com/catalogue/c6fada3e-1991-35c9-85ca-f9fa854fa583/

U2 - 10.18699/vjgb-24-70

DO - 10.18699/vjgb-24-70

M3 - Article

C2 - 39440308

VL - 28

SP - 628

EP - 639

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 6

ER -