RNA sequencing

Overview

Bulk RNA sequencing of tumor (and where available matched normal) tissue for gene expression quantification, fusion detection, and downstream signature/classifier analysis.

Used by

  • PMID:35927489 — RNA-seq on n=712 CLL samples (603 treatment-naive used for clustering); unsupervised clustering identified 8 robust expression clusters that are independent prognostic factors beyond IGHV/epitype PMID:35927489.
  • PMID:36862133 — select targeted RNA sequencing alongside MSK-IMPACT in the Make-an-IMPACT program; detected actionable fusions including a PRDX1-NTRK1 fusion in histiocytosis only via targeted RNA-seq, plus MS4A6A-BRAF, DOCK8-BRAF, HLA-A-BRAF, and TFG-ALK PMID:36862133.
  • PMID:37202560 — bulk RNA-seq on 348 AC-ICAM colon cancer tumor/normal pairs; underpins the ICR signature, ConsensusTME deconvolution, and CMS classification used for prognostic analysis PMID:37202560.
  • PMID:27634761 — RNA-seq (platform-independent, multiple normalization schemes including RSEM, FPKM, RPKM, TPM) used as the sole molecular feature (~500 features for site of origin, ~200 for lineage) in the ATLAS tumor classification model; trained on 8,249 TCGA/CCLE samples and validated on 10,376 samples PMID:27634761.
  • PMID:34433969 — mRNA-seq on 121 fresh-frozen meningiomas from the University Health Network Brain Tumor BioBank; integrated with WES, EPIC methylation array, and snRNA-seq to define four stable molecular groups PMID:34433969.
  • PMID:38117484 — RNA-seq on 54 glioma patients in the GLASS International consortium; paired with 450K/EPIC methylation arrays and WES/WGS; identified HOXD13 as master regulator of IDH-mutant astrocytoma progression PMID:38117484.
  • PMID:38412093 — RNA-seq on 24 primary anaplastic thyroid carcinomas and 13 cell lines, integrated with TCGA PTC data PMID:38412093.
  • PMID:38488813 — RNA-seq on 44 prostate cancer PDX models; paired with WGS (30X) and targeted sequencing for integrative multi-platform analysis; confirmed ETS fusion-driven expression changes PMID:38488813.
  • PMID:38895302 — RNA-seq paired with WES using G&T-seq protocol on single-cell clones from normal skin melanocytes; supported mutation calling via RNA evidence and phasing PMID:38895302.
  • PMID:30325352 — Illumina HiSeq 2500 RNA-seq (TruSeq Total Stranded RNA + Ribo-Zero) on 130 of 211 NSCLC subjects; reads aligned to hg19 with STAR v2.3, quantified with Cufflinks v2.0.2 in FPKM; RIN <2.5 excluded; part of the nsclc-radiogenomics-stanford public radiogenomic resource PMID:30325352.
  • PMID:39214094 — bulk RNA-seq on 100 upfront resected PAAD tumors (63 KRASG12D, 37 KRASG12R) from the Canadian COMPASS trial (NCT02750657) plus consortium-resected patients; aligned to GRCh38 via STAR; revealed KRASG12D enrichment for EMT, mTORC1, and E2F/G2M Hallmarks versus KRASG12R enrichment for NF-κB/TNFα signaling PMID:39214094.
  • PMID:39305899 — bulk RNA-seq (KAPA Hyper Prep, NovaSeq6000, STAR, GRCh38.108) on sarcoma specimens from the UCLA biobank (194 total, subset sequenced); deposited on Synapse (PDTOSarcoma); used alongside WGS and targeted DNA panel sequencing to characterize 24 bone and soft-tissue sarcoma subtypes PMID:39305899.
  • PMID:39753968 — bulk RNA-seq applied to 11 MAPK-WT PAAD tumors for fusion discovery (FusionCatcher v1.20 + Arriba v2.1.0); also used for the COMPASS trial transcriptomics arm referenced within the study; identified activating BRAF and NRG1 fusions in 2/11 MAPK-WT tumors PMID:39753968.
