More about parents and self

I would be interested to learn more about the rate of non-matching parent-child SNP assays (preferably Affymetrix technology as current Illumina chips do not include low MAF variants).

This could tell us something about the role of de novo somatic mutations: Read more in a recent TIGS paper by Kenneth Weiss. Has anyone checked different tissues of the same individual and looked for mosaics? Or traced the fate of blood transfusions? Or followed up a single individuals over a couple of years?

This idea is also fuelled by a recent Cell paper that shows Sticker’s sarcoma to be transmitted among dogs by licking or biting tumor-affected areas. Yea, yea.

Pater emon o en tois ouranois – About paternity testing

The Lord’s prayer has been translated into nearly all languages (where 1,377 languages are online). Having a father in heaven is comforting but from a genetic standpoint we don´t take it literally (in contrast to some other family relationships in the Lutheran tradition).

Although pedigrees usually list only father names, the absolute amount of DNA transmitted from father to children is less than for women, who always transmit a long X as well as mitochondrial DNA. When testing for paternity in family studies, my experience is that about 3% of the children do not match with their fathers (while I have never found a mother that did not match). This fact does not seem to be new: Already the Romans knew that “Mater certa, pater semper incertus“.

Is DNA testing for paternity really so important as many commercial websites make you to believe? Genes are part of our existence, environment is another as well as what WE want to achieve in life. Nay, nay, genes are not so important knowing so many wonderful non-genetic fathers.

From misunderstanding to dogma

The Nature Reviews Genetics Timeline features an interesting story on human chromosome numbers. Theophilus Painter in his 1921 Science paper wrote: “In my own materials the counts range from 45 to 48 apparent chromosomes” which was interpreted for obvious reasons to be 46 or 48 (Painter probably saw a bended chr1 as 2 different ones). Textbooks then reported 48 human chromosomes for 3 decades until the classical paper of Tijo in 1956 paper who confirmed 46 human chromosomes. Gartler believes that Tijos unusal background have made him likely to question authority. Yea, yea.

What’s in a name?

What’s in a name? That which we call a rose. By any other word would smell as sweet. From Romeo and Juliet (II, ii, 1-2).

Geographical distribution of names may indicate spreading of gene variants – a fact that has been ignored so far in genetic research. If you are interested in European names, here are some interesting links. It is now even possible to draw your name on a map – on the fly. Yea, yea.

Here is map of my name (yes, a couple of errors, but the locations are close to what I have found in our 70 year old family register).

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Not invited to Lindau?

Lindau at Lake Constance hosts the annual Nobel laureate meeting. In addition some 500 young students from all over the world can listen to the Laureates’ lectures and to engage in discussions with them. Not invited? There are some excellent interviews available (for 2003-2005 but we are all waiting for 2006).

Interested in the history of DNA discovery? There is a wonderful Linus Pauling website that has it all: A wealth of primary sources – over three hundred letters, manuscripts, photographs, published papers, audio-visual snippets and more – provide an important scholarly perspective on the DNA story. Yea, yea.

Doorlink

Ever failed with a grant application? Sad? Don´t worry, submit your grant somewhere else.

This will, however not work in Bornemouth. As the local newspaper says: “A new telephone system has been launched in Bournemouth town centre that aims to stop troublemakers from getting into bars, clubs and pubs. Doorlink enables doorstaff to take pictures of any problem drinkers via their mobile phones and within seconds circulate them to other venues in a bid to stamp out violent behaviour.” Yea, yea.

Matchcode

If you are invited to a party just mention genetically modified (GM) food and you will be center of the crowd. There are many national and internationally bodies that deal with GM food (see the dissertation of Scholderer). As far as we do not know what makes and allergen and allergen, I would always care when introducing any modification. There is a way round, however, that GM food can also have less allergen content – just found a preprint of a gene-silenced tomato. This German-Spanish group managed by RNAi silencing to reduce protein Lyc e 3 with led to reduced skin reactivity of tomato allergic probands. BTW – do you renember our fake food hypothesis? Yea, yea. BTW The best tomato bread can be found in Barcelona.

