Posts Tagged ‘from’
Whole-genome reconstruction and mutational signatures in gastric cancer – Genome Biol.
Saturday, October 12th, 2013Genome Biol. 2012 Dec 13;13(12):R115.
Whole-genome reconstruction and mutational signatures in gastric cancer. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y.
http://www.ncbi.nlm.nih.gov/pubmed/23237666
Some thoughts, much from WC:
Looks like the data is freely available via GEO ID : GSE30833 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30833
The article by Nagarajan et al. highlights the authors efforts to utilize de novo genome assembly of gastric cancer genomes to detect not only single nucleotide variants (SNV’s) and short
insertions/deletions (indels), but also larger scale genomic structural variation (SV) that could be signatures of cancer genomes. It is to be applauded that this is a whole genome analysis.
The authors present several interesting findings such as enrichment for C->A and T->A mutations in both cancer genomes, enrichment for C->A and C->T mutations in the H. pylori infected cancer genome (evidence of cytosine specific transcription mediated DNA repair due to deamination), and amplification and deletion of regions on chromosome 12 in the non-H. pylori infected genome.
Although copy number variants (CNV) could potentially be detected by exome sequencing alone, whole genome sequence enables the precise localization of such events, as well as the detection of variation in non-coding regions.
Their methodology relies on combining high-throughput short-read sequencing with longer DNA-PET (paired end tags) in order to construct higher confidence de novo assemblies with longer contiguous regions.
Adventures of a Serial Trespasser – In Focus – The Atlantic
Friday, October 11th, 2013Interesting review on exRNA
Wednesday, October 2nd, 2013mostly focussed on microRNAs, but it goes into the role of exRNAs on cancer:
http://www.frontiersin.org/Journal/10.3389/fgene.2013.00173/abstract
RNA editing in Drosophila
Wednesday, October 2nd, 2013http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2675.html
They say most editing sites identified by modENCODE are technical artifacts !
Would you pass the wallet test?
Saturday, September 28th, 2013Helsinki is the world’s most honest city while Lisbon is the least in lost wallet test
NY is #3
Exosomes mediate the cell-to-cell transmission of IFN-α-induced antiviral activity
Saturday, September 28th, 2013Would you pass the wallet test?
Saturday, September 28th, 2013Systematic identification of trans eQTLs as putative drivers of known disease associations
Sunday, September 15th, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2756.html
“They found SNPs that regulate one gene (Ikaros) in different cell types, meaning they found different cis-regulatory regions for a single gene, that map to different pathways…. they used the cell-type specific information from ENCODE data.”
Papers about retroduplications (variable pseudogenes)
Friday, September 13th, 2013here are three more relevant papers about retroduplications :
http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1810.html http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003242 http://genomebiology.com/content/14/3/R22