http://www.ncbi.nlm.nih.gov/pubmed/23176822
Am J Hum Genet. 2012 Dec 7;91(6):1033-40. doi:
10.1016/j.ajhg.2012.10.018. Epub 2012 Nov 21.
Differential relationship of DNA replication timing to different forms of human mutation and variation.
Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA.
Posts Tagged ‘from’
Differential relationship of DNA replication timing to different forms of human mutation and variation.
December 6, 2013FYI: IEEE Spectrum “data sexual”
November 30, 2013Datasexual, the latest incarnation of metrosexual. Other related terms: narb (=narrative bits), data hygiene, QSer
http://spectrum.ieee.org/at-work/test-and-measurement/meet-the-datasexual
Meet the Datasexual
Dropbox Gets Down To Business
November 29, 2013Dropbox Gets Down To Business
November 29, 2013Interesting way to peer review
November 29, 2013Bubble Popper !
By allowing peers to test some of the hypotheses stated in a theoretical paper (or stating that some statement(s) in the paper need additional justification)…
Epigenomic alterations in localized and advanced prostate cancer – Neoplasia
November 27, 2013Summary 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.
100,000 UK whole genome sequenced
November 19, 2013RGASP papers online
November 11, 2013The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!
Some notes from a senior author:
* Due to space constraints unfortunately most of the results are in the supplemental data.
* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.
* The papers are not open access, unfortunately.
0-cell RNAseq
November 10, 2013Interesting title
http://liorpachter.wordpress.com/2013/11/07/zero-cell-rna-seq
HPV integration and SVs
November 10, 2013http://genome.cshlp.org/content/early/2013/11/05/gr.164806.113.abstract Interesting association of viral integration, relevant to bkpts
linkstream2 microblog 