Category Archives: Genetics

PLINK: Bug or feature?

I am struggling now for 4 weeks with some unusual behaviour in PLINK that gives me different results with a trait of the alternate phenotype files either by calling that trait directly

plink –file mydata –tdt –pheno pheno2.txt –mpheno 1

or from a loop over all traits

plink –file mydata –tdt –pheno pheno2.txt –all-pheno

It seems that I am working with different numbers at both occasions – click to enlarge the log Continue reading PLINK: Bug or feature?

 

CC-BY-NC Science Surf , accessed 18.07.2026

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“.

 

CC-BY-NC Science Surf , accessed 18.07.2026

How we inherit acquired traits – all about non random mutations in the human genome

This is just a material collection for a forthcoming review. I am collecting links to studies showing an increased mutation rate in CpG islands that may possibly fix gene activation status. Continue reading How we inherit acquired traits – all about non random mutations in the human genome

 

CC-BY-NC Science Surf , accessed 18.07.2026

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 18.07.2026

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 18.07.2026

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 18.07.2026

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 18.07.2026

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 18.07.2026