  • rRNA-depletion RNA-seq applied to breast cancer primaries and metastases (AURORA cohort); expression subtype switching detected in 13/39 (33%) of paired cases; basal-like was the most stable subtype (15/16 concordant) PMID:36585450
  • Performed on one sample per MEC patient for fusion validation; confirmed EWSR1::KLF15 fusion (Patient 2) and novel ASCC2::GGNBP2 fusion (Patient 1) PMID:36577525
  • Total RNA-seq (Illumina TruSeq RiboZero Gold on HiSeq 4000) performed on 176 of 218 metastatic UC patients in UC-GENOME; enabled molecular subtyping and immune cell deconvolution (CIBERSORTx) PMID:36333289
  • Used to sequence transcriptomes of 113 additional NHL cases (DLBCL and FL) in the BCGSC study; provided mutation calls and expression data complementing WGS/WES in 14 matched pairs PMID:21796119
  • Bulk RNA-seq used across SCLC and LUAD cell lines (CCLE/DepMap) to characterize ARID1A expression levels and correlate with JQ1 sensitivity; SCLC lines showed markedly higher ARID1A expression than LUAD lines (p < 0.0001) PMID:22037554
  • Bulk RNA-seq used across 14 ccRCC cohorts (n=3,621) to define HiTME molecular subtypes and train ICI/TKI response prediction models; WU-RCC independent validation cohort included 157 samples with bulk RNA-seq PMID:22138691
  • Used alongside WES in breast cancer to detect splice-site consequences of SF3B1 mutations and quantify allele-specific expression PMID:22158541
  • RNA-seq applied alongside WGS in BCCRC breast tumor cohort to characterize transcriptomic landscape PMID:22495314
  • RNA-seq used in HCC studies to characterize hepatocellular carcinoma transcriptome alongside WGS PMID:22634756
  • Strand-specific high-coverage RNA sequencing performed on 28 pediatric medulloblastoma cases (ICGC); identified first medulloblastoma fusion transcripts (DNAJB6-SHH, LCLAT1-ERBB4); only 48% of non-synonymous DNA mutations detectable at RNA level PMID:22832583
  • Applied to Genentech colorectal cohort to detect RSPO2/RSPO3 fusion transcripts and characterise expression profiles PMID:22895193
  • Used in CLCGP SCLC study (29 tumors) to complement WES/WGS and characterise transcriptome of TP53/RB1-deficient tumors PMID:22941188
  • Applied in JHU SCLC study (36 tumors) to validate SOX2 and MYCL amplification at the transcriptional level PMID:22941189
  • Used in TCGA LUSC study (178 tumors) for expression profiling alongside WES to characterise the CDKN2A/TP53/KEAP1/NFE2L2 mutational landscape PMID:22960745
  • RNA-seq profiling of 510 breast tumors enabled mRNA subtype classification and identified outlier expression events in known cancer genes PMID:23000897
  • RNA-seq used in neuroblastoma study to detect gene fusions and outlier expression; confirmed ALK overexpression in cases lacking ALK point mutations PMID:23334666
  • RNA-seq performed on 20 prostate tumors with matched benign prostate tissue (16 matched cases) as part of the WGS chromoplexy characterization study PMID:23622249
  • RNA-seq performed on 179 of 200 AML samples in TCGA AML analysis; used for de novo assembly identifying 118 fusions in 80 samples and NMF consensus clustering yielding 7 expression groups PMID:23634996
  • RNA-seq applied to 333 endometrial carcinoma tumors; combined with microRNA-seq, RPPA, and DNA-methylation for iCluster and consensus clustering defining four molecular subtypes PMID:23636398
  • Used in TCGA CCRCC study for transcriptome profiling; multi-platform integration with WES, copy-number arrays, methylation, miRNA-seq, and RPPA identified four mRNA expression subtypes (m1-m4) with distinct genomic correlates and survival differences PMID:23792563
  • Applied in 73/96 pediatric pilocytic astrocytoma cases (ICGC cohort) for matched RNA sequencing alongside WGS; used for fusion discovery via TopHat-Fusion and deFuse, identifying novel NTRK2 fusions (QKI:NTRK2, NACC2:NTRK2) and novel BRAF fusion partners PMID:23817572
  • Applied to 164 GBM transcriptomes; analyzed with PRADA to detect fusion transcripts (228 total in 106/164 samples) including recurrent EGFR-SEPT14, FGFR3-TACC3, and PDGFRA intragenic splice variants PMID:24120142
  • Applied to 42 TCC bladder tumors with 16 matched normal bladder tissues; detected FGFR3-TACC3 in-frame fusion in 2/42 (5%) cases with outlier TACC3 expression PMID:24121792
  • Performed alongside whole-genome sequencing (STAR hg38 alignment + RSEM quantification) for 28 metastatic NENs in the BC Cancer POG program; expression data drove 6 of 10 clinical benefit outcomes through independent transcriptome-based therapy recommendations PMID:24326773.
