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Updated: Jun 3, 2025

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

Artem Podvalnyi1,2, Arina Kopernik1, Mariia Sayganova1

  • 1Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia.

International Journal of Molecular Sciences
|January 11, 2025
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Summary

Processed pseudogenes cause variant calling errors in human genome analysis. DeepVariant showed the most effectiveness in correcting these errors, improving variant identification accuracy.

Keywords:
ACMGSNPsprocessed pseudogenes

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Processed pseudogenes are non-functional gene copies that pose challenges in genome analysis due to high sequence similarity.
  • Their homology to parent genes can lead to incorrect variant identification and complicate accurate variant calling.
  • Pseudogenes are frequently absent in reference genomes, further hindering analysis.

Purpose of the Study:

  • To quantify variant calling errors introduced by processed pseudogenes.
  • To evaluate the performance of popular germline variant callers in handling pseudogene-associated errors.
  • To identify the most effective variant caller for mitigating pseudogene interference.

Main Methods:

  • Analysis of 30x human whole-genome sequencing data from 13,307 individuals.
  • Quantification of variant calling errors generated by GATK-HC, DRAGEN, and DeepVariant.
  • Comparative assessment of variant caller performance in the presence of processed pseudogenes.

Main Results:

  • Processed pseudogenes significantly interfere with germline variant calling, leading to false positive variant identifications.
  • The presence of pseudogenes can result in the misassignment of variants to parental genes.
  • DeepVariant demonstrated superior performance in correcting pseudogene-associated variant calling errors compared to GATK-HC and DRAGEN.

Conclusions:

  • Pseudogenes represent a critical challenge for accurate variant calling in human whole-genome sequencing.
  • Variant callers differ in their ability to handle pseudogene interference, with DeepVariant showing the best performance.
  • Improved methods for pseudogene handling are essential for reliable variant identification, especially for clinically relevant variants.