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Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling.

Authors :
Podvalnyi, Artem
Kopernik, Arina
Sayganova, Mariia
Woroncow, Mary
Zobkova, Gauhar
Smirnova, Anna
Esibov, Anton
Deviatkin, Andrey
Volchkov, Pavel
Albert, Eugene
Source :
International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 1, p363. 10p.
Publication Year :
2025

Abstract

A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a significant challenge in genome analysis due to their high sequence similarity to the parent genes and their frequent absence in the reference genome. This homology can lead to errors in variant identification, as sequences derived from processed pseudogenes can be incorrectly assigned to parental genes, complicating correct variant calling. In this study, we quantified the occurrence of variant calling errors associated with pseudogenes, generated by the most popular germline variant callers, namely GATK-HC, DRAGEN, and DeepVariant, when analysing 30x human whole-genome sequencing data (n = 13,307). The results show that the presence of pseudogenes can interfere with variant calling, leading to false positive identifications of potentially clinically relevant variants. Compared to other approaches, DeepVariant was the most effective in correcting these errors. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
16616596
Volume :
26
Issue :
1
Database :
Academic Search Index
Journal :
International Journal of Molecular Sciences
Publication Type :
Academic Journal
Accession number :
182451466
Full Text :
https://doi.org/10.3390/ijms26010363