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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Variant calling tools often assume human genome characteristics, limiting their effectiveness in diverse species.
  • DeepVariant (DV) is a powerful variant caller, but its performance with non-human genomes is not fully understood.
  • The development of universal algorithms necessitates evaluating their impact across different species.

Purpose of the Study:

  • To assess the performance of human-trained variant callers, including DeepVariant with allele frequency (DV-AF) and DeepTrio (DT), on bovine genomes.
  • To develop and validate a novel approach, TrioTrain, for extending DV to diploid species lacking established reference resources like Genome-in-a-Bottle (GIAB).
  • To create the first multispecies-trained DV-AF checkpoint using bovine trios.

Main Methods:

  • The TrioTrain approach automates DV extension for diploid species by using a region shuffling strategy to overcome SLURM-based cluster limitations.
  • Animal truth labels were curated to exclude Mendelian discordant sites before training DV for accurate offspring genotyping.
  • Bovine trios (cattle, yak, bison) were utilized to generate a multispecies-trained DV-AF checkpoint.

Main Results:

  • A multispecies-trained DV-AF checkpoint achieved a mean SNV F1 score >0.990 during GIAB benchmarking, despite limitations in bovine truth sets for repetitive regions.
  • A bovine-trained DV checkpoint (checkpoint 28) reduced the Mendelian inheritance error (MIE) rate by 50% compared to the default human-trained DV when tested on HG002.
  • Checkpoint 28 demonstrated a mean MIE rate of 0.03% across three bovine interspecies cross genomes.

Conclusions:

  • A multispecies, trio-based training strategy effectively reduces inheritance errors in single-sample variant calling.
  • Exclusively human-trained models hinder the application of deep learning-based variant calling to new species.
  • The diverse ancestry within bovids highlights the need for advanced comparative genomics tools tailored for non-human species.