Screening for LOH from CNV results

[Bio-WYX]

Can I determine which regions are LOH(Loss of Heterozygosity)) based on the results of CNV analysis?

[holtjma]

Hi @Bio-WYX,

At this time, HiFiCNV is only reporting copy number changes (i.e. CNVs) based on changes in the read depth signal. Loss of heterozygosity is not reported in the output files. Are you looking for general purpose LOH calling or is it something specific to CNV calls?

Matt

[Bio-WYX]

Thank you for your reply. I want to do general purpose LOH calling, but I have not found a detection tool that does not require control samples and is suitable for PacBio data. I saw that HifiCNV can perform CNV detection and parse vcf files. I wonder if it is possible to perform LOH detection based on this.

[ctsa]

Thanks @Bio-WYX , it is not possible at this time and we don't have a timeline for any such improvement. The depth and minor allele frequency tracks produced by HiFiCNV can be loaded in IGV to visually determine whether a segment is LOH.

[Bio-WYX]

OK, thank you.