[GET-dev] Re: [GET-Editors] Problem with raw genome data of PGP6:hu04FD18

[Madeleine Ball]

PGP6 requested to have his APOE status redacted. To do this, we removed a
large region surrounding the location (otherwise it would be possible to
infer the genotype based on surrounding information):
http://www.nature.com/ejhg/journal/v17/n2/full/ejhg2008198a.html

This is the only redaction in PGP data and we no longer allow participants
to do this (it is very impractical to redact information, especially if we
want to be releasing raw read data as well). It would be ideal if PGP6
reconsidered this request... we haven't actually approached him and asked,
maybe we should.

  -- Madeleine

On Wed, May 23, 2012 at 4:41 AM, Clara Tang <Clara.Tang at qimr.edu.au> wrote:

> Hi,
>
> I am sorry if this is not the right email list to send. When examining
> the raw genome data of PGP6:hu04FD18, I found a whole region of chr19
> missing (line number:26852942-26852943; loci 22831700-22854093;
> chr19:44411884-46412254).
>
> 22831700 2 1    chr19    44411884    44411884    no-call        ?
> 22831700 2 2    chr19    44411884    44411884    ins        A
> 46    46    VQHIGH
> dbsnp.130:rs68104991;dbsnp.130:rs72528703;dbsnp.129:rs56310260
> 22854093 2 1    chr19    46412254    46412255    ref    A    A
> 182    182    VQHIGH    6318897
>
> As the locus number is not contiguous, I assume there are quite a number
> of variants in between. May I know whether and how I can get the data of
> this region?
>
> Thanks a lot.
>
> Best wishes,
> Clara
>
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