Manta analysis in WES

Question

[Eduardo]

Hello, I am analyzing exome sequencing from one patient (paired ends) using Illumina NovaSeq 6000 and Illumina DNA Prep with Enrichment kit. All quality control software used were Falco and MultiQC. The Bioinformatics pipeline used SAREK (Nextflow) with an exome kit bed file (capture regions).

I did a pipeline with GATK and MANTA. The MANTA results (vcf) were filtered with DUPHOLD to exclude bad-quality structural variants. After analyzing MANTA results in Exomiser, I found multiple deletions (heterozygote) in a candidate gene (PRKRA gene, which is highly connected with the symptoms).

Therefore, I screened the PRKRA gene alignment in IGV, and the deletions (detected from MANTA) span almost the whole gene.

Is this evidence that there might be one deletion that covers most of the gene?

Exomiser results with MANTA data:

IGV on PRKRA gene (the deletions found by manta were marked with a red box on top):

[Pierre Lindenbaum]

DUPHOLD for WES ? as duphold looks at the boundaries and you may not have captured those regions in the exome, I don't think that is the tool of choice ? Are you sure it works with WES ?

[Eduardo]

Sorry, my bad. You are right. I forgot to check before using it in the exome data. It will not work...

Answer 1

[GokalpC]

Those het deletions are not really deletions. If you can take a look at in those variants with more detail you will see that those breakpoints are at the exon-intron boundaries almost making it look like you sequenced RNA libraries. PRKRA gene is known to have a retro integration copy in certain HLA haplotypes therefore a non-functional retro copy of the gene is actually contaminating your capture. You can certainly ignore these variants.

For more information you may want to take a look at the below article. Impact of gene retrocopies

[Eduardo]

Thank you so much! I didn't knew it. It help me a lot!

Best regards, Eduardo.