Gene sequences for a cell line

Question

[jszkodon]

Hi all! I am looking for HLA gene sequences for a specific cell line (GM12878). Does anyone have any info about where I can find them? Thanks!

Answer 1

[Amos Bairoch]

The genome and exome sequence of GM12878 is available from:

https://www.internationalgenome.org/data-portal/sample/NA12878

You will also find links to Nanopore sequencing data in: PubMed=29431738 (DOI=10.1038/nbt.4060):

https://github.com/nanopore-wgs-consortium/NA12878

https://www.ebi.ac.uk/ena/browser/view/PRJEB23027

They seem to have a better assembly for the HLA region:

"Exon sequences belonging to the six classical HLA genes were extracted from the phased assembly, and HLA types called at G group resolution. These results were compared to GM12878 HLA type reference data. For the class I and II HLA genes, with the exception of one DRB1 haplotype, there was good agreement between the best-matching reference type and the alleles called from the assembly (edit distance 0–1). Detailed examination of HLA-DRB1, however, showed that one exon (exon 2) is different from all reference types in the assembly, a likely error in the assembly sequence."

Software to specifically analyze the HLA region is described in:

https://pubmed.ncbi.nlm.nih.gov/27792722/

Which as examples analyze GM12878 and her two parents

This will allow me to add an HLA typing info for these cell lines in the next release of the Cellosaurus entry:

https://web.expasy.org/cellosaurus/CVCL_7526

HLA typing: A01,11; B08,56; C01,07; DPA101:03:01,02:01:01; DPB104:01:01,14:01; DQA101,05; DQB102,05; DRB101,03:01 (PubMed=27792722).