  • Used to validate aberrant splicing in grade II glioma, including confirmation of RB1 c.2520+1G>A splice-site mutation-driven premature termination and loss of growth-suppression domain in a TMZ-treated hypermutated recurrence PMID:24336570
  • PolyA RNA-seq on Illumina HiSeq2000 (100 bp PE) applied to 80 rhabdomyosarcoma tumors; mapped with TopHat2; fusions called via tophat-fusion and deFuse; showed 58% of DNA-level somatic mutations had RNA expression evidence; identified cryptic PAX rearrangements including PAX3-INO80D PMID:24436047
  • Applied to all 131 TCGA bladder carcinoma tumors (n=129 for mRNA clustering); miRNA-seq also performed; identified 4 mRNA expression clusters including papillary-like (cluster I, enriched for FGFR3 mutations) and basal/squamous-like (cluster III, expressing KRT14/KRT5/EGFR); viral integration transcripts detected in 5/122 PMID:24476821
  • Performed on 4 of the 20 Discovery Cohort ESCC tumors to support transcriptomic analysis of mutated genes (e.g., APOBEC3B expression, XPO1 mRNA levels) PMID:24686850
  • Applied to 196 HCC patients as part of the TCGA integrated molecular characterisation (DNA copy number, methylation, mRNA, miRNA, RPPA) PMID:24798001
  • Transcriptome RNA-seq performed on 25 thymic epithelial tumors (Illumina Genome Analyzer II / HiSeq2000) using TopHat + Cufflinks; identified BCL2 focal amplification correlated with increased BCL2 mRNA; both GTF2I alleles expressed (mean mutant allele fraction 47%) PMID:24974848
  • Used for bulk RNA-seq of primary human gallbladder fibroblasts (GFs) cultured on 0.5 vs 16 kPa silicon hydrogels (NCBI SRA PRJNA1182410), identifying SEMA7A as the most strongly upregulated semaphorin under stiff matrix conditions in GBC stroma PMID:24997986
  • Six-platform TCGA profiling of 295 gastric adenocarcinomas (stad_tcga_pub) included mRNA-seq (RNA-seq) to define transcriptional subtypes and pathway activity across EBV, MSI, GS, and CIN molecular subgroups PMID:25079317
  • Multi-platform TCGA profiling of 230 lung adenocarcinomas (luad_tcga_pub) included mRNA sequencing to identify transcriptional subtypes (TRU, PI, PP) and MET exon 14 skipping events PMID:25079552
  • Used in TCGA ChRCC project (66 tumors) to profile gene expression, identify distal-nephron cell-of-origin signatures, characterize mtDNA-mutant transcriptomes, and assess TERT expression levels. PMID:25155756
  • Used on Illumina HiSeq 2500 (GEO GSE272957) to profile transcriptomes of EWS::FLI1-transduced heMSCs vs controls, identifying 3,836 DEGs and Ewing sarcoma gene-expression signatures. PMID:25186949
  • Used on Illumina HiSeq to profile seven prostate cancer organoid lines; identified TMPRSS2-ERG fusion status, SPINK1 overexpression, and confirmed gene-expression concordance between organoids and parental tumor tissue. PMID:25201530
  • Used in MPNST discovery cohort (15 tumors, 51 bp PE, Illumina HiSeq-2500, hg19, STAR v2.3); RNA-seq was essential to detect SUZ12 structural rearrangements missed by WES, and revealed 455/479 differentially expressed genes upregulated in PRC2-loss tumors PMID:25240281
  • Applied to 159 nccRCC tumors (TruSeq, HiSeq 2000, ~68M PE reads/sample); enabled a 5-gene classifier (ASB1, GLYAT, PDZK1IP1, PLCG2, SDCBP2) achieving 95.3% subtype accuracy and detection of novel ACTG1-MITF and CLTC-TFEB fusions PMID:25401301
  • Used in TCGA papillary thyroid carcinoma (THPA) multiplatform study to derive BRAFV600E-RAS Score (BRS) from a 71-gene expression signature and Thyroid Differentiation Score (TDS) from 16 metabolism genes, enabling molecular reclassification of 496 PTCs PMID:25417114
  • Applied to 279 HNSC tumors for HPV status determination (E6/E7 read mapping; threshold >1,000 reads) and expression subtype classification (atypical/mesenchymal/basal/classical), as well as structural variant detection including MET exon-14 skipping PMID:25631445
  • Paired-end RNA-seq (Illumina HiSeq 2500, 2×100 nt, ~50M paired reads) performed on 150 mCRPC biopsies alongside WES, enabling fusion detection via Tophat-Fusion and FPKM quantification by Cufflinks. PMID:26000489
  • mRNA sequencing (Illumina TruSeq, HiSeq 2000) on 331 melanoma samples enabled identification of three transcriptomic subclasses (Immune, Keratin, MITF-low) and 224 candidate fusion drivers. PMID:26091043
