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.
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.
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.
Pollen contamination may have been the reason for the Lolle/Pruitt results.
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.
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?
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.
Another company has some thoughts on the same problem: Illumina and Veracode.
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, my first web page (on a ftp! server) 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 havenÂ´t done anything useful during the past 3 years.
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 private archive of ~16,000 scientific papers that I have collected since 1986 when starting my thesis.