Hi,

Just wanted to add in a little more on the "normal" adjacent samples that
TCGA uses.

I work with breast cancer samples, and it has appeared that some(if not
many) of these "normal" adjacent samples are really similar to the tumour
themselves. This has been reported earlier (see
http://cancerres.aacrjournals.org/cgi/content/meeting_abstract/72/24_MeetingAbstracts/P1-03-02
).

Just thought it will be worth sharing.

Cheers,
Jeremy



On Thu, Feb 6, 2014 at 7:23 AM, Steve Lianoglou <lianoglou.steve@gene.com>wrote:

> Hi,
>
> Just wanted to comment on the "paired" TCGA data:
>
> On Wed, Feb 5, 2014 at 2:38 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:
> [snip]
> > I have analysed similar data from TCGA, and the separation is really much
> > too good.  Furthermore there is little evidence of matching.  It would
> > appear that the matched normal cells are not really comparable cells to
> the
> > tumours.  The matched normal samples may actually be profiles of whole
> > blood, a cell type which has a radically different expression profile to
> > epithelial cells.  I really wonder what one can hope to learn about
> cancer
> > by comparing epithelial tumours to blood.
>
> There are samples where you have the "correct" matched sample for gene
> expression, as indeed comparing a solid tumor to "normal blood" to
> identify changes in gene expression would make very little sense.
>
> You just need to be careful in parsing the sample barcodes to ensure
> you are working with the correct stuff.
>
> An explanation of the barcode scheme is here:
> https://wiki.nci.nih.gov/display/TCGA/TCGA+Barcode
>
> You are interested in decoding the "sample" value, which ranges from 01-29.
>
> Explanation is here:
>
> https://tcga-data.nci.nih.gov/datareports/codeTablesReport.htm?codeTable=Sample%20type
>
> There are samples taken from "normal blood" (code = 10), however
> code=11 are solid tissue normals (presumably from the correct tissue
> ;-)
>
> The preponderance of blood samples is, I believe, primarily to be used
> in order to identify somatic mutations -- presumably using the
> exome-seq from "normal blood" would be cleaner than primary tissue,
> depending on how close to the tumor the tissue was taken from.
>
> To figure out what was extracted from the "sample" (DNA, RNA, etc),
> you just decode the "Analyte" part of the barcode:
>
> https://tcga-data.nci.nih.gov/datareports/codeTablesReport.htm?codeTable=portion%20analyte
>
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>
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