Month: December 2017

HRD Signatures

[PMID: 29262283] [New England Journal of Medicine]

Signatures of DNA-Repair Deficiencies in Breast Cancer

Mini review of HRDetect and Paz’s paper.



[PMID: 29272339] [Bioinformatics]

Personal Cancer Genome Reporter: variant interpretation report for precision oncology  

“The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual cancer genomes for precision oncology. It interprets both somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl’s Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations retrieved flexibly through vcfanno, and produces interactive HTML reports intended for clinical interpretation.”

HRD Predicts BRCA1/2

[PMID: 29246904] [Clinical Cancer Research]

Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer

WGS on 93 T/N (100x/60x) in advanced breast cancer. They called the mutation signatures and looked into how HRD predicts BRCA1/2 status and outcomes of platinum-based chemo. Basically they used HRDetect to generate a score (aggregated metric) to represent six HRD signatures for correlation tests. They also examined how signatures differ across PAM50 subtypes.

Field Cancerization

[PMID: 29217838] [Nature Reviews Cancer]

An evolutionary perspective on field cancerization

“Field cancerization, which is the replacement of the normal cell population by a cancer-primed cell population that may show no morphological change, is now recognized to underlie the development of many types of cancer, including the common carcinomas of the lung, colon, skin, prostate and bladder. Field cancerization is the consequence of the evolution of somatic cells in the body that results in cells that carry some but not all phenotypes required for malignancy.”