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The Great Health Data Deficit: Are Environmental causes for Disease a Mirage?

Ever since I was a child the message has been eat your greens (we got caned at primary school if we didn’t), you need to exercise, carrots will make you see in the dark, an apple a day keeps the doctor away. It continues today with the “5 a day”, all the healthy food pyramids, anti-junk foods, and so on. Yes the environment can be dangerous, it can kill us. There are some indisputable examples, a bullet in the head for example, or getting hit by a car is an environmental impact that almost always results in injury and death. There are others on which we more or less agree, like smoking is harmful (evidence is very strong, although it has never actually been proven, who knows, it could be the regular movement of hand to mouth that causes all the damage, we need to do the proper controlled trial…)For the rest we have always sort of somehow known that eating badly can cause disease – it seemed so obvious, and all the little research studies just confirmed what we knew and lead to the ris…

Personal Genetics & Utility: Round 2 – Mind the EGAPP

Yesterday I wrote about the false Family History vs. Personal Genetics battle, today I look at the old chestnut of traditional risk factors. There seems to be a lot of fear among some professions that personal genetics is attempting to take over their jobs – it’s been like this from the beginning mainly due to misunderstanding (wilful or otherwise) exactly what personal genetics is and what it’s role in healthcare can be.
The latest salvo is from the EGAPP Working group who published their assessment of genetics vs. traditional risk factors (TRF) in cardiovascular disease risk. They looked at the 9p21 variant as well as 57 other variants in 28 genes associated with CVD and they sought to document
“the extent to which genomic profiling alters CVD risk estimation, alone and in combination with traditional risk factors, and the extent to which risk reclassification improves health outcomes”. Some conclusions from EGAPP:
The magnitude of net health benefit from use of any of these tes…

Personal Genetics has a Family History of getting beaten up

Over the last few days personal genetics has come in for a bit of a bashing, first it was knocked out by family history then it was clearly nailed into the coffin by traditional risk factors.Also have a look at Genesherpa’s blog for some more putting the boot in here and here.Update: Nov 12th, here is the 23andMe blog on the subjectBut what is behind the hype and the headlines? In this post I will look at family history and deal with EGAPP in the next.The latest attack was sparked by a press release of some work presented at the ASHG. We don’t know too much because all we have is an abstract and a video but we have enough. FH was compared to the Navigenics genetic profile (PGS). From the abstract“None of the 3 hereditary prostate cancer subjects were assessed as high risk on PGS. Based on FHRA, 10 subjects had hereditary breast cancer risk and PGS only identified 1 as high risk (K=0.12). None of the 9 hereditary colon cancer subjects were high risk on PGS.”Sounds awful and this was th…

Nutrigenetics–a little bit of history, but no miracles

Reading The $1,000 Genome by Kevin Davies, as expected it’s a fascinating story and right at the beginning in Chapter 1 there was something that I liked. The first personal genome to be sequenced and interpreted was that of Jim Watson (Craig Venter was first but no interpretation). Davies describes the presentation of Watson’s genome to the man himself and reports that the sequencing was performed by 454 and the interpretation was handled by the team directed by Richard Gibbs of the Baylor Genome Center. Watson’s genome inventory, for example, revealed 310 genes with likely mutations and 23 with known disease causing mutations, increasing his risk for cancer and heart disease. The Baylor team recommended that he should take folic acid and other vitamins and minimize his exposure to sunlight, particularly during his daily tennis matches. p19So there you have it, the first advice based on the first interpretation of a human genome sequence was nutrigenetic!But then I read later in the b…

The murky side of physician prescribed LDTs

Apparently the LDT community are not too happy with DTC genomics for having stirred up the regulatory hornets nest, well maybe that’s not such a bad thing. I have argued previously that physician prescribed tests can be more dangerous and more necessary of regulation than DTC and below is a good case for the argument.First a huge huge thanks to @laikas for a) her excellent beautifully detailed and analytical posts on the CFS virus story (XMRV & MRV: here, here and here) and b) for specifically asking me and others to comment. I had been aware of the controversy but no more than that so Laika’s request made me read more – my first inclination was that it reminded me of the helicobacter story, scepticism followed by acceptance, cures and nobel prizes, but reading further it unfortunately looks more like the MMR / Autism debacle which was Laika’s comparison.I’m not going to discuss the various findings here, no point as Laika has done that far better – what I do want to talk about is…

FDA – Personal Genetics: Is it safe? It’s a marathon, man…

It’s nearly 10 years now and still there is no clarity about the position of personal genetics in the regulatory framework. Maybe that’s going to change soon with the FDA activity and the recently published HGC Principles. It would be good to get it settled one way or another, the uncertainly doesn’t help anyone except those who exploit it to exploit the gullible.Some elements:DTC vs. DTMD (via physician) – I will argue that DTMD is actually higher risk and needs closer scrutiny Is it medicine? I think this question is a waste of time, it will not be resolved, the definition is too broad, medicine is practised everywhere by everyone - if I take my son’s temperature, put a plaster on a cut or administer medication I am practising medicine. What is the FDA duty bound to do and what will they decide? No regulation – more or less the current situation Tight regulation – medium/high risk requiring pre market approval (PMA) Somewhere in between – the “light touch” The questions are wha…

DNA Dilemma, dissecting the FDA

Mary Carmichael (General Editor, Newsweek) has this week been running a very interesting series of articles about the “dilemma” of whether or not to undergo a 23andMe type DTC genetic test. As part of that she interviewed the FDA and with journalistic cunning recorded the whole interview and published the full transcript (here). It was a very good thing too that she has the tapes because the interview was in some places quite revealing. Mary asked me to comment/dissect the interview and I have done so below – I look forward to seeing the comments of others that Mary has asked on their blogs as well.In a sentence the interview came over to me as unnecessarily vague and evasive (unless for some reason it was necessary!) – certainly lacking in clarity and not answering some of the questions asked but giving up some useful information. DNA Dilemma: The Full Interview With the FDA on DTC Genetic TestsNEWSWEEK: During the recent congressional hearing, 23andMe’s general counselsaid that the …

DTC, FDA, GAO…2006 and all that

I wrote a post below a few months ago but for various reasons got cold feet about posting it. Yesterday made me angry (like Daniel Macarthur), warmed them up and so after sleeping on it decided to go ahead. It is about events of 4 years ago but it needs hardly anything changed to make it perfect for today. I have made some slight modifications and added an introduction specifically about yesterdays US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry.

The Congress hearing was eerily familiar. There were a few differences, in 2006 it in the Senate and was all out attack by a single senator (a committee of 1), yesterday at least there was balance and some sensible questions from some members of congress. I felt Henry Waxman was OK as was Burgess.
The whole hearing was based around the GAO investigation and this was just a mirror image of what happened in 2006. Just the same – selected evidence, highlight the most headline grabbing b…