Month: July 2016

Small RNA-Seq Workflow

[PMID: 27317696] [Nucleic Acids Research]

Toward reliable biomarker signatures in the age of liquid biopsies – how to standardize the small RNA-Seq workflow



[] [Genomic Medicine]

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

“…whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. ” “uitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs).”

Cancer Genes Through WES

[PMID: 27417679] [Nature Communications]

Challenges in identifying cancer genes by analysis of exome sequencing data

“While some cancer genes are identified by analysis of recurrence, spatial clustering or predicted impact of somatic mutations, many remain undetected due to lack of power to discriminate driver mutations from the background mutational load (13–60% recall of cancer genes impacted by somatic single-nucleotide variants, depending on the method). Cancer genes not detected by mutation recurrence also tend to be missed by all types of exome analysis.”

HER2+ Breast Cancer WGS

[PMID: 27406316] [Nature Communications]

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers

“an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal–basal breast cancer spectrum rather than standing apart.”