Category Archives: Genetics

Genetics, Philosophy

Formal proof is difficult if not impossible

At least in medicine but also in many other fields, formal proof of a scientific hypothesis is difficult if not impossible. Reading again Greaves’ cancer book, I discover even more insights there. Talking about the hormonal stress leading to breast cancer he makes the point that

there is no ’cause’ in the straightforward, singular, or usually perceived meaning of the word; no tubercle bacillus equivalent. Neither is a mutant gene the common cause. Chronic hormonal stimulation driving persistent epithelial stem cell division seems to be a major factor (cycles driving cycles) and this reflects in large measure our social divorce from evolutionary adaptations for reproduction … Superimpose some degree of inherited predisposition and chance itself on this prescription and a very plausible causal network imbued with evolutionary principles becomes evident.

This is a very different view to the current sequencing headlines like “Lung cancer and melanoma laid bare“.

 

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Allergy, Genetics

On the tasseography of lung function genes

Having done lung function testing on hundreds, even thousands of children, I believe that this is not an easy task – it’s not only about abdominal mechanics and airway diameter but also about physical fitness – and let’s be cruel – also about intelligence. Even worse, I remember a long discussion how to adjust lung function parameter appropriately – should we use standing or sitting height? Two new papers large ignore these questions. But read first what the Charge consortium writes Continue reading On the tasseography of lung function genes →

 

CC-BY-NC Science Surf accessed 19.02.2026
Genetics

100 cases of inherited epigenetic inheritance

I was searching quite long for a review on that – but only to discover in the print version of a QRB article a reference to an online table. In homo sapiens, the author reports an increased cardiovascular mortality slash diabetes susceptibility (INS-IGF2-H19) through male germline and Angelman/Prader/Willi syndrome (from paternal grandmother). So there are only limited human examples so far, which is certainly due to the lack of appropriate sample collections yea, yea.

Addendum 29-Dec-2009

Video Link to an interview with Lars Olov Bygren.
I am still not sure about Angelman/Prader/Willi (as this is more with imprinting) – otherwise the updated list consists of

 

CC-BY-NC Science Surf accessed 19.02.2026
Genetics

One for all

A research article in Science reports a new CML cell line

We used insertional mutagenesis to develop a screening method to generate null alleles in a human cell line haploid for all chromosomes except chromosome 8.

I couldn’t figure out why chromosome 8 remained but are nevertheless fascinated by the opportunities, yea, yea.

 

CC-BY-NC Science Surf accessed 19.02.2026
Allergy, Genetics

GWAS integrator: HuGENavigator

At HuGe there runs an Apache Tomcat displaying by 01 Dec 2009 a total of 2460 GWAS hits, 14 of these for asthma which will be more or less my genotyping program for the next year.

rs7216389 rs4950928 rs12619285 rs1420101 rs2269426 rs2416257 rs3184504 rs4143832 rs4857855 rs10762058 rs16937883 rs9319321 rs1588265 rs2378383

Unfortunately the HuGENavigator missed published GWAS data, Continue reading GWAS integrator: HuGENavigator →

 

CC-BY-NC Science Surf accessed 19.02.2026
Genetics

Best NGS alignment viewer

Bild 2Heng Li has an excellent overview table on next generation sequence alignment viewers (as well as alignment programs) – thanks to TB for pointing me to that site. The Broad Institute has just bought another 30 Illumina Genome Analyzer – they now own 89 so the Broad people might have clearly a need for visualizing data.
The best choice is not easy to make – I am trying now the IGV in my lung sequence project. Annother interesting piece of software not listed by the Heng Li table is annoj that looks promising too, yea, yea.

 

CC-BY-NC Science Surf accessed 19.02.2026
Allergy, Genetics, Vitamins

ORMDL3 graduated

Given my sceptical view that ORMDL3 is really an asthma gene (that may be even shared by the authors of the initial association) the train has now departed with more groups speculating about ORMDL3 function.
For example this new paper by Gerard Cantero-Recasens is about the unfolded protein response (UPR) that may be triggered by a putative loss of function mutation in ORMDL3 via a Ca2+ decrease in the ER. Although I am quite intrigued about the fact that the story now moves to calcium and vitamin D, we are far away from any conclusive evidence.

Addenddum 3.3.2010

And here is another paper that associates ORMDL3 to the sphingolipid metabolism. Although that may be also an interesting pathway (given a bulk of literature not cited in the paper ( more, more, more, more) I still wonder if this is wishful thinking. The authors do not touch the main problem – the weak connection of some genomic variants in that region to ORMDL3 function to asthma pathogenesis.

 

CC-BY-NC Science Surf accessed 19.02.2026