PLoS ONE may revolutionize science communication. Have a first look at www.plosone.org. As they write: “Be one of the first to appear in this new Open Access 2.0 online forum—and qualify for a great low pre-launch price. We’ll peer review your work and publish it online as soon as possible so that it can start a conversation within the community that will enhance scientific progress.” Will it still be traditional, 1:1 translated publishing system? Or can we even edit any text? What about lists of open questions? And a true synopsis – like the one theologians use to compare the four canonical gospels? Yea, yea.
How deep is deep enough?
In case that the common disease / common variant is leading to nirvana, we urgently need to resequence common genes in large populations. 2kb long CRP is a particular good candidate which might be a reason why Crawford from Uwash resequenced ~500 individuals. They found indeed potentially relevant codings SNPs – of course rare (<1%) but they are there! There is a greater number in African-Americans than other populations and more than half are private to a single population (BTW more than half in dbSNP can not be validated). Of course tag SNPs would not discover them. Yea, yea.
Nothing but skin and bone…
… was the title of a recent editorial in JCI. Clearly that’s not true for vitamin D as you may know of the many immunological functions. A new study now shows, that mice get atopic dermatitis by applying vitamin D ointment. A EJCN paper published on the same day concludes that “the national fortification of fluid milks and margarines with vitamin D safely improved the vitamin D status of children”. Nay, nay.
Exact tests for R
If you are looking for exact tests, I have some links: an unbiased allelic test dedicated to case-control association studies and another for testing Hardy Weinberg equilibrium. Yea, yea.
At-Home Genetic Tests
FTC now warns that a healthy dose of skepticism may be the best prescription: Having also reviewed many sites that are offering genetic testing either for health outcome or genealogy I could not find anything that is worth the money. Do you believe in horoscopes? Nay, nay.
Where we recombine
Finally, and long awaited, there is a first detailed analysis of mutational hotspots in the human genome by Myers from the McVean group in Oxford. There are roughly 1k-2k hotspots per chromosome, each 1kb-2kb long while there are no 200 kb without apparent recombination. Recombination avoids repeats, exons and L1 elements but likes GC as well as the THE1A/B 7mer CCT.CCC.T and the 8mer CCA.CGT.GG. As rec laways needs double strand breaks, are these also the first cancer motifs found? Yea, yea.
Looking for 100 year old DNA
You can probably find hundreds of times the argument in the medical literature that the main cause of asthma is the environment – as genes can not spread within 1 or 2 generations. While this might be true for de novo mutations it is certainly not true with pre-existing variations and recent population dynamics. In a review how asthma came into live, I argued that introduction of antibiotics and improved child care extremely shaped our genome by suppressing purifying selection. In developing countries respiratory infections are among the main killers. Who can help with 1,000 unbiased 100 year old DNA samples to prove this hypothesis? I have an excellent dentist to punch holes in bones.
Again paranormal inheritance?
Following the exciting Lolle paper, now again non-chromosomal transfer of genetic information in a new study of Mary Alleman. Yes, of course, humans inherit mito DNa, there is imprinting, but also siRNA (not found in maize) or RNA polymerases (found!)? BTW much fuss of maternal imprinting in genetic epidemiology is simply preferential maternal reporting.
Addendum
Pollen contamination may have been the reason for the Lolle/Pruitt results.
Once in a lifetime
You may think twice about participating in a genetic study. Science magazine makes the point: If you have been ever been profiled by a SNP scan that is now (even anonymous) in the public domain, every further study (or anyone else who has access to trace amounts of your DNA) can re-identify you by 20 – 70 characteristic SNPs. This is even problematic as likelihoods for your disease risk can be calculated from SNP arrays of distant relatives, yea, yea.
Is there any sense of genetic association studies?
The International Journal of Epidemiology has some extreme views of the Philosopher’s stone – have to confess that I am a fan of Keneth Weiss and Anne Buchanan. Did we waist millions of $ for nothing?
Well organized
Just came across a company called Genvault – they are advocating to add a short DNA sequence to the DNA samples as a identity tag. The oligos are mixed to represent binary numbers, see online docu for description.
Addendum
Another company has some thoughts on the same problem: Illumina and Veracode.
Hello world!
Setting up this blog was a matter of 10 minutes while filling it will probably take some more time. I have been a net citizen since its beginning. Having sent out my first (stored) email on Jan 18, 1993, while my first web page dates back to Feb 1, 1995. I was running one of the worlds largest websites on asthma and also a gene database for many years but haven’t done anything useful during the past years.
Addendum
This blog serves as a testbed for the next few months if this kind of information exchange is of any use (except for paying bills of a lawyer). I will broaden here my view on science and refer to my archive of ~16,000 scientific papers that I have collected since 1986 when starting my thesis.
Is there an association of CARD15 variants with allergy?
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