Question: ExAC non-TCGA mean
0
gravatar for oghzzang
15 months ago by
oghzzang40
oghzzang40 wrote:

Greetings,

Hi.

I have questions.

I really want to know what "ExAC non-TCGA" means.

As I know, TCGA ExAC is derived from matched germline sample of "cancer patients" and this is annotated by "cancer" samples.

Can I understand that "ExAC non-TCGA" is derived from probably healthy samples?

Thanks.

Oh.

dna db • 806 views
ADD COMMENTlink modified 14 months ago by igor10k • written 15 months ago by oghzzang40

And where did you read that term?

ADD REPLYlink written 14 months ago by WouterDeCoster43k

In case anyone else is wondering, you can get the subset here: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/subsets/

Curiously release 0.3 also has a non-psych subset like @igor mentioned but I'm not sure why release 0.3.1 doesn't include it. I e-mailed them about it a while back and never got a response.

ADD REPLYlink written 14 months ago by manuel.belmadani1.2k

Good point. I am not sure why they got rid of that subset.

ADD REPLYlink written 14 months ago by igor10k

In this web-site. http://exac.broadinstitute.org/faq

ADD REPLYlink modified 3 months ago by RamRS27k • written 13 months ago by oghzzang40
2
gravatar for dagsbio
14 months ago by
dagsbio20
dagsbio20 wrote:

From http://exac.broadinstitute.org/faq:

Do the cancer samples in the database include tumor exomes, or is this from germline samples only? All of the "cancer" samples in the current release of ExAC are blood ("germline") samples from TCGA. We excluded any sample labeled as tumor. However, note that some sample/label swaps may have occurred in TCGA; in addition, it is possible that in some patients the blood samples are contaminated by circulating tumor cells.

So I believe the "ExaC non-TCGA" term comes from taking out the TCGA cohort of 7,601 samples from the total of 60,706 for population-based variant filtering purposes.

ADD COMMENTlink written 14 months ago by dagsbio20

Thanks for your reply. :)

ADD REPLYlink written 13 months ago by oghzzang40
1
gravatar for igor
14 months ago by
igor10k
United States
igor10k wrote:

ExAC is only using normals from TCGA. The non-TCGA subset excludes those samples.

Since the TCGA normals are normal tissue from cancer patients, those samples are not really healthy. That is why you may want to exclude them. They also provide a non-psych cohort for a similar reason.

You may find this previous discussion helpful as well: ExAC variant data

ADD COMMENTlink written 14 months ago by igor10k

Thanks for your help.

ADD REPLYlink written 13 months ago by oghzzang40
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