Regarding to the assumingly missing "HLA-DRB1" gene on the loci grch38 Alt_loci chr6_GL000254v2

[Field Tian]

Dear USCS genome browser group.

Thank you for the effort to maintain such a helpful database. I'm Field (Ye Tian). We perform HLA typing service at Hangzhou, China. 

We used to rely on IMGT database heavily until we found the importance to understand the whole assembly of a haplotype. 

I looked into the gene HLA-DRB1 when I had some doubt. I found the alt loci GL000251v2 to GL000256v2 on chr6 should encompass the HLA-I and HLA-II area. Surprisingly, I didn't find the HLA-DRB1 gene on locus GL000254v2. I know really little about the genome browser, so I don't know how to validate my finding. 

Very few publications report the phenomenon of missing DRB1 gene on a haplotype. I occasionally found one, "OR47 The mystery of the missing DRB1 allele – solved by NGS!!!", reporting a deleted version of HLA-DRB1*15 allele that's associated with a HLA-A*25:01. That's obviously not the case of GL000254v2.

I wonder how I may validate. 

Thank you very much. 

Field

[Gerardo Perez]

Hello, Field.

Thank you for your interest in the Genome Browser and your question regarding the HLA-DRB1 gene.

According to the Alt Haplotypes track, the HLA-DRB1 gene is missing in the GL000254v2 and GL000250v2 alternate haplotypes. You can view this in the following session: https://genome.ucsc.edu/s/gperez2/mlq_34430_1.

Additionally, you may find the HPRC pairwise alignments (chains) track helpful. This track shows regions of the human genome that are alignable to other Homo sapiens genomes. Alignable parts are represented by thick blocks (look like exons), while alignable parts between these are shown with thin lines (look like introns). You can explore these alignments in the DRB1 locus using the following session: https://genome.ucsc.edu/s/Max/hladrb1.

If you have any questions or need further assistance, please feel free to reach out to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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