Main Session
Sep
30
PQA 09 - Hematologic Malignancies, Health Services Research, Digital Health Innovation and Informatics
3729 - Determining Cancer Biomarker Status by RNA Sequencing
Presenter(s)
Steven Tau, PhD - Dartmouth College, Hanover, NH
S. Tau1, L. D. Gangiredla2, R. S. Vyas3, Z. Cieslak4, D. T. Bergman1, and P. S. Shah3; 1Geisel School of Medicine at Dartmouth, Hanover, NH, 2Dartmouth College, Lebanon, NH, 3Dartmouth Health, Lebanon, NH, 4Dartmouth Geisel School of Medicine, Lebanon, NH
Purpose/Objective(s):
Immunohistochemistry (IHC) is the mainstay diagnostic to determine cancer biomarkers for identification, prognostication, and therapy selection. As part of precision oncology efforts to adopt personalized treatment strategies for cancer patients, more tumors undergo next-generation sequencing as standard-of-care. We hypothesized that RNA sequencing (RNA-seq) can discern biomarker status across a wide array of biomarkers and cancer types and can serve as an additional tool for accurate tumor diagnostics.Materials/Methods:
RNA-seq was performed on tumors from patients seeking routine care. RNA was extracted from FFPE tissue by the Illumina RNA Prep with Enrichment kit and Illumina Exome Panel. Sequencing was performed on the Novaseq-600, and data were processed through the AUGMET informatics platform for demultiplexing, quality control, pseudoalignment, and counting. IHC results of biomarkers were abstracted from the medical record and tested for associations with RNA-seq.Results:
Corresponding gene and protein levels were made by RNA-sequencing and IHC intensity on 200 tumors from 10 cancer types. RNA-seq counts were significantly correlated with the percentage of cells positive for PD-L1 (Spearman ? = 0.473, p < 0.001, n = 20 tumors). Additionally, RNA-seq counts are significantly greater in samples positive for TTF-1 (p = 5.75e-8, n = 59), CDX2 (p = 2.11e-4, n = 40), CK20 (p = 2.06e-4, n = 48), CK7 (p = 8.78e-7, n = 61), GATA3 (p = 3.15e-7, n = 39), ER (p = 0.001, n = 43), and PR (p = 0.012, n = 43). RNA-seq counts significantly correlated with HER2 staining intensity (Spearman ? = 0.689, p = 6.07e-5).Conclusion:
RNA-seq showed significant association to IHC staining intensity, supporting its role in determining biomarker status as part of tumor characterization. This would enable an additional method of cancer diagnostics including determining tissue of origin, immunotherapy benefit and breast cancer molecular subtype. Further studies will seek to determine gene-specific thresholds that would enable accurate prediction of biomarker status, and determining the minimum tumor cellularity needed for RNA-seq results to remain accurate.