hg18, hg19, hg38

Question

[GG]

Hi everyone,

I need to map hg18 HGNC gene symbols into ENSGs. My ENSG files are hg38 but my gene names are in hg18. Would I need to first change my hg18 HGNC gene symbols into hg38 HGNC gene symbols and then map to ENSGs or would it be ok to directly map hg18 HGNC symbols to hg38 ENSGs? I am confused because I don't know if gene names change according to the version of the genome assembly. If I do need to change from hg18 HGNC gene symbols into hg38 first, please could you let me know how to do this too? Thank you very much.

Answer 1

[GenoMax]

Your best bet is to use archival copy of Ensembl for hg18 and BioMart to do this mapping. While gene names could have changed across assemblies the changes should be rare and the old names would likely be retained as an alias.

[GG]

I see, thank you very much for your reply. Do you know if there is a way to directly change/compare hg18 ENSGs to hg38 ENSGs? I would like to be sure that there haven't been significant changes.

[GenoMax]

If you are only interested in ENSG id's then you could spot check a few. They would likely have new version numbers at the end but otherwise should be identical. You will run into some that may be retired and no longer valid.

BRCA2 in hg18: http://may2009.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618 There was one transcript in 2009.
BRCA2 in GRCh38: http://www.ensembl.org/Human/Search/Results?q=ENSG00000139618 There are 10 transcripts now.

[GG]

Great. Thank you very much!