[PMID: 28911107] [Nucleic Acids Research]
Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs
“provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%.”
[PMID: 28904067] [Cancer Research]
Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
“11 of 640 tumors as MMR deficient”. Work by Michael Stratton & Serena Nik-Zainal.
[PMID: 28886379] [Cell]
Putting p53 in Context
Great review about P53 in human cancers.
[PMID: 28892075] [Nature Biotechnology]
Analysis of somatic microsatellite indels identifies driver events in human tumors
“MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance.” Work from Gad Getz.
[PMID: 28873162] [JAMA]
Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing
“Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing.”
[PMID: 28851873] [Nature Communications]
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes
“Here, we present ALoFT (annotation of loss-of-function transcripts), a method to annotate and predict the disease-causing potential of loss-of-function variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between loss-of-function variants that are deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. ” Work from Daniel MacArthur & Mark Gerstein.
[PMID: 28714863] [The Journal of Clinical Investigation]
DNA methylation-based immune response signature improves patient diagnosis in multiple cancers
“the evaluation of tumor-infiltrating lymphocytes (TILs) relies on histopathological measurements with limited accuracy and reproducibility. Here, we profiled DNA methylation markers to identify a methylation of TIL (MeTIL) signature that recapitulates TIL evaluations” Glad to see the methylation becomes a good surrogate of pathological TIL measurement.