http://database.oxfordjournals.org/content/2013/bat069.abstract.html
Archive for the 'SciLit' Category
Nencki Genomics Database-Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs
October 13, 2013The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line Nature. 2013 – PubMed – NCBI
October 12, 2013http://www.ncbi.nlm.nih.gov/pubmed/23925245
Contains a personal-genome like construction for HeLa
with 100X shotgun and then paired ends used for variant discovery and sequencing of pools of fosmid clones for haplotype resolution. Finally, low-freq. somatic and passage variants layered onto this.
Haplotype-resolved genome… of #HeLa: Has mapping of #ENCODE RNA- & chIP-seq against a personal genome
http://dx.doi.org/10.1038/nature12213 via @aemonten
Cell – A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk
October 12, 2013Cell, Volume 155, Issue 1, 70-80, 26 September 2013
10.1016/j.cell.2013.08.030
David R. Blair,Christopher S. Lyttle,Jonathan M. Mortensen,Charles F. Bearden,Anders Boeck Jensen,Hossein Khiabanian,Rachel Melamed,Raul Rabadan,Elmer V. Bernstam,Søren Brunak,Lars Juhl Jensen,Dan
Nicolae,Nigam H. Shah,Robert L. Grossman,Nancy J. Cox,Kevin P. White,Andrey Rzhetsky
http://www.cell.com/retrieve/pii/S0092867413010246
Variants in #Mendelian Loci Contribute to Complex Disease Risk: connecting rare & common diseases
http://www.cell.com/retrieve/pii/S0092867413010246 via @neilfws
CiteULike: Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers
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.
Clan genomics and the complex architecture of human dis… Cell. 2011 – PubMed – NCBI
October 11, 2013QT:”One implication of this realization is that recent mutation may have a greater influence on disease susceptibility or protection than is conferred by variations that arose in distant ancestors.” http://www.ncbi.nlm.nih.gov/pubmed/21962505
Replicative mechanisms for CNV formation are error prone : Nature Genetics : Nature Publishing Group
October 11, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2768.html Replicative mechanisms for #CNV formation are error prone: CNVs associated with SNVs in 67 cases http://dx.doi.org/10.1038/ng.2768 MT @LeucineRichBio
Lupski paper
Interesting 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
RNA editing in Drosophila
October 2, 2013http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2675.html
They say most editing sites identified by modENCODE are technical artifacts !
linkstream2 microblog 