http://www.genomesunzipped.org/2013/10/genomics-england-and-the-100000-genomes.php
Posts Tagged ‘from’
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
100,000 British invited to post their genomes online – in the name of science — RT News
November 10, 2013Nencki Genomics Database-Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs
October 13, 2013WildCat
October 12, 2013Whole-genome reconstruction and mutational signatures in gastric cancer – Genome Biol.
October 12, 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
October 11, 2013Interesting review on exRNA
October 2, 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
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