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Once again genetic testing

I have argued earlier that the free decision of an individual to allow genetic testing, will also reveal data on genetic relatives that have never consented to that procedure.
A new review by Bruce Weir now confirms that “it is reasonably straightforward to find the probability of the genotypes of individuals when their relationship is known…” My current work lets me also assume that with 500,000 SNP data at hand, much individual characteristics of the donor can be reconstructed – there are no anonymous DNAs datasets as some people still believe.
I even fear that genetic testing will increase for example in “homeless” (in vitro fertilized) individuals as these people will want to prevent sibling marriage – see for example the a-China DNA project. Other people may be curious about their genealogy, others about drug side effect prediction, lifestyle, assurance questions…
With every new dataset, available datasets will gradually decrease their anonymity level. I fear that anonymity is not so much a dichotomous property, it is much more a likelihood ratio to stay unknown under the probability to be known. Yea, yea.

Addendum

Time online of Dec 17, 2006 reports that the British police is holding the DNA records of more than 1m innocent people — eight times more than ministers have previously admitted. I wonder if this will affect participation rate of the UK Biobank that targets health of lifestyle, environment and genes in 500,000 people.

Sleep well

Just came to my attention that there is research of sleep related genes, the usual stuff of protein kinases, dopaminergic receptor, and serotonine transporter. Also this research community seem to have the common difficulty of the complex disease gene mappers – to understand a phenomenon (not a trait) as systemic function, an intrinsic property of a multicellular and multiwired brain, yea, yea.

Addendum

More strange phenotypes orgasm frequency, pain, human memory performance.

Addendum

Read also the what-we-could-have-learned-from-linkage-studies.

Heritable mutation or not?

moblog – Tsun Leung Chan is now reporting a heritable germline epimutation of MSH2 in a family with hereditary colorectal cancer another case of “paranormal” inheritance. They find a mosaic germline methylation pattern (which might even be a symptom of another mutation that affects the demethylation-de novo methylation pattern of MSH2 during embryogenesis?). If my hypothesis is true these families should even show more genes with different methylation patterns, yea, yea.

Addendum 28/5/08

Another attempt to answer this question comes by a study of the MLH1 promotor

Pro: MLH1 promoter methylation was found in a patient and his mother giving evidence for a familial predisposition for an epimutation in MLH1. Contra: a de novo set-up of methylation in one patient, a mosaic or incomplete methylation pattern in six patients, and no evidence for inheritance of MLH1 promoter methylation in the remaining families.

Science projects, glue projects

Reading about science projects, glue projects and platform projects, all with minority, gender, public communication and ethics modules while including large administrative overheads, travel and meeting costs, I even wonder how much money is finally going to real research – careful experimentation and thoughtful interpretation. Some people seem to spend more time on creating logos than in study design, yea, yea.

What could have been learned from linkage studies

What makes the difference between genetic linkage and association studies? Simply speaking, for linkage you need to inherit a particular marker allele from your parents where it does not matter if a child in another family inherits another allele (pending it shares it with its affected sibling). With association studies this matters.

As we found with the much relaxed linkage strategy so many minor diverse loci, I assume a rather heterogeneous origin of complex diseases. There is no doubt about the importance of genes, but about the sharing of the same genetic abnormality. An (anonymous) position paper on basic Asthma Research Strategy II in Clin Exp All 2006; 36: 1326 says

The average size of effect on asthma and related traits from common SNPs is small. For instance, seven common SNPs in the IL13 gene jointly accounted for only 0,5% of the variance of total IgE … With a heritability of circa 60% for total IgE this implies that hundreds of genes, each with small effects, may be involved in IgE regulation.

Families presenting with a complex system disease will all have unique patterns how they arrive at the same clinical endpoint. Alpha-delta-gamma asthma, theta-kappa-jota schizophrenia or $%&# diabetes – are they combining lets say 3000 variations in 300 genes of 30 metabolic-signalling pathways to 1 disease of variable onset, severity and prognosis? Yea, yea.

Free for all

A report describing some first experience with GWAs (that means genomewide association studies by single nucleotide polymorphism) is listing several websites that will offer soon public data

There are many opportunities to do research without ever writing a grant application, yea, yea.

Addendum

A German paper gives some updates – you may also check www.p3gconsortium.org and www.wtccc.org.

A zebra takes its stripes wherever it goes

This week ends with another African proverb and some thoughts on transcription factor binding sites.