Taqman ® based genotyping – What´s new?

You may have read the contribution of Monika Werner and me in “Pharmacogenetics” about “Methods of Genotyping”.

A point that we did not cover when describing the 5-prime-nuclease assay is the neverending miniaturisation of assays. At a recent HUGO meeting I have already seen British Kbioscience offering an extremely flat, black, ca. 8 x 12 x 0.2 cm, 1,536 well plastic plate (size recalled from memory) that is sealed after filling in primer / mastermix and DNA. Up to 1,000 sealed plates are then water-bathed for temperature cycling.

A few days ago another system made it on my desk: U.S. BioTrove sent me a demo array that is about 6,4 x 2 x 0,01 cm has precoated primer holes for 3,072 assays where you just add your DNA + mastermix before sealing and cycling it on a conventional thermocycler.

Just a barf bag

Following the 8/10 discussion, some politicians now advocate that all hand-luggage should be prohibited on airplanes. What will happen if all frequent traveller scientists are no more allowed to take anything inside of planes? No laptop, no organizer, no paper to read, nothing to review, nothing to administrate? Imagine that the inflight magazine is only good for 5 minutes and that there are no interesting flight attendants anymore. Just a pencil and a barf bag in front of the seat. Would that revolutionize science? If yo say yea, yea, let come that true ASAP. If you say nay, nay, do we need these VIP scientists anymore?

Nylenna-Simonsen-Chalmers Misconduct Diagram

The Lancet (10 June 2006, p 1882) had one of the best descriptions of scientific misconduct that I have ever seen (yes, I am also admiring Geoffrey Rose). The authors argue that our current view of misconduction is wrong those caught for fraud being a few “bad apples”. Instead we are facing a continuum ranging from honest and inevitable errors to outright fraud. I agree up to here, however, I do not believe so much in a “slippery slope” – in my experience the intentional selection of certain entry and exit levels is more common.

Here is my expansion of the original N-S-C diagram:
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Yea, yea.

No fool like an old fool

PLOS Genetics – one of the ever rising stars – reports detailed expression profiling of aging human, mouse, fly and worm. When looking at muscle (in part also brain and kidney), Jacob Zahn et al from Stanford UMC found chloride transport and mitochondrial electron transport chain most severely affected by age. Is that a biological explanation for two common geriatric problems, e.g. exsicosis and falls? BTW detoxification by CYP26B1 increased, so aging does not necessarily mean involution. Most frightening: a 41 y old expressed like 10-20 y older and a 64 y old like 30 y younger. Yea, yea.

Bigger is better

John Todd has always been advocating that we should use larger sample sizes in our genetic association studies. I agree, it is also true that larger sample sizes will lead to smaller p-values. In his recent nature genetics comment he now suggest a p of less than 10 up minus 8 to be relevant. Yes, all of his 6 examples show that significance level but only 1 provides functional evidence (the SLE study). All other studies including Todd`s own studies are number-crunchers. I fear that in the absence of functional data 10-8 may not even be sufficient. Think of 500,000 SNPs, 20 possible traits, 5 genetic models and 20 competing groups – this multiplies to 10-9. Interestingly, the SLE study, showed a p of 10-16! Having good functional evidence I would be even willing to accept 10-2. May I point you to an excellent study describing a new rSNP by means of CHIP and expression analysis of de Gobbi – using just a couple of families. Yea, yea.

Le abia o non le bia

One of my favorite stories that I heard in Venice two years ago (and recall it only from memory, please correct me if I am wrong): The rich Venice merchandiser Labia arranged big parties for his guests. With his temper at height, he was throwing golden plates through the window, crying: “Le abia, o non le bia, saró sempre Labia” – “if I have them or if I have them not, I am always a Labia”. (It turned out that some of his servants were waiting at Canale Grande to pick up the golden plates coming through the window). Yea, yea.