Category Archives: Genetics

Genetics

Common disease + common variant = common misunderstanding?

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? →

 

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Genetics, Software

WikiPathways

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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.

 

CC-BY-NC Science Surf , accessed 16.08.2026
Allergy, Genetics

Probability that a genetic association is false positive

An (anonymous) reviewer of our forthcoming EJHG paper on IgE and STAT3 pointed me towards a JNCI paper that has a nice supplement – an excel sheet to calculate the probability that a positive report is false. It basically relies on (i) the magnitude of the p-value (ii) statistical power and (iii) fraction of tested hypothesis. While we certainly know (i) and (ii), (iii) is always hard to know with many datasets including hundreds of traits that allow indefinite numbers of subgroups. Are you really interested in a new paper about “An African-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity” that encompasses 1 of virtually 100 ethnic groups; 1 or virtually 25000 genes; 1 of 2 sexes; 1 or virtually 50 asthma related traits, yea, yea.

 

CC-BY-NC Science Surf , accessed 16.08.2026
Allergy, Genetics, Philosophy

Will the Data Deluge Make the Scientific Method Obsolete?

A new Edge article answers this question. According to Chris Anderson, we are at “the end of science”, that is, science as we know it.

The quest for knowledge used to begin with grand theories. Now it begins with massive amounts of data. Welcome to the Petabyte Age.

Yesterday I reviewed a paper that crunches massive amount of data (and even found a new pathway for asthma). Nevertheless I was asking the question if this wishful thinking? Just take the next gene in one region and the overnext in another one and I would come up with a completely different pathway. This is all about association and not by the traditional “theorize, model, test it” way of science we have been brought along, yea, yea.

 

CC-BY-NC Science Surf , accessed 16.08.2026
Genetics

German Human geneticist warns against personal genomics

Wolfram Henn, Vorsitzender der Kommission für Grundpositionen und ethische Fragen der Deutschen Gesellschaft für Humangenetik, warnt im Interview mit Technology Review (Ausgabe 07/08 […]) vor persönlichen Genomanalysen, die über das Internet angeboten werden. So bietet beispielsweise das Unternehmen 23andMe seit kurzem eine Genomanalyse für nur 999 Dollar an.

Welcome in the club! Just to let you know that 23andme has been stopped 2 days ago as reported by Spiegel magazine.

 

CC-BY-NC Science Surf , accessed 16.08.2026
Allergy, Genetics

The many problems of GWAs

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genetic-future has an excellent article why the recent genome scans failed (i) alleles with small effects? (ii) population differences? (iii) epistatic interactions? (iv) cnvs more relevant than snps? (v) epigenetic inheritance? (vi) disease heterogeneity? It is a thorough review better than everything Continue reading The many problems of GWAs →

 

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Allergy, Genetics, Vitamins

CD 14 now also on the vitamin+allergy list

Just for curiosity I am collecting a list of allergy genes that are vitamin D dependent. The list is already rather long but now there is a prominent addition: CD14. Known as asthma gene for many years the vitamin D dependency isn’t such clear. A clever analysis, however, now shows that there is an intermediate step involved Continue reading CD 14 now also on the vitamin+allergy list →

 

CC-BY-NC Science Surf , accessed 16.08.2026
Genetics, Software

Orientation of genomic sequence and SNP allele designation

… permanently leading to errors – the plus / minus strand orientation and the consecutive sequence / allele designation of SNPs. Only recently I came across a fancy way how to define strand direction – from a tech note Continue reading Orientation of genomic sequence and SNP allele designation →

 

CC-BY-NC Science Surf , accessed 16.08.2026