Segmental Duplication FISH test results?
Lilit Atanesyan
Dear Sir/Madam,
We have been busy with taking closer look at the segmental duplication regions as annotated in the hg38 (see the previous email for details).
By MLPA technique (for gene copy number detection) we had a look at several of these regions. Strangely, as compared to “non-segmental duplicated” genomic regions, we did not detect additional copy number as expected.
Do you possibly have access to experimental evidence to this duplication: any array or FISH results?
Your support is highly appreciated.
With kind regards,
Lilit
Lilit Atanesyan, Ph.D
Senior Product Developer
MRC-Holland - Amsterdam, the Netherlands
email: l.ata...@mlpa.com
web: www.mlpa.com
Tel: +31 88 865 7228
Fax: +31 88 865 7201
Out of office: Tuesdays
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From: Matthew Speir [mailto:msp...@soe.ucsc.edu]
Sent: dinsdag 2 juni 2015 18:41
To: Lilit Atanesyan; gen...@soe.ucsc.edu
Cc: Suvi Savola
Subject: Re: [genome] Chromosome 21p arm genes in GRCh38
Hi Lilit,
Thank you for your question about these duplicated genes on chr21. The example you provided, U2AF1, falls within a contig that was newly added in hg38. It also happens that this gene is part of a segmental duplication that maps to the other U2AF1 location on chr21. In the following session, you can see the newly added contig at the top in red, the U2AF1 transcripts in various shades of blue in the center, and the segmental duplications track in orange at the bottom: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Matt%20Speir&hgS_otherUserSessionName=hg38_U2AF1segDup. If you turn on the "Hg19 Diff" and "Segmental Dups" tracks at look at the other genes that you noted were duplicated on the p-arm, you may see a similar situation where the new contigs added in hg38 that are also part of a segmental duplication.
If a prediction in the UCSC Genes track ever looks suspicious to you, I recommend turning on some of the other gene prediction tracks like GENCODE, RefSeq, or CCDS to see if they also contain a similar gene prediction at that position. In the case of both U2AF1 locations on chr21, all of three of these gene prediction tracks contain transcripts similar to those in UCSC Genes. For the UCSC and GENCODE Genes tracks, you can also click on a particular transcript to see more detailed information about it, including transcript support information. The UCSC Genes track includes transcript support information under the section titled "Gene Model Information". GENCODE Genes includes the "Annotation Method" and "Transcript Support Level" fields which detail how the gene prediction was generated and the level of support for a particular transcript.
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.
Matthew Speir
UCSC Genome Bioinformatics Group
On 5/29/15 5:06 AM, Lilit Atanesyan wrote:
Dear Sir/madam,
As compared to the GRCh37, there are many more genes indicated on the p-arm of chromosome 21.
However, after carefully looking at them, one can see that these genes (especially those close to telomere) are exactly the same as on the 21q arm, with the same exact sequence.
An example is U2AF1 gene; below a blat search of a sequence form that gene in the GRCh38:
BLAT Search Results
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN---------------------------------------------------------------------------------------------------browser details YourSeq 50 1 50 50 100.0% 21 - 43104268 43104317 50browser details YourSeq 50 1 50 50 100.0% 21 - 6495946 6495995 50
Is there any finding supporting this?
Many thanks for your support and consideration.
With best regards,
Lilit
Lilit Atanesyan, Ph.D
Senior Product Developer
MRC-Holland - Amsterdam, the Netherlands
email: l.ata...@mlpa.com
web: www.mlpa.com
Tel: +31 88 865 7228
Fax: +31 88 865 7201
Out of office: Tuesdays
Subscribe here to our periodic newsletter, to receive the latest information about our products, technology and website.
Interested in learning more about MLPA? Please visit our MLPA workshops. More information about our workshops can be found on our website.
Christopher Lee
Hi Lilit,
Thank you for your question about experimental evidence supporting the segmental duplications
track data.
You can read the segmental duplications track description page for information
on how the track was produced.
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genomicSuperDups
Please note that UCSC did not actually generate the data underlying this track, we are only
displaying it. If you have specific questions about how the track was created you can contact
the providers listed in the Credits section of the track description page.
Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.
Christopher Lee
UCSC Genomics Institute
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