Month: December 2015


[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”.


[PMID:26704973] [Nucleic Acids Research]

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

“to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data.”


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.



[PMID:26691984] [Nature Genetics]

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

“SMRs reveal recurrent alterations across a spectrum of coding and noncoding elements, including transcription factor binding sites and untranslated regions mutated in up to ~15% of specific tumor types.” Work from Michael Snyder.



[PMID:26630308] [PLoS Genetics]

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

Cancer mutation signature R package from Matthew Stephens.


Pathogenic Variants in NGS

[PMID:26681312] [Genetics in Medicine]

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing

Summary work from Wendy Chunk.