I have no idea how 23andme got its name but the business model of this company seems to rely on a rather haploid view of the world.
I had the pleasure this weekend to listen to a talk by Joanna Mountain(senior research director at 23andMe, the company that was founded by Googles Sergey Brin‘ s wife Anne Wojcicki). For whatever reasons Brin Continue reading 46andyou
Nature magazine has a collection of interesting opinions about future developments of science. My favorite contribution is open content management Continue reading Invention is the mother of necessity
What is the fastest acceleration in Nature? It seems that high-speed spore discharge mechanisms are winning the race. From a PLoS press release Continue reading 9,69
I wondered if Chorea Huntington may be unintentionally diagnosed by current SNP chips used in research projects of other diseases. On a first glance, this seems to be unlikely – we are dealing with repeated CAG repeats in huntingtin located on chromosome 4p16.3 that are not easily accessible by SNP panels. Continue reading Will current SNP chips unintentionally diagnose Huntington?
The new Lancet has a paper from our own group as well as another one from ISAAC. We have already suggested earlier that asthma is a iatrogenic disease- the ISAAC paper now confirms at least the long suspected association with paracetamol use – gratulations to my London friend who had been working so long on this hypothesis. The accompanying editorial puts in into context:
Furthermore, although many important potential confounders were included in multivariate analyses, confounding by underlying respiratory disease, differences in hygiene, and use of other antipyretics might also explain the findings.
To put it more on a general level – more iatrogenic factors cannot be excluded, yea, yea.
PLoS medicine publishes today a piece that we wrote already last summer. As we have removed the narrative abstract (PLoS uses keypoints instead of an abstract) here is it – pleading for an update of traditional informed consent. Continue reading Informed Consent 2.0
It seems that CEA just published my rather critical view of the recent ORMDL3 association paper. My letter had been first submitted to “Nature” but rejected after review.
A rebuttal seemed to be necessary as the authors repeatedly highlight ORMDL3 as a new asthma gene – in the printed Nature paper, in the Nature podcast and in the accompanying press releases. They even continue with reviews saying that
Completion of the human genome sequence and the advent of genome-wide association studies have resulted in the identification of two novel asthma susceptibility genes, ORMDL3 and CHI3L1, in the past year.
Continue reading ORMDL3 – more inconsistencies in the Nature paper
Physics gets now a lot of attention with the largest experiment ever done with the LHC (pictures+data).
* largest machine (26.659 m diameter)
* largest freezer (60 tons helium)
* fastest runaway (99,99999 % speed of light)
* highest energy consumption (7 TeV)
* most lonely place – vaccum (10^-13 at)
* hottest place 100.000-fold temperature of the sun
* coldest place onearth (-271,3°C)
* largest supercomputer
Gratulations from the biomedical field that produced much less records in this week.
Genowatch (paper|website) is doing pretty well by annotating large SNP sets that would require otherwise numerous hours to map their position on genes, biological function and pathways. Continue reading SNP batch annotation of GWAs
Galaxy, one of my favorite bioinformatics websites now offers the conversion of existing history into a work flow. Obviously source data (by UCSC or Ensembl) may be produced in the same format but everything else can then be delegated to a workflow – just a set of instructions how to modify your data.
Having a free copy of the Lancet at the moment, I found a nice book review about “Dissent over Descent” by Steven Rose.
[He] takes a pleasure, which in part I share, in puncturing the often hyperbolic claims of natural scientists to be unimpeachable purveyors of absolute truth Continue reading Dissent over descent
The experts in the field will immediately notice what I am suggesting here – an improved GWA plot that does not take into account p values alone but also effect sizes. I was experimenting some time with smile plots but finally ended with this bubble plot. Bubble size for 0.5<OR>2 is set to a minimum while all other ORs get increasing bubbles (BTW use for OR<1 a 1/OR transformation beforehand). Chromosomal colors are from a self defined palette using the colorRampPalette function in R which makes it look like pointillism art. The real question: Did the previous GWA p value screening miss some important effects? For example the important dot at x=4 and y=4?
Three large studies on schizophrenia now all agree that rare structural variants (CNVs) have a causal role in disease causation – probably by affecting large regions at 1q21 and 15q11 that contain all some “neuro”-genes (Harvard, Decode, Seattle). There are two major points that let me wonder if these papers even mark a turning point in our understanding of genetic causes of human diseases that is largely influenced by the Chakravarti hypothesis of common disease and common variants (CDVC). The Seattle paper had the most clever comment on that
We propose an alternative model: that some mutations predisposing to schizophrenia are highly penetrant, individually rare, and of recent origin, even specific to single cases or families.
Continue reading Common disease + common variant = common misunderstanding?
As somebody who is dealing most time with large datasets I always arrive at genes and proteins that I do not know. Using Biocarta, Keggs and other services in the past, I find the new WikiPathways exciting and hope that it will grow over the years. A companion paper in PLoS biology describes its roots in GenMAPP and the current work of the authors on bots that identifiy inconsistencies but also pick up loose ends. Hopefully I will find some time to work a bit on nuclear receptors, yea, yea.
Sequence logos are fun: www-lmmb.ncifcrf.gov is the ultimate site for many demo figures. It provides even a link where you can manufacture your own logo. Here is mine which is derived from a TCR consensus sequence:
