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closeVague and perhaps misleading
Posted by bertgold on 17 Feb 2011 at 01:43 GMT
The level of contamination found in these databases is significant and worrisome.
http://plosone.org/article/info:doi/10.1371/journal.pone.0016410#article1.body1.sec3.p1
I read this paper as a consequence of Nicholas Wade's NYTimes article. The popular press is susceptible to misinterpreting the science, so i thought I would see for myself. My thought upon reading the Wade reportage and this sentence in the discussion, is that patients and doctors considering molecular medical genetic testing will falsely suspect that their medical test results are incorrect. That many checks and balances are present in a clinical molecular genetic laboratory to make certain that only correct results will be delivered should have been clearly articulated in the paper. Further, the fears expressed by one of the co-authors in the news article are clearly subjective and have no clear implications for the analytic or clinical validity of any medical test. I would hope that is well understood by any reader of this article or of the news story.
RE: Vague and perhaps misleading
mjoneill replied to bertgold on 17 Feb 2011 at 15:07 GMT
Nicholas Wade wanted to play up the controversy with questions like, "Should the public be upset?", and fishing for a response to the flip comments by Gibbs and Lipman. (I was present during Wade's phone interview of Rachel.) For a more cogent analysis see Melissa Lee Phillips' feature at nature.com.
Responding to your statement, "That many checks and balances are present in a clinical molecular genetic laboratory...". Are they? Results for current clinical genetic tests targeted to known infectious agents or Mendelian disorders can easily be validated by repetition. Likewise, paternity SNP profiles. For a 23andMe profile, you literally spit into a tube and send it to them in the mail (but see 23andMe's Terms of Service and Disclaimer of Warranties). As clinical genetic diagnoses evolve toward multilocus profiling for complex disease susceptibilities and/or variant drug responses via personal genome sequencing, problems associated with archiving, curation and validation are orders of magnitude greater in complexity and expense. Moving forward do we cop the attitude of Gibbs and Lipman, i.e. "we don't see a problem", or of UCSC's David Haussler, i.e. "filters can fail".
RE: RE: Vague and perhaps misleading
bertgold replied to mjoneill on 17 Feb 2011 at 20:26 GMT
A large problem with Reporter - Scientist interactions is that the former are motivated to sell newspapers while the other wants to tell the truth. I am empathic to those issues.
However, I want to both inform and enlighten that: (1) there are standards for molecular genetic testing in the US that are done for clinical purposes, (2) these standards are subject to CLIA and many State, and other Federal and Organizational (ACMG, ABMG, ACOG, CAP) requirements and that (3) 23andme is NOT a certified clinical laboratory that physicians send samples to for clinical testing and that, although I have enormous respect for David Haussler and David Lippman, neither are Board Certified in Clinical Molecular Genetics (as am I) and neither are very familiar with the methods validation process for molecular testing, nor the elaborate process for communicating actual clinical laboratory results to physicians for clinical purposes. I would therefore assure you that the problems that you have pointed out are simply not relevant for clinical testing as now practiced. Whether these problems become relevant in the future remains to be seen. My understanding is that the few NextGen tests that are being done for clinical purposes (GeneDx comes to mind), are targeted gene sequencing tests, that are likely confirmed using conventional sequencing when abnormalities are found. Again, if you think the molecular testing community is poorly organized, that is the community that actually provides clinical molecular diagnoses to physicians, please think again.
Thanks for the opportunity to expound on this.