ArticleJCO precision oncology2018
Biological Validation of RNA Sequencing Data from Formalin-Fixed Paraffin-Embedded Primary Melanomas.
Article in JCO precision oncology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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Who cites it
24 citing papers in PubMed.
- Global patterns of mutational profiles in biliary tract cancer.Journal of hepatology · 2026Article
- Multi-omic analysis identifies a multi-step pathology in a case of multiple chorangioma syndrome in monochorionic twins.Orphanet journal of rare diseases · 2026Article
- Machine learning identifies glycosphingolipid signature linking immune dysregulation and clinical prognosis in uveal melanoma.Discover oncology · 2026Article
- Characterizing malignant prognostic signatures in primary glioma based on single-cell and bulk transcriptome sequencing.PloS one · 2026Article
- A comprehensive, multi-center, immunogenomic analysis of melanoma brain metastases.Acta neuropathologica communications · 2025Article
- Article
- KRAS Allelic Variants in Biliary Tract Cancers.JAMA network open · 2024Article
- Comprehensive Immunogenomic Profiling ofJCO precision oncology · 2024Article
- Multiplatform Analysis of Intratumoral PTEN Heterogeneity in Melanoma.The Journal of investigative dermatology · 2023Article
- Characterization of gene expression profiles in the mouse brain after 35 days of spaceflight mission.NPJ microgravity · 2022Article
- Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- High-Plex Spatial RNA Profiling Reveals Cell Type‒Specific Biomarker Expression during Melanoma Development.The Journal of investigative dermatology · 2022Article
- Evaluation of the EdgeSeq Precision Immuno-Oncology Panel for Gene Expression Profiling From Clinical Formalin-Fixed Paraffin-Embedded Tumor Specimens.Frontiers in cell and developmental biology · 2022Article
- Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors.NPJ genomic medicine · 2021Article
- Reduced expression of innate immunity-related genes in lymph node metastases of luminal breast cancer patients.Scientific reports · 2021Article
- High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis.Human genomics · 2021Article
- Distribution pattern of tumor infiltrating lymphocytes and tumor microenvironment composition as prognostic indicators in anorectal malignant melanoma.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2021Article
- Ginsenoside ameliorated ventilator-induced lung injury in rats.Journal of intensive care · 2020Article
- Molecular and immunological associations of elevated serum lactate dehydrogenase in metastatic melanoma patients: A fresh look at an old biomarker.Cancer medicine · 2020Article
- Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
purposeInitiatives such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) have generated high-quality, multi-platform molecular data from thousands of frozen tumor samples. While these initiatives have provided invaluable insight into cancer biology, a tremendous potential resource remains largely untapped in formalin-fixed, paraffin-embedded (FFPE) samples that are more readily available, but which can present technical challenges due to crosslinking of fragile molecules such as RNA. MATERIALS AND
methodsWe extracted RNA from FFPE primary melanomas and assessed two gene expression platforms -- genome-wide RNA sequencing (RNA-seq) and targeted NanoString -- for their ability to generate coherent biological signals. To do so, we generated an improved approach to quantifying gene expression pathways, in which we refine pathway scores through correlation-guided gene subsetting. We also make comparisons to the TCGA and other publicly available melanoma datasets.
resultsComparison of the gene expression patterns to each other, to established biological modules, and to clinical and immunohistochemical data confirmed the fidelity of biological signals from both platforms using FFPE samples to known biology. Moreover, correlations with patient outcome data were consistent with previous frozen-tissue-based studies.
conclusionFFPE samples from previously difficult-to-access cancer types - such as small primary melanomas - represents a valuable and previously unexploited source of analyte for RNA-seq and NanoString platforms. This work provides an important step towards the use of such platforms to unlock novel molecular underpinnings and inform future biologically-driven clinical decisions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.