Comments on: The PGP and me, Part I http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/ Thu, 11 Mar 2010 21:29:08 +0000 http://wordpress.org/?v=2.2.1 By: MicrobiologyBytes » Blog Archive » Gene Genie #14: Bugs and Beyond http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-14316 MicrobiologyBytes » Blog Archive » Gene Genie #14: Bugs and Beyond Mon, 06 Apr 2009 10:46:27 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-14316 [...] considerations from an intriguingly personal standpoint are the subject of the description of the Personal Genome Project by GenomeBoy. Sandwalk believes that aside from the safety issue, there doesn’t seem to be [...] […] considerations from an intriguingly personal standpoint are the subject of the description of the Personal Genome Project by GenomeBoy. Sandwalk believes that aside from the safety issue, there doesn’t seem to be […]

]]> By: Way To Test Paternity http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-804 Way To Test Paternity Mon, 04 Feb 2008 16:30:58 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-804 <strong>DNA Paternity Testing and Child Support...</strong> Part One of a two-part series about the legal implications of DNA paternity testing... DNA Paternity Testing and Child Support…

Part One of a two-part series about the legal implications of DNA paternity testing…

]]> By: Pack of Sensations » Blog Archive » What’s on the web? (26 August 2007) http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-14 Pack of Sensations » Blog Archive » What’s on the web? (26 August 2007) Sun, 26 Aug 2007 22:21:24 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-14 [...] The PGP and me, Part I (GenomeBoy): I have yet to articulate the appeal of the Personal Genome Project in a way that really captures how I feel. [...] […] The PGP and me, Part I (GenomeBoy): I have yet to articulate the appeal of the Personal Genome Project in a way that really captures how I feel. […]

]]> By: Gene Genie #14: Bugs and Beyond « MicrobiologyBytes http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-12 Gene Genie #14: Bugs and Beyond « MicrobiologyBytes Sun, 26 Aug 2007 02:28:12 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-12 [...] considerations from an intriguingly personal standpoint are the subject of the description of the Personal Genome Project by GenomeBoy. Sandwalk believes that aside from the safety issue, there doesn’t seem to be [...] […] considerations from an intriguingly personal standpoint are the subject of the description of the Personal Genome Project by GenomeBoy. Sandwalk believes that aside from the safety issue, there doesn’t seem to be […]

]]> By: misha http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-11 misha Fri, 24 Aug 2007 03:02:56 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-11 <p>Hi Lee--</p> <p>First of all, I hope you're healthy and that the nodule is nothing more than an "incidentaloma." (By the way, if you haven't read it already, I highly recommend Zak Kohane's paper on "the incidentalome," JAMA. 2006 Jul 12;296(2):212-5.) </p> <p>Second, while it's nice of you to say, I don't think my participation in the PGP is particularly bold, to say nothing of this blog. Perhaps when I've gotten my sea legs and have had a chance to really push the bounds of good taste, then maybe it will be hailed--or derided--as bold. For now, it may be immodest and narcissistic, but I wouldn't call it bold. I think, as Esther Dyson has said so eloquently in various outlets, the PGP is about reassuring people that genomic information is not a voodoo doll. If we thought it would rise up and bite us in the ass, we wouldn't have signed on the dotted line. </p> <p>Finally, I think ClinSeq is an interesting test case for medical sequencing and I hope to learn more about it--I hope you'll keep us updated. I think you wanting access to your own sequence may be exceptional for the moment, but it won't be for very long. It seems to me this is really about disclosure of research results--or are they even research results? In any case, I believe we're still in the top or perhaps bottom of the first inning as far all of that stuff goes: defining genomic human subjects research beyond conventional IRB definitions, deciding what subjects have a right to expect, re-identification, etc.</p> Hi Lee–

First of all, I hope you’re healthy and that the nodule is nothing more than an “incidentaloma.” (By the way, if you haven’t read it already, I highly recommend Zak Kohane’s paper on “the incidentalome,” JAMA. 2006 Jul 12;296(2):212-5.)

Second, while it’s nice of you to say, I don’t think my participation in the PGP is particularly bold, to say nothing of this blog. Perhaps when I’ve gotten my sea legs and have had a chance to really push the bounds of good taste, then maybe it will be hailed–or derided–as bold. For now, it may be immodest and narcissistic, but I wouldn’t call it bold. I think, as Esther Dyson has said so eloquently in various outlets, the PGP is about reassuring people that genomic information is not a voodoo doll. If we thought it would rise up and bite us in the ass, we wouldn’t have signed on the dotted line.

Finally, I think ClinSeq is an interesting test case for medical sequencing and I hope to learn more about it–I hope you’ll keep us updated. I think you wanting access to your own sequence may be exceptional for the moment, but it won’t be for very long. It seems to me this is really about disclosure of research results–or are they even research results? In any case, I believe we’re still in the top or perhaps bottom of the first inning as far all of that stuff goes: defining genomic human subjects research beyond conventional IRB definitions, deciding what subjects have a right to expect, re-identification, etc.

