Papers of the week 50-51 – Pre-Christmas extended edition

clip_image002Back from Israel. This week I will send you on holidays with a lot of interesting papers for the the time off. Hopefully you will find time to read some of these papers and won’t get overwhelmed by the amount of studies this week. Here we go:

Twenty tips for interpreting scientific claims. Does correlation imply causation? Sutherland and colleagues list 20 issues to “keep in mind” when interpreting scientific results. From my point of view this article is relevant for non-scientists reading about science in newspapers, early-stage scientists planning their experiments and even experienced scientist when writing the discussion of their latest paper.

Incomplete penetrance of CNVs. For those of you who participated in the Sde Boker Meeting or work with me know that I am a CNV research lover. Therefore, a paper by Stefansson et al. is my favorite paper of the week. The authors demonstrate that control subjects carrying CNVs perform cognitively at a level that is between that of patients and population controls. Furthermore, they could show that the individual cognitive defects are CNV specific.

Phenome-wide association study (PheWAS). Even clinicians can enter the x-WAS field by analyzing their electronic medical records (EMRs) statistically. For an alternative and complementary analysis to investigate genotype-phenotype associations and to detect pleiotropy, read the article by Denny and colleges about PheWAS.

Are sodium channel polymorphisms are associated with epilepsy? In a recent paper in Human Genetics, Baum and colleagues show an association with disease for SNPs in SCN1A and SCN1B in 1529 Asian epilepsy patients compared to1935 controls. More and more epilepsy SNP association studies support the association for variants in SCN1A for a broad range of epilepsy types. How do we interpret this observation? How do we interpret the low effective size of epilepsy associated SNPs, especially in context of rare variants with large effect in SCN1A-dependent encephalopathies?

Epilepsy genes, new technologies and the insights of 2013 in a nutshell. Tired of reading tons of papers? in the January edition of Lancet Neurology, Lee and Heo review  mayor epilepsy research advances in 2013. Topics from genetics of encephalopathies, the post-stroke epilepsy rat model, advances in translational research, the mTor pathway in epilepsy and mortality in epilepsy patients are covered.

Methylation canyons. In a new article in Nature Genetics by Jeong and colleagues, extended regions of low methylation are identified. These regions are distinct from CpG islands and shores and span conserved domains. Genes deregulated in leukemias are enriched in these “canyons”.

Exonic Transcription Factor Binding. Do you remember my post entitled The human genome is way too complicated for me? It gets worse. In the new edition of Science Stergachis et al. present dual-use codons referred to as “duons”. Duons are simultaneously specific for both amino acids and transcription factor (TF) recognition sites. They show that both synonymous and nonsynonymous mutations within coding footprints are significantly younger than those outside of footprints, indicating that coding TF binding constrains both codon and amino acid evolution. Do mutations in duons predispose to epilepsy?

Somatic mtDNA mutation spectra in the aging putamen. Somatic mutations and CNVs are frequently encountered in neurons and likely play a role in the etiology of disease. Whether these somatic alterations play a role in epilepsy is not well studied. It is possible that future studies will explore this area of research by large scale post mortem brain studies. Williams and colleagues investigated the mtDNA mutation spectra of putamen of young and aged donors, showing an increased amount and of complex genomic alterations gained during ageing. This study highlights the importance of study design and sample selection for investigation of somatic disease related variants for early onset epilepsies. Neurons from post mortem brains of adult patients might already harbor aging-related and not epilepsy-related genomic variants.

Papers of the week 50-51 pre Christmas extended edition on noninvasive diagnostic tool in cancer. In the latest edition of PNAS Ni and colleagues show that different circulating tumor cells (CTCs) in peripheral blood exhibit reproducible copy number variation (CNV) but not single-nucleotide variation (SNV) pattern. The finding of reproducible cancer-specific CNVs might offer potential for CTC-based cancer diagnostics in blood.

I hope you enjoyed this extended edition of papers of the week and I wish you a merry Christmas!

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