  • RNA-seq used for transcriptome profiling in breast cancer genomic analysis PMID:26168399
  • RNA-seq used for transcriptome profiling as part of multi-omic characterization of ovarian cancer PMID:26200345
  • Used in 40-42 of 110 metastatic melanoma pretreatment tumors (skcm_dfci_2015) to measure cytolytic activity (GZMA+PRF1 geometric mean) and immune checkpoint expression (CTLA4, PDCD1LG2); each independently associated with ipilimumab clinical benefit PMID:26359337
  • Performed on 35 AAV-CRISPR-edited rat mammary tumors across six genotype groups; ANOVA (FDR<1%) identified 1,579 differentially expressed genes; intrinsic subtype assignment classified most tumors as Luminal A or B; GSEA of fulvestrant-responsive DEGs showed significant concordance with human patient neoadjuvant endocrine therapy datasets PMID:26437033
  • Used in the TCGA breast ILC/IDC multi-platform study (n=817) for mRNA expression profiling; enabled definition of three ILC transcriptional subtypes (reactive-like, immune-related, proliferative) and orthogonal validation of mutation calls (78.1% of CLL gene mutations detected at sites with >90% detection power) PMID:26451490
  • Performed on neuroblastoma tumors (Illumina HiSeq 2000) alongside custom 4x44K Agilent oligonucleotide microarrays; quantified TERT expression showing 92-fold higher levels in TERT-rearranged vs low-risk tumors and higher than MYCN-amplified tumors (P=0.028) PMID:26466568
  • Used in 156 of 538 CLL whole-exome samples for orthogonal validation; 78.1% of CLL gene mutations detected in matched RNA-seq at sites with >90% detection power; MGA-mutant CLLs showed downregulation of MYC-suppressed B-cell gene sets PMID:26466571
  • Profiled mRNA expression in 333 primary prostate adenocarcinomas (TCGA) as part of multi-platform characterization; 19 matched non-malignant adjacent samples profiled for methylation and RNA/miRNA expression PMID:26544944.
  • TruSeq Stranded Total RNA, 100 bp paired-end, ≥50 M reads applied to 30 periampullary tumors (28 AMPAC + 2 DUOAC) to characterize WNT-pathway transcriptional dysregulation PMID:26804919
  • Applied to 1,045 diffuse gliomas in the TCGA pan-glioma study; TERT mRNA quantified as a 91% sensitive / 95% specific surrogate for TERTp mutation status; also used for LGr1–4 expression cluster derivation PMID:26824661
  • Used alongside WGS and ChIP-seq in adenoid cystic carcinoma (ACC) primagrafts and primary tumors to characterize MYB-driven transcriptional programs and the BRD4 super-enhancer landscape PMID:26829750
  • TruSeq, HiSeq 2500, 2×75 bp paired-end applied to 49 metastatic CRPC specimens (Adeno + NE) to identify the 70-gene NEPC classifier and characterize EZH2/PRC2 target dysregulation PMID:26855148
  • Illumina HiSeq 2000, ≥50M paired 100×100 bp reads applied to 17 adenoid cystic carcinoma (ACC) tumors; NFIB overexpression confirmed independent of fusion status (p=0.002 vs normal tissue); quantification by RSEM PMID:26862087
  • Applied to 40 MRT cases plus 3 hESC lines (with 4 fetal cerebellum normals); NMF on top-25% most-variable protein-coding genes identified 2 mRNA sub-groups recapitulating the AT/RT vs RTK distinction, with organ site associated with sub-group 1 (all 6 extra-renal cases; Fisher p=0.04). PMID:26977886
  • Performed on 28-tumor subset of anti-PD-1-treated metastatic melanomas to identify the IPRES transcriptional resistance program via GSVA/GSEA enrichment analysis PMID:26997480
  • Performed on 495 lung ADC and 476 lung SqCC samples; used for fusion calling via PRADA and for mutational-signature transcriptional cross-validation in the NSCLC landscape study PMID:27158780
  • Applied on 7 uRCC tumours (4 NF2-loss, 3 NF2-WT) using Illumina HiSeq 2500, with STAR alignment, to evaluate YAP/TAZ transcriptional signatures via GSEA. PMID:27713405
  • Transcriptome sequencing (RNA-seq) on N=54 cases used to characterize the DUX4/ERG B-ALL subtype; identified ERGalt from a novel non-canonical first exon and distinguished this subtype from other B-ALL classes. PMID:27776115
  • Used as tumor transcriptome profiling (TruSeq Stranded Total RNA LT) in the PIPseq program; RNA-seq independently contributed ~40% of clinically impactful findings including fusion detection, BCR-ABL1-like signature identification, and expression-based subtyping across 65 pediatric patients PMID:28007021.
