OAC RNASeq

Please see our related publication, 'Molecular profiling to predict immunochemotherapy outcomes in esophageal adenocarcinoma'

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 2 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009399	This dataset contains bulk transcriptomes from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). Transcriptomes were prepared from pre-treatment oesophageal tumour biopsies using a ribodepletion approach in order to assess both previously reported (e.g. PD-L1 expression) and novel predictive expression-based biomarkers for immunochemotherapy treatment in this setting. On-treatment and post-treatment biopsies were generated as well to characterize response to therapy, and samples were also prepared from paired normal GI tissues for a subset of patients. scRNA-seq based deconvolution was also applied to bulk transcriptomes in this study to estimate the cell composition of tumour biopsies and assess the link between the presence of specific cell types with immunochemotherapy outcomes.	Illumina HiSeq 4000	144

Publications	Citations
Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma. Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X, LUD2015-005 Project Team. Cancer Cell 41: 2023 1222-1241.e7	30
Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma. Yates J, Mathey-Andrews C, Park J, Garza A, Gagné A, Hoffman S, Bi K, Titchen B, Hennessey C, Remland J, Carnes M, Shannon E, Camp S, Balamurali S, Cavale SK, Li Z, Raghawan AK, Kraft A, Boland G, Aguirre AJ, Sethi NS, Boeva V, Van Allen EM. Cell Rep Med 6: 2025 102188	1

Publications

Citations

Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma.
Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Xie PF, Chang J, Roth A, Amess B, James SA, Rei M, Fuchs HS, McCann KJ, Omiyale AO, Jacobs BA, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Schuster-Böckler B, Middleton MR, Lu X, LUD2015-005 Project Team. Cancer Cell 41: 2023 1222-1241.e7

Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.
Yates J, Mathey-Andrews C, Park J, Garza A, Gagné A, Hoffman S, Bi K, Titchen B, Hennessey C, Remland J, Carnes M, Shannon E, Camp S, Balamurali S, Cavale SK, Li Z, Raghawan AK, Kraft A, Boland G, Aguirre AJ, Sethi NS, Boeva V, Van Allen EM. Cell Rep Med 6: 2025 102188