Mutational landscape and significance across 12 major #cancer types: Common genes mutated in different cancers
http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
http://www.sciencedaily.com/releases/2013/10/131016132143.htm
Mutational landscape and significance across 12 major cancer types http://www.nature.com/nature/journal/v502/n7471/full/nature12634.html
Summary for:
“Epigenomic Alterations in Localized and Advanced Prostate Cancer” Lin PC, Giannopoulou E, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA*, Elemento O*. 2013. Epigenomic alterations in localized and advanced prostate cancer. Neoplasia
http://www.ncbi.nlm.nih.gov/pubmed/23555183
In this paper, the authors take advantage of new advances in reduced representation bisulfite sequencing, a method for measuring DNA methylation patterns genome-wide, with high coverage and
single-nucleotide resolution, to study methylation patterns in prostate cancer. Working with a prostate cancer cohort already studied with DNA-Seq and RNA-Seq analyses, the authors identified
differentially methylated regions (DMRs), comparing the methylation of prostate cancer samples to benign prostate samples. The analysis found an increase in DNA methylation in prostate cancer samples, and that the methylation was more diverse and heterogeneous compared to the patterns of benign samples. Furthermore, it was found that genes near hypermethylated DMRs tended to have decreased expression, while genes near hypomethylated DMRs tended to have increased expression. Additional analyses revealed that breakpoints associated with prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue. Finally, a study of CpG islands at different stages of prostate cancer (benign vs. PCa vs. CRPC (castration-resistant prostate cancer)) revealed that certain islands become increasingly methylated with disease severity. The authors used this data as the basis for two classification models: one to discriminate between benign prostate tissue and PCa tissue, and another to discriminate between PCa tissue and CRPC tissue. Both models demonstrated high sensitivity and specificity, indicating that CpG islands with high discriminatory power could serve as a diagnostic basis for predicting disease aggressiveness. Finally, additional analyses revealed that breakpoints associated with
prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue.
http://nar.oxfordjournals.org/content/40/D1/D930.long
HaploReg explores functional annotations, such as chromatin states in varied cell types, sequence conservation, regulatory motif
alterations and eQTLs, of linked SNPs or indels within LD block of queried SNPs. The output provides a the guide to develop hypotheses of functional impact of non-coding variants, especially GWAS SNPs. HaploReg is currently limited to known variants (e.g. 1000 Genome variants and dbSNPs) and is unable to deal with private variants.
Interesting discussion of a new sleep medication related to orexin, which is a protein that when removed is associated with narcolepsy.
http://stm.sciencemag.org/content/5/179/179ra44
Genome Res. 2001 Apr;11(4):531-9.
Identification and functional analysis of mutations in the hypocretin (orexin) genes of narcoleptic canines.
Hungs M, Fan J, Lin L, Lin X, Maki RA, Mignot E.
http://www.ncbi.nlm.nih.gov/pubmed/11282968
#Orexin Receptor Antagonists Differ from Standard #Sleep Drugs… Interesting discussion of a new insomnia medication
http://stm.sciencemag.org/content/5/179/179ra44
Worth a read for large-scale project:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285
Ten Simple Rules for Reproducible Computational Research
Geir Kjetil Sandve,
Anton Nekrutenko,
James Taylor,
Eivind Hovig
and related :
http://www.slideshare.net/dullhunk/the-seven-deadly-sins-of-bioinformatics
[tag ReproducibleResearch,from,kbase]
Interesting discussion by Ken Dill reviewing the field of protein folding over the past 50 years. Dr Dill links it to a number of diseases such as Alzheimer’s, Parkinson’s and type II diabetes, which are transmitted by aberrantly folding proteins. There is also a bit of discussion about folding landscapes in the funnel.
http://www.sciencemag.org/content/338/6110/1042
The #Protein-Folding Problem, 50 Years On: Broad review, ranging from funnels to misfolded proteins & Alzheimer’s
http://www.sciencemag.org/content/338/6110/1042
Interesting discussion about the creation of smart rocks and smart pebbles, which allow the tracking of current. These contain a data logger embedded in either aluminum or plastic. The tricky bit is how one finds them after they have been dropped off. Some ways might be radio transmitters, metal detectors and so forth but all of these have downsides.
How to Build a Smarter #Rock? Put a data #logger into aluminum or plastic; then track via radio or metal detector
http://www.sciencemag.org/content/338/6113/1412.summary
Half a Million DVDs in Your #DNA: Nice writeup of Goldman et al paper, highlighting 3X density incr. to >2 PB / g DNA
http://news.sciencemag.org/biology/2013/01/half-million-dvds-your-dna
Very interesting discussion outside of science about the potential of storing large quantities of archival data on DNA. The statistic is that you can store a little more than 2 petabytes in a gram of DNA. This is actually cost effective relative to magnetic tape if one wants to do storage for >500 years. However one imagines that as the price of DNA sequencing and synthesis goes down this will become more favorable, perhaps being reasonable for archival storage in the ~50 year regimen. One of the issues with DNA storage, of course, is the lack of random access and the inability to rewrite over already stored media. But for long-term archival storage DNA is considerably more stable than the magnetic storage on tape or disk.
http://news.sciencemag.org/biology/2013/01/half-million-dvds-your-dna http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html
http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2728.html
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
HaploSeq: #haplotype reconstruction using proximity-ligation. Nice adaptation of functional genomics tech to assembly
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2728.html
~400 top authors by h-score & citations from 15K in biomed.
http://onlinelibrary.wiley.com/doi/10.1111/eci.12171/abstract