E-MTAB-6729
Analysis of HER3-EGFR score among pretreatment triple-negative breast cancer resection samples from the Georgia State University/University of Nottingham RNA-sequencing study (ICART1-2 cohort)
The goal of the RNA-sequencing experiment was to identify differentially expressed genes, ontologies, and pathways based on HER3-EGFR score in pre-treatment resection samples from patients with primary operable invasive triple-negative breast cancer (TNBC). TNBC patients belonged to the well-characterized Nottingham Primary Breast Carcinoma series, the database of which was prospectively maintained for another study, although its design accommodates the present retrospective analysis. All patients received chemotherapy with cyclophosphamide-methotrexate- 5-fluoruracil after surgery (radical mastectomy or breast-conserving surgery). Stained slides were used for quantitation of HER3 and EGFR H-scores, which were scored independently by two pathologists blinded to clinical annotation, whose scores were averaged. Separate slides from the same formalin-fixed paraffin-embedded malignant samples were used for RNA-sequencing based on the availability of sufficient tissue for analysis. Only tissue from pre-marked tumor areas in these slides were used for RNA-sequencing. RNA was extracted from deparaffinized tissue and first- and second- strand synthesis were performed using commercial kits. Pair-read sequencing was performed using the Illumina HiSeq2500 instrument. The Human Genome Assembly GRCh38.P10 was used as the reference genome for mapping sequence reads. Transcript expression was quantified using Salmon. Differentially expressed genes, ontologies, and pathways were determined based on median HER3-EGFR.
The goal of the RNA-sequencing experiment was to identify differentially expressed genes, ontologies, and pathways based on HER3-EGFR score in pre-treatment resection samples from patients with primary operable invasive triple-negative breast cancer (TNBC). TNBC patients belonged to the well-characterized Nottingham Primary Breast Carcinoma series, the database of which was prospectively maintained for another study, although its design accommodates the present retrospective analysis. All patients received chemotherapy with cyclophosphamide-methotrexate- 5-fluoruracil after surgery (radical mastectomy or breast-conserving surgery). Stained slides were used for quantitation of HER3 and EGFR H-scores, which were scored independently by two pathologists blinded to clinical annotation, whose scores were averaged. Separate slides from the same formalin-fixed paraffin-embedded malignant samples were used for RNA-sequencing based on the availability of sufficient tissue for analysis. Only tissue from pre-marked tumor areas in these slides were used for RNA-sequencing. RNA was extracted from deparaffinized tissue and first- and second- strand synthesis were performed using commercial kits. Pair-read sequencing was performed using the Illumina HiSeq2500 instrument. The Human Genome Assembly GRCh38.P10 was used as the reference genome for mapping sequence reads. Transcript expression was quantified using Salmon. Differentially expressed genes, ontologies, and pathways were determined based on median HER3-EGFR.