Stream: genomics
Topic: HLA Haplotype from NGS data
Bob Dolin (Oct 05 2020 at 21:27):
Hi @ Bob Milius . Is there open source software that computes HLA haplotypes from short-read NGS data?
Joel Schneider (Oct 05 2020 at 23:02):
I haven't followed it closely, but some work has been done on deriving HLA genotyping from typical WGS data, e.g.:
https://doi.org/10.1016/j.humimm.2015.07.183
However, the HLA genotyping computable from typical (short read) WGS data appears to have limited accuracy.
My understanding is, to get really accurate HLA results via NGS methods, custom amplicons/probes are needed.
(I'm not aware of open source software for this, but the short-read NGS data may have intrinsic limitations regarding HLA.)
Joel Schneider (Oct 05 2020 at 23:08):
Another related article:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3575-z
Joel Schneider (Oct 05 2020 at 23:29):
If you're interested in (probabilistic) HLA haplotype predictions based on population-level haplotype frequencies, HaploStats may be of some use:
https://haplostats.org
Bob Dolin (Oct 05 2020 at 23:32):
Thanks @Joel Schneider , I will take a look at these. I was kinda suspecting limited accuracy, but thought it might still be an interesting exercise.
Bob Milius (Oct 06 2020 at 20:21):
Most (if not all) clinical labs reporting HLA genotyping use commercial software, e.g., GenDx NGSengine, CareDx Assign TruSight HLA, Omixon HLA Explore, etc. NMDP spent some time working on an open-source pipeline for HLA allele assignment, but it's still pretty incomplete. As part of our Sync4Genes project, we're developing a GenDx to FHIR tool to create HLA reports compliant with our HLA Reporting IG. We hope to work with other vendors to develop similar tools.
Bob Milius (Oct 06 2020 at 20:25):
btw, I assume when @Bob Dolin mentioned HLA haplotypes, you meant HLA alleles (gene level variation). In the HLA community, HLA haplotypes refer to different gene-level alleles from different HLA genes on the same chromosome (e.g., HLA-A, HLA-B, HLA-C)
Bob Dolin (Oct 06 2020 at 21:44):
Thanks @ Bob Milius , yes, that's what I meant. And thanks for the info.
Bob Dolin (Nov 25 2020 at 22:00):
@ Bob Milius @Joel Schneider Just a quick fyi, I did find some open source software, xHLA [https://github.com/humanlongevity/HLA], that allowed me to compute HLA alleles from WGS sequencing data.
Bob Milius (Nov 30 2020 at 16:32):
Thanks @Bob Dolin . I'm not familiar with that code. I'll ask our bioinformatics group to see if they have any opinions about it.
Joel Schneider (Dec 01 2020 at 02:58):
HLA- A, B, C, DPB1, DQB1, and DRB1 are indeed the main HLA genes we currently use for tissue type matching and transplantation.
However, it looks like the license from Human Longevity, Inc. ("HLI") only allows for non-commercial academic research use.
Last updated: Apr 12 2022 at 19:14 UTC
