Enquiry about new/putative pseudogene KCNE1b

[Ivo van Bostelen]

Dear Sir/Madam,

 

I hope you can help me as I have a question regarding a change between the current genome build (hg38) and previous versions. In hg38 there is a pseudogene annotated as KCNE1b (chr21:7,816,678-7,829,592) that has not been there in previous builds. I am a geneticist with an interest in the KCNE1 gene (chr21:34,446,688-34,511,339) which is associated to a disease called Long-QT syndrome (LQTS). The two exons of the pseudogene KCNE1b are 100% homologous to exon 3 and 4 of KCNE1. As I said, none of the previous genome builds have the pseudogene.

 

At the company I work (MRC Holland) we have developed an MLPA assay to determine copy numbers of genes (and their exons) that are associated to LQTS (MLPA probemix P114; link to the product on our website). All data we obtained from healthy individuals and positive controls support the notion that the pseudogene KCNE1b is not really present in the human genome. Could it be an error in the hg38 genome build? Or is there another likely explanation?

 

Thank you in advance for your time.

 

All the best,

 

Ivo van Bostelen

Project Leader | IVD development | MRC Holland BV

Tel: +31 (0) 88 865 7200 | Willem Schoutenstraat 1 | 1057 DL | Amsterdam

 

 

[Jairo Navarro Gonzalez]

Hello Ivo,

Thank you for using the UCSC Genome Browser and your inquiry.

The discrepancy you are seeing between the different human assemblies is due to the different tracks that are on by default. The knownGene track for hg38 uses the GENCODE, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene, dataset whereas hg19 uses the UCSC Genes, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene, dataset. You can see that the KCNE1b gene is present on both assemblies, but you can only view the annotation if you use the GENCODE dataset.

hg19: https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr21:35,818,986-35,828,107&hideTracks=1&knownGene=full&wgEncodeGencodeV28lift37=full&wgEncodeGencodeSuper=full

hg38: https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr21:7,816,678-7,829,592&hideTracks=1&knownGene=full

You can read more about this change from our blog post:

http://genome.ucsc.edu/blog/new-default-gene-set-on-grch38-gencode-basic-genes/

If you do believe this could be an error in the hg38 genome build, you can contact the Genome Reference Consortium (GRC) that produced the assembly GRCh38 from which we built the hg38 database: https://www.ncbi.nlm.nih.gov/grc/contact-us

I hope this is helpful. If you have any further questions, please reply 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.

Jairo Navarro 
UCSC Genome Browser

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