{"entity":{"id":"rna-seq","kind":"technology","name":"RNA sequencing & expression profiling","aka":[],"tldr":"Measuring which genes a tumour is actively using, which reveals its subtype and finds gene fusions.","summary":"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.","status":"established","asOf":"2026-09-04","wikipedia":"https://en.wikipedia.org/wiki/RNA-Seq","links":[{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/RNA-Seq"}],"tags":[],"related":["gene-expression-prognostic-assays"],"cancers":["pancreatic","nsclc","sclc"],"sections":["diagnostics"],"technologies":[],"targets":[],"drugs":[],"companies":["blank-bio","cofactor-genomics","data-driven-bioscience","exai-bio","insight-molecular-diagnostics","isabl","lucence","oncobox"],"institutions":[],"pathways":[],"terms":["gene-fusion","pam50"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":["paper-okane-gata6-basal-like-compass-ccr-2020","paper-rashid-purist-pancreatic-subtype-classifier-ccr-2020","paper-philip-kras-wild-type-pancreatic-ccr-2022","paper-jonna-nrg1-fusions-solid-tumours-ccr-2019","paper-fernandez-cuesta-cd74-nrg1-fusion-lung-cancer-discov-2014","paper-gay-sclc-subtypes-inflamed-cancer-cell-2021"],"journals":[],"dependsOn":[],"notes":["Pancreatic cancer: RNA sequencing does two jobs here, calling the classical versus basal-like subtype that predicts chemotherapy response (O'Kane 2020, Rashid 2020) and catching the NRG1, ALK, NTRK, FGFR2 and RET fusions that DNA panels miss in KRAS wild-type tumours (Philip 2022).","Lung cancer: RNA is the only reliable route to the fusions with heterogeneous partners. NRG1 fusions were found in 41 of 21,858 tumours by anchored multiplex RNA sequencing with a different partner almost every time (Jonna 2019), and the founding CD74-NRG1 discovery came from transcriptome sequencing of driver-negative tumours (Fernandez-Cuesta 2014). In small-cell disease RNA is also how the four transcriptional subtypes are called (Gay 2021)."],"principle":"Reverse transcription of RNA to cDNA and sequencing; counts per gene quantify expression.","strengths":["Fusion detection","Functional state, not just genotype"],"limitations":["RNA degrades in FFPE","Bulk averages over cell types"]},"route":"/technologies/rna-seq/","neighbours":{"technology":[{"id":"gene-expression-prognostic-assays","kind":"technology","name":"Gene-expression prognostic assays","route":"/technologies/gene-expression-prognostic-assays/"},{"id":"sarcoma-methylation-classifier","kind":"technology","name":"Methylation classifier for sarcomas","route":"/technologies/sarcoma-methylation-classifier/"},{"id":"multitarget-stool-rna-test","kind":"technology","name":"Multitarget stool RNA test (ColoSense)","route":"/technologies/multitarget-stool-rna-test/"},{"id":"neoantigen-mrna-vaccine","kind":"technology","name":"Personalised neoantigen (mRNA) 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