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Question: ExAC non-TCGA mean
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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.

ADD COMMENTlink 11 months ago oghzzang • 40 • updated 10 months ago igor 7.7k
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And where did you read that term?

ADD REPLYlink 10 months ago
WouterDeCoster
39k
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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 10 months ago
manuel.belmadani
• 830
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Good point. I am not sure why they got rid of that subset.

ADD REPLYlink 10 months ago
igor
7.7k
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In this web-site.http://exac.broadinstitute.org/faq

ADD REPLYlink 9 months ago
oghzzang
• 40
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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 10 months ago dagsbio • 20
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Thanks for your reply. :)

ADD REPLYlink 9 months ago
oghzzang
• 40
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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 10 months ago igor 7.7k
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Thanks for your help.

ADD REPLYlink 9 months ago
oghzzang
• 40

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