Hello,
I work in the clinical genetics laboratory at Women & Infants Hospital in Providence, RI. I have often used the UCSC browser and also the University of Miami/Oklahoma SNP evaluation tool (Genomic Oligoarray and SNP array evaluation tool v3.0. http://firefly.ccs.miami.edu/cgi-bin/ROH/ROH_analysis_tool.cgi) and found them very useful in my analysis of microarray data.
Today (6/9/2017 at 10 am) I have used both websites and have noticed a discrepancy between the list of genes provided by the SNP evaluation tool in comparison to the list of genes identified by the UCSC genome browser/NCBI link. I have examined the coordinates chr1:146016526-147929323 (set to GRCh37/hg19 for both websites). Using the SNP evaluation tool v3.0 tool, 23 OMIM genes are identified (GPR89A > NBPF11), while using the UCSC browser 10 OMIM genes are identified (NBPF11 > GPR89B). I think that I am inputting the data to the websites correctly, and wonder if there may be an error with one of websites. I will also contact the authors of the Genomic Oligoarray and SNP array evaluation tool v3.0 about this observation.
I hope you will be able to help in this matter.
Thank you.
John
John Pepperell, Ph.D.
Associate Research Scientist
Genetics Division, Department of Pathology and Laboratory Medicine
Women & Infants Hospital
Providence, Rhode Island 02905
Tel: 401-453-7652.
FAX 401-453-7547.
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Dear Brian,
Thank you for your quick reply. I also received a reply from the author of the Miami/Oklahoma SNP tool and have copied and pasted it below. I did try to convert the coordinates chr1:146016526-147929323 using the lift over tool to version hg38, but received a “#Split in new” error message so was unable to try the different build comparison as suggested by the author. However, I am glad that it looks like there is no fundamental problem with either site.
Thanks again.
John
>>
The main reason for the differences is that you compared between different genome assembly versions. Our tool converts the input gene coordinates
into genome version hg38, then looks for OMIM gene located in these coordinates. And the genome assembly version in the UCSC Genome Browser you mentioned is very like set at hg19 as default, if you change the genome version to hg38 in UCSC genome browser
like this,
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A145512842%2D148457202&hgsid=595207749_7InAFcqbA6Oij1FOarezXlLd5qMi
then you should see the similar OMIM ids.
But our tool provides six more OMIM ids (#108770, #116200, #274000, #602390,#614049, #614920 ), which are OMIM phenotype ids, and are usually not provided by UCSC genome browser.
Hope this answers your question.
Best,
Zhijie
From: Brian Lee [mailto:bria...@soe.ucsc.edu]
Sent: Friday, June 09, 2017 1:05 PM
To: Pepperell, John
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] UCSC genome browser error?
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