]]> By: Lee Watkins Jr http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-9 Lee Watkins Jr Thu, 23 Aug 2007 22:11:11 +0000 http://genomeboy.com/2007/08/22/the-pgp-and-me-part-i/#comment-9 You are very bold to do this; I mean, to participate in the PGP and also to blog about it. But given the public nature and stated goals of this project, it seems really important for participants like yourself to carry on a public dialog. I had a conversation with George about all this after a related talk he gave in late 2005, when I was agonizing over similar issues related to depositing high-res SNP data into public databases like dbSNP (you don't need a whole genome for most of the consent issues you list above to apply!). This was before NIH decided that GWAS data should go into dbGaP and solicited comments on the <a href="http://grants.nih.gov/grants/gwas/" rel="nofollow">proposed policy.</a> You see, I work in a high-throughput genotyping lab, the <a href="http://www.cidr.jhmi.edu" rel="nofollow"> Center for Inherited Disease Research</a> at Johns Hopkins, where most of our work is done under contract to the NHGRI. Like you, I think about these issues every single day, and it is not at all abstract but it has always bothered me that all the thousands of people whose DNA samples we process will forever be anonymous to me even though we are handling and discussing such fundamental aspects of their lives. Also like you, I made a similar decision in order to gain a more direct and complete understanding of these matters, which was to volunteer for the NIH <a href="http://www.genome.gov/25521313" rel="nofollow">ClinSeq </a> project, whose objective is to <i> "explore the fundamental medical, molecular and bioinformatic challenges facing individualized gene sequencing in a clinical research setting." </i> The first thing I did was meet with a genetic counselor who was very thorough about explaining the implications of study participation and what I could and probably couldn't expect to learn from the sequencing results in terms of disease risk. But the one question she wasn't prepared for was when I asked "So, how do I get my sequence?" to which the answer was something like, "We really haven't discussed that." To which I replied, "Well, you probably should... I may be unusual in that I want it and know what to do with it, but certainly other people will eventually want it too." Especially since in this case my sequence will be part of my medical record - at least the parts that harbor a potentially significant result, which will then be re-sequenced in a CLIA-approved lab. I've already talked to my personal care physician about it and he's actually quite excited about the prospect of actually being able to practice "personalized genomic medicine" of sorts... after all, it has to start somewhere with somebody. Another surprise to me was that the first real issue that came up wasn't related to the medical sequencing at all, but was a purely medical issue that turned up in the (very thorough and elaborate) testing they did and will continue to do. This hadn't really occurred to me as a possibility. A high-res CT scan found a 2mm "nodule" on my left lung, which is probably nothing but has to be followed up in a few months just in case. I'm not particularly worried but if it does turn out to be something I'll be very glad they found it at 2mm rather than later. You are very bold to do this; I mean, to participate in the PGP and also to blog about it. But given the public nature and stated goals of this project, it seems really important for participants like yourself to carry on a public dialog. I had a conversation with George about all this after a related talk he gave in late 2005, when I was agonizing over similar issues related to depositing high-res SNP data into public databases like dbSNP (you don’t need a whole genome for most of the consent issues you list above to apply!). This was before NIH decided that GWAS data should go into dbGaP and solicited comments on the proposed policy. You see, I work in a high-throughput genotyping lab, the Center for Inherited Disease Research at Johns Hopkins, where most of our work is done under contract to the NHGRI. Like you, I think about these issues every single day, and it is not at all abstract but it has always bothered me that all the thousands of people whose DNA samples we process will forever be anonymous to me even though we are handling and discussing such fundamental aspects of their lives. Also like you, I made a similar decision in order to gain a more direct and complete understanding of these matters, which was to volunteer for the NIH ClinSeq project, whose objective is to “explore the fundamental medical, molecular and bioinformatic challenges facing individualized gene sequencing in a clinical research setting.” The first thing I did was meet with a genetic counselor who was very thorough about explaining the implications of study participation and what I could and probably couldn’t expect to learn from the sequencing results in terms of disease risk. But the one question she wasn’t prepared for was when I asked “So, how do I get my sequence?” to which the answer was something like, “We really haven’t discussed that.” To which I replied, “Well, you probably should… I may be unusual in that I want it and know what to do with it, but certainly other people will eventually want it too.” Especially since in this case my sequence will be part of my medical record - at least the parts that harbor a potentially significant result, which will then be re-sequenced in a CLIA-approved lab. I’ve already talked to my personal care physician about it and he’s actually quite excited about the prospect of actually being able to practice “personalized genomic medicine” of sorts… after all, it has to start somewhere with somebody. Another surprise to me was that the first real issue that came up wasn’t related to the medical sequencing at all, but was a purely medical issue that turned up in the (very thorough and elaborate) testing they did and will continue to do. This hadn’t really occurred to me as a possibility. A high-res CT scan found a 2mm “nodule” on my left lung, which is probably nothing but has to be followed up in a few months just in case. I’m not particularly worried but if it does turn out to be something I’ll be very glad they found it at 2mm rather than later.

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