Commenting on the work of Janssens that “there is no inherent reason that CRMs [cis regulatory modules] must lie on a contiguous segment of DNA or that they must contain clusters of sites”, Halfon still expresses the hope that “we should be able to identify the regulatory elements for any gene starting with only the DNA sequence”.

Although an old dream, I am now rather sceptical if this prediction will ever work. Recognize the differences of my drawing compared to original figure: I am introducing even another level of temporal relationships. There might be even a close relationship to yesterdays post on “retaliation“, yea, yea.

zwischenablage0131.png 

Do not run after a cart that will not take you

Starting with another African proverb, here are some thoughts about evolution, design and the difference of chimps and humans. Yes, I am biased, I know.

I have learned that there are mainly three differences between chimps and human – the ability to run, a larger brain size and the language/speech capability. The only trait that can directly observed is the ability to run (check Munich marathon: Neither brain size and language can be directly observed :-) BTW, I renember having seen a family that walk on feet and hands – quadrupedal locomotion is a recessive trait linked to chromosome 17p, the way we all start our lifes).

So genetics is playing a big role in the human < -> ape differentiation. Or did the differentation select the genes?

You will understand my great expectations when now reading one of the first serious papers about the chimp and the human lineage. It is about pseudogenization, the gene loss during separation of species. The authors show 80 non-processed pseudogenes inactivated in the human lineage – while gently negelecting the fact of another 7868 or so pseudogenes in the human pseudogene database.

There is also nothing about my favorite trait bipedalism (only a ridiculous quote of pseudogenization of the sarcomeric myosin gene MYH16 that should relate to hominin masticatory muscles that “may have allowed the brain size expansion”, uhhh. It is also hard to understand how gain of ability should be caused by loss of gene function, yea, yea.

Dr. Livingstone, I presume?

Asthma in Africa: I will touch this issue in more detail in a forthcoming editorial in PLos Medicine. Africa has fascinated me since childhood when I read books of Paul White, Albert Schweitzer and tried to get everything our library had about David Livingstone and Morton Stanley. Here is a further link that we couldn’t place in the editorial – a 2 month helicopter trip from Hamburg to Kapstadt including daily GPS data to watch a heli flying in Google Earth, simply the best, I have seen in the internet this year, yea.

And the winner is…

Don´t miss the Ig Noble Ceremony. For example:

  • Why woodpeckers don’t get headaches
  • An electromechanical teenager repellant
  • Calculating the number of photographs you must take to (almost) ensure
    that nobody in a group photo will have their eyes closed
  • Consequences of erudite vernacular utilized irrespective of necessity:
    problems with using long words needlessly
  • Termination of intractable hiccups with digital rectal massage

yea, yea.

Are randomized clinical trials gold standard?

A new paper in the Deutsche Ärzteblatt argues that there should be alternatives to RCTs. The reasons are manifold

  • selection bias towards more severely ill patients
  • selection towards too homogeneous samples
  • patients may decline participation
  • physician may decline participation
  • bias towards larger cities and universities
  • usually “hard” endpoints that ignore quality of life, compliance, side effects
  • usually only short time studies
  • protocol may deviate from daily practice in medical routine

Community-based studies may therefore not be as bad, yea, yea.

Addendum

An extended and reworked version of this blog can be found in issue 45 of the “Deutsche Ärzteblatt“, page A3019, 10th November 2006.

Genetic archaeology

While doing a study of European population stratification, I came across an older but interesting study of old testament priests that compares the Levi tribe (where Moses was a member) with the Cohanim tribe (descendents of Moses’s brother Aaron who served as priests). The investigators traced patrilineal inheritance since the temple period 3,000 -2,000 years until present, and showed current levites unlike the Cohanin having a heterogeneous origin. The coalescence of of Cohanim chromosomes is dated to between Exodus and the destruction of the first temple in 586 BC.

Most current research is dedicated to between species comparisons but unfortunately the wonderful older Y and mtDNA approaches haven´t kept pace with the current SNP technology developement. There would be many intersting studies possible following the timeline of European history, yea, yea.

Beauty is skin deep but ugly goes all the way to the bones

Sorry, the original title of this paper is “Nothing but skin and bone“. It is an excellent JCI review of two diverse systems that do not seem to have so many common denominators. As the authors state a recurring theme is Wnt (a family of secreted glycoproteins) signalling during early patterning and for morphogenesis of skin appendages – common mesenchymal progenitors support both tissues. What the authors neglected is the effect of vitamin D signal in skin and bone, yea, yea.