  • Used for mRNA profiling of 164 oesophageal carcinomas and 359 gastric adenocarcinomas in the TCGA esophageal/stomach study; mRNA-seq confirmed no HPV transcripts in ESCC and provided expression data for iCluster integrative subtyping PMID:28052061.
  • Applied to 173 PCPG tumors in the TCGA PCPG study; mRNA-seq revealed four molecular subtypes (kinase signaling, pseudohypoxia, Wnt-altered, cortical admixture) and confirmed CSDE1 splice-site mutation effects via intron retention and exon skipping PMID:28162975.
  • Used RNA-seq to profile transcriptional changes in tumor models PMID:28196596
  • Employed RNA-seq for transcriptome profiling in sarcoma tumor samples PMID:28199314
  • Used RNA-seq for transcriptome profiling and fusion detection in cancer specimens PMID:28373299
  • Poly(A)+ transcriptomes generated for 164 medulloblastoma cases; recurrent fusions targeting GLI2, PTEN, and PVT1 identified by integrating SV breakpoints with RNA-seq data PMID:28726821
  • Poly(A)+ and exome-capture transcriptomes generated for 868 libraries from 496 MET500 metastatic tumors (40–50M paired reads on Illumina HiSeq 2000/2500); enabled fusion calling (CODAC), immune deconvolution, and MImmScore derivation PMID:28783718
  • Applied to NOL10-knockdown LNCaP cells to identify 71 downregulated cell-cycle genes (DLGAP5, MCM4, KIF20B, DIAPH3, SUV39H1, CENPE, GINS2, HMGB3, CDC6); also used for GSEA and eQTL/sQTL analyses across CPGEA and TCGA PRAD cohorts PMID:28927585
  • Performed on 775 DLBCL cases (625 used in core analysis) for cell-of-origin assignment (ABC vs GCB) and integrated prognostic modeling PMID:28985567
  • Performed on 408/412 BLCA tumors enabling five mRNA expression subtype classification (luminal-papillary, luminal-infiltrated, luminal, basal-squamous, neuronal) with subtype-associated survival p=4×10⁻⁴ PMID:28988769
  • Performed on 45 baseline and 26 paired pre/on-therapy melanoma biopsies (STAR-aligned, hg19); 189 pre-therapy DEGs distinguished CR/PR from PD and 475 on-therapy DEGs captured pharmacodynamic immune response to nivolumab PMID:29033130
  • Performed on 206 TCGA sarcomas; revealed that UPS and MFS are transcriptomically indistinguishable and identified miR-181b-5p as an independent recurrence-free survival predictor in LMS (HR=7.4, p=9×10⁻⁶) PMID:29100075
  • Performed on 18 PBRM1-LOF vs. 14 PBRM1-intact pre-treatment CCRCC tumors; GSEA confirmed up-regulation of hypoxia and IL6/JAK-STAT3 gene sets in PBRM1-deficient tumors PMID:29301960
  • RNA-seq fusion calling across 9,624 TCGA tumor samples and 713 normal samples (33 cancer types) using STAR-Fusion, EricScript, and BREAKFAST pipelines; GRCh38 reference; yielded 25,664 filtered fusions PMID:29617662
  • HiSeq 2500 PE100 RNA-seq performed on AALE chr_3p-deleted cells; processed via STAR + RSEM + edgeR for differential expression analysis PMID:29622463

Notes

  • In the CLL-map study, RNA-seq is one arm of an integrated WES/WGS + RNA-seq + methylation analysis used to derive an integrated outcome model PMID:35927489.
  • In the AC-ICAM atlas, RNA-seq drives both immune signature scoring and downstream microbiome integration PMID:37202560.
  • In the NSCLC radiogenomics dataset, RNA-seq (n=130) complements CT/PET-CT imaging and SNaPshot mutational testing for EGFR/KRAS/ALK, with 17 subjects having both RNA-seq and microarray expression data PMID:30325352.

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