Month: December 2015

OASIS

[PMID:26716558] [Nature Methods]

OASIS: web-based platform for exploring cancer multi-omics data

“Currently OASIS contains sample-level annotations and gene-level mutation, copy number variation (CNV) and expression data on 12,108 primary tumor, 13,007 normal samples and 1,054 cell lines across 55 cancers and 43 tissues from The Cancer Genome Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE), the Genotype-Tissue Expression (GTEx) project and four published genomics studies of liver, gastric and breast cancers”

Tissues vs. Species

[PMID:26694591] [Genome Biology]

Meta-analysis of RNA-seq expression data across species, tissues and studies

Analyses from mouse ENCODE [PMID:25409824] and Michael Synder’s group [PMID:25413365] suggested that gene expression data from human and mouse tend to cluster more by species rather than by tissue, whereas Yoav Gilad disagreed [F1000Research]. This meta-analysis of RNA-Seq work supported the latter, “samples clustered exclusively by tissue rather than by species or study, supporting conservation of organ physiology in mammals”.

Tumor Germline and Somatic Mutations

[PMID:26689913] [Nature Communications]

Patterns and functional implications of rare germline variants across 12 cancer types

“Germline variant calling was conducted using VarScan, GATK and Pindel for TCGA discovery (4,034) and validation (1,627) samples and Women’s Health Initiative (WHI) (1,039) controls.” “We followed stringent filtering strategies for standardizing specificity across the Pan-Cancer somatic variant calls for 3,368 cases in this study” Work from Li Ding.