what's the best sequencing read length based NGS for HLA typing ?

Question

[demolidd77]

Hi, I got a question , how to choose the best sequencing strategy for a better downstream HLA typing tool analysis,like hlascan,optitype,etc . how long the read length should be ?

Thanks

Answer 1

[Charles Warden]

Maybe it depends upon which HLA gene you are trying to type?

For example, I could get consistent HLA assignments for HLA-A, HLA-B, and HLA-C (which I believe are the main ones used for organ transplant compatibility).

However, I got discordant results for SNP chip imputed types versus NGS assigned types for 3 of the HLA-D genes.

https://github.com/cwarden45/DTC_Scripts/tree/master/AncestryDNA

(scroll down a little bit to see the various HLA assignments for my samples)