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Measuring which genes a tumour is actively using, which reveals its subtype and finds gene fusions.
RNA sequencing reverse-transcribes a tumour's RNA to cDNA and sequences it, so read counts per gene quantify which genes are actively expressed rather than merely present. Bulk RNA-seq detects gene fusions (NTRK, RET, NRG1) that DNA panels can miss, defines expression subtypes such as PAM50 in breast cancer, TNBC subtypes and the consensus molecular subtypes in colorectal cancer, and measures immune signatures. Commercial prognostic assays including Oncotype DX, MammaPrint and Prosigna are expression-based and guide chemotherapy de-escalation in HR-positive breast cancer. The strengths are fusion detection and a readout of functional state rather than genotype alone. RNA degrades in formalin-fixed tissue, and bulk measurements average over all cell types. It measures which genes a tumour is using, revealing its subtype and finding fusions a DNA test can overlook.
Reverse transcription of RNA to cDNA and sequencing; counts per gene quantify expression.
Nothing recorded yet: a foundation, or a gap to fill.
Dependencies are what this technology cannot be delivered without: manufacturing steps, instruments, software, upstream methods. See its full chain on the map.
A gene test on the needle sample from a thyroid lump that can safely call an 'uncertain' result benign and spare an operation.
The only test designed to tell a woman who has finished five years of hormone therapy whether another five years is worth the side effects.
A urine test that can rule out bladder cancer in people with blood in their urine, so fewer need a camera examination of the bladder.
A 22-gene test on the biopsy or surgical specimen that predicts spread and death, used to decide on surveillance or adding hormone therapy.
A 12-gene test that combines gene activity with tumour size and lymph nodes to say whether hormone therapy alone is enough, and whether to continue it beyond five years.
A 70-gene test that tells whether an early breast cancer is genomically low or high risk, used to decide who can skip chemotherapy.
The first FDA-approved test that sequences all of a tumour's genes and gene activity at once, used to match patients to several targeted drugs.
A 21-gene test that tells most women with early hormone-positive breast cancer whether they can safely skip chemotherapy.
A 17-gene biopsy test that helps men with newly diagnosed low-risk prostate cancer decide whether to watch or treat.
A gene test on a prostate biopsy that estimates how aggressive the cancer is, to help decide between active surveillance and treatment.
A 50-gene test run in local hospital laboratories that estimates the ten-year risk of a hormone-positive breast cancer coming back.
This is the fusion and immune-marker table for the wild-type minority, the group in which RNA sequencing pays for itself.
It offers the first credible explanation for why only a minority of small-cell patients get a durable benefit from checkpoint blockade, and it introduces subtype switching, which would mean retesting at relapse rather than typing once.
A subtype report should carry a confidence, and a trial that dichotomises subtype will misplace about one patient in eight.
It is the number behind 'basal-like is chemoresistant' and the validation of the GATA6 stain that lets a pathology laboratory call the subtype without RNA sequencing.
It shows that the driver frequencies quoted in Western guidelines are population statistics rather than facts about the disease, which matters for how many patients anywhere are expected to benefit from a given medicine.
PurIST is the assay form of the Moffitt subtypes and the tool prospective subtype-stratified trials use.
It explains why single-sample classifiers disagree on about one tumour in eight and why KRAS allelic imbalance and GATA6 copy number are being read alongside expression.
It put a number on how rare NRG1 fusions are and showed that heterogeneous partners make RNA-based testing the only reliable way to find them, which is the practical argument for adding a fusion panel to a driver-negative lung cancer work-up.
Query for this technology: (TITLE:"RNA sequencing" OR ABSTRACT:"RNA sequencing" OR TITLE:"transcriptomic profiling" OR ABSTRACT:"transcriptomic profiling" OR TITLE:"gene expression signature" OR ABSTRACT:"gene expression signature") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about RNA sequencing & expression profiling, not a curated reading list.
Shares Isabl, BostonGene, Carlos Caldas, Genomics-driven precision medicine for advanced pancreatic cancer: early results from the COMPASS trial.
Shares CD74-NRG1 fusions in lung adenocarcinoma, Genomic correlates of clinical outcome in advanced prostate cancer, Whole-genome and transcriptome sequencing of prostate cancer identifies new genetic alterations driving disease progression, Genomic landscape of lung adenocarcinoma in East Asians.
Shares Genomic correlates of clinical outcome in advanced prostate cancer, Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer, Substantial interindividual and limited intraindividual genomic diversity among tumours from men with metastatic prostate cancer, Whole-genome and transcriptome sequencing of prostate cancer identifies new genetic alterations driving disease progression.
Shares Detection of NRG1 gene fusions in solid tumors, CD74-NRG1 fusions in lung adenocarcinoma, Jones 2019: NRG1 gene fusions are recurrent, clinically actionable rearrangements in KRAS wild-type pancreatic ductal adenocarcinoma, Recurrent R-spondin fusions in colon cancer.
Shares Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection, Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer, Genomic correlates of clinical outcome in advanced prostate cancer, Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer.
Shares Oncobox, Data Driven Bioscience (Duoseq), Takashi Kohno, BostonGene.
Shares Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection, Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer, Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma, Detect tumours changing cell type from RNA in the blood.
Shares FOXO1 fusion status and IRS group (rhabdomyosarcoma), SS18::SSX fusion (synovial sarcoma), Ph-like (BCR::ABL1-like) acute lymphoblastic leukaemia, Molecular characterisation of neuroendocrine prostate cancer and identification of new drug targets.
Open-source projects that implement or serve this technology, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
The community-standard Nextflow pipeline for bulk RNA sequencing: quality control, alignment or pseudo-alignment and gene counts, used across cancer transcriptomics.
A single R interface to several methods that estimate immune cell fractions in bulk tumour transcriptomes.
Fast fusion detection from RNA-seq built for clinical use, with a curated list of known cancer fusions and publication-quality plots.
Fusion transcript detection from RNA-seq using STAR chimeric alignments, part of the Trinity CTAT toolkit.
Cell-type enrichment scores for 64 immune and stromal cell types from gene expression.
Finds somatic fusion genes and translocations in RNA-seq from tumour samples.
Estimates the abundance of immune and stromal cell populations in a tumour from bulk expression data.
Commercial and regulated products that serve this technology. Each card says what is behind it: a regulator's database, the literature, a public body's list, or only the company's own words. Listing is not endorsement, and a clearance is a regulatory fact, not a clinical one.
Caris's approved whole-exome and whole-transcriptome profiling test, with the reporting layer that turns it into treatment options.
Deconvolution of bulk expression data into cell type proportions, the standard way to ask what immune cells were in a tumour sample.
Extraction of T-cell and B-cell receptor repertoires from sequencing data, used to measure clonality in tumours and after cell therapy.
Open-source software, hardware and data projects catalogued by a third party, the Open Medical Registry, that bear on this technology. Listing is not endorsement; check each project's own licence and validation before clinical use.
Fast and accurate gene fusion detection from RNA-Seq data
From the Open Medical Registry (openmedical.sh), an MIT-licensed catalogue of open-source medicine. Blurbs are one line from each registry record; every project keeps its own licence.