Genotype imputation in human genomic studies
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 studie...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2024-10-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4292 |
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| author | A. A. Berdnikova I. V. Zorkoltseva Y. A. Tsepilov E. E. Elgaeva |
| author_facet | A. A. Berdnikova I. V. Zorkoltseva Y. A. Tsepilov E. E. Elgaeva |
| author_sort | A. A. Berdnikova |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-b57429621ce048328e9fc2884d9d69d3 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-b57429621ce048328e9fc2884d9d69d32025-02-01T09:58:13ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592024-10-0128662863910.18699/vjgb-24-701498Genotype imputation in human genomic studiesA. A. Berdnikova0I. V. Zorkoltseva1Y. A. Tsepilov2E. E. Elgaeva3Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University,Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University,Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesImputation 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.https://vavilov.elpub.ru/jour/article/view/4292imputationgenotypingsequencinggenome-wide association studyhumandna-microarray |
| spellingShingle | A. A. Berdnikova I. V. Zorkoltseva Y. A. Tsepilov E. E. Elgaeva Genotype imputation in human genomic studies Вавиловский журнал генетики и селекции imputation genotyping sequencing genome-wide association study human dna-microarray |
| title | Genotype imputation in human genomic studies |
| title_full | Genotype imputation in human genomic studies |
| title_fullStr | Genotype imputation in human genomic studies |
| title_full_unstemmed | Genotype imputation in human genomic studies |
| title_short | Genotype imputation in human genomic studies |
| title_sort | genotype imputation in human genomic studies |
| topic | imputation genotyping sequencing genome-wide association study human dna-microarray |
| url | https://vavilov.elpub.ru/jour/article/view/4292 |
| work_keys_str_mv | AT aaberdnikova genotypeimputationinhumangenomicstudies AT ivzorkoltseva genotypeimputationinhumangenomicstudies AT yatsepilov genotypeimputationinhumangenomicstudies AT eeelgaeva genotypeimputationinhumangenomicstudies |