Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains
tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the …
tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the …
Alternative tumour-specific antigens
The study of tumour-specific antigens (TSAs) as targets for antitumour therapies has
accelerated within the past decade. The most commonly studied class of TSAs are those …
accelerated within the past decade. The most commonly studied class of TSAs are those …
Accuracy assessment of fusion transcript detection via read-map** and de novo fusion transcript assembly-based methods
Background Accurate fusion transcript detection is essential for comprehensive
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools …
MET-dependent solid tumours—molecular diagnosis and targeted therapy
Attempts to develop MET-targeted therapies have historically focused on MET-expressing
cancers, with limited success. Thus, MET expression in the absence of a genomic marker of …
cancers, with limited success. Thus, MET expression in the absence of a genomic marker of …
Biogenesis, identification, and function of exonic circular RNAs
Circular RNAs (circRNAs) arise during post‐transcriptional processes, in which a single‐
stranded RNA molecule forms a circle through covalent binding. Previously, circRNA …
stranded RNA molecule forms a circle through covalent binding. Previously, circRNA …
STAR-Fusion: fast and accurate fusion transcript detection from RNA-Seq
Motivation Fusion genes created by genomic rearrangements can be potent drivers of
tumorigenesis. However, accurate identification of functionally fusion genes from genomic …
tumorigenesis. However, accurate identification of functionally fusion genes from genomic …
Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data
Background: Fusion transcripts are formed by either fusion genes (DNA level) or trans-
splicing events (RNA level). They have been recognized as a promising tool for diagnosing …
splicing events (RNA level). They have been recognized as a promising tool for diagnosing …
JAFFA: High sensitivity transcriptome-focused fusion gene detection
NM Davidson, IJ Majewski, A Oshlack - Genome medicine, 2015 - Springer
Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion
genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a …
genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a …
Discovering and understanding oncogenic gene fusions through data intensive computational approaches
NS Latysheva, MM Babu - Nucleic acids research, 2016 - academic.oup.com
Although gene fusions have been recognized as important drivers of cancer for decades,
our understanding of the prevalence and function of gene fusions has been revolutionized …
our understanding of the prevalence and function of gene fusions has been revolutionized …
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide
variants, small insertions or deletions, gene fusions, copy-number variations, and large …
variants, small insertions or deletions, gene fusions, copy-number variations, and large …