Convert to genome location

[nguyendofx]

All,

I've googled but could not get the answer. Hopefully, the experts may help. How to figure out a location on hg19 genome giving a mutation region ?

E.g:
Exon 19
2235-2249 del 15
2235-2252>AAT del18


Ref: http://www.entrogen.com/web2/egfr-mutation-analysis-kit


Thanks,
Ng

[dlgoode]

It would be best if you could get an accession # for the transcript that Entrogen is basing these mutation coordinates on.

Then you can try to retrieve the transcript and map it back to the reference genome using BLAST or BLAT.

[nguyendofx]

How to get an accession #?
I managed to get a Cosmic ID associates with a deletion regions, then I able to get its location on the Ensembl Human genome ref.
e.g 2235-2249 del 15 =>chr7:55244550-55244564 (Ensembl)

The question now is how to find out 'chr7:55244550-55244564 ' on Ensembl is on hg19 (ucsc or ncbi) ? BAMs files aligned with hg19.

Best,
Ng

[DZhang]

Ng,

If you have a BAM file aligned with hg19, use any genome browser (e.g., IGV) and point it to the location for manual examination. I assume you can find the neighboring sequences of that deletion from somewhere else and use them as land marks.

Best regards,
Douglas

https://www.contigexpress.com

[nguyendofx]

Hi Douglas,

Thanks for your input. However, how to get it done with 1000+ coordinates/locations.

How to get the hg19 coordinate from here http://www.sanger.ac.uk/perl/genetic...mmary&id=12560

Thanks,
Ng

[dlgoode]

Hi Ng,

You can download and install a local version of BLAT. It's pretty easy. All you need is the executable and a local FASTA copy of hg19.

Both Ensembl and UCSC should have tools for retrieving sequences for multiple loci from a genome. Have a look around their sites.

To answer the first question in your response to my post, you may have to ask Enterogen what transcript they're basing their mutation annotations on.

Best of luck.