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LUD2015-005 Trial Data Access Committee

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Xin Lu
xin.lu@ludwig.ox.ac.uk

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This DAC controls 8 datasets

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
EGAD00001009400	This dataset contains whole genome sequencing (WGS) generated from the inoperable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). WGS data were generated with the aim to assess previously reported (e.g. tumour mutational burden) and novel predictive genomic markers for immunochemotherapy treatment in this setting. Using these data, mutation and copy number profiles were generated for the LUD2015-005 study, which were assessed for correlation with patient outcomes from this trial.	HiSeq X Ten Illumina NovaSeq 6000	102
EGAD00001009401	This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.	NextSeq 500	59
EGAD00001010306	This dataset contains bulk transcriptomes from the operable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19), used to verify the deconvolution method used for the scRNA-seq dataset.	NextSeq 2000	24
EGAD00001016161	RNA-Seq data generated from normal tissue from patients from the operable cohorts of the LUD2015-005 Oesophageal cancer study (NCT02735239, EudraCT 2015-005298-19).	NextSeq 2000	10
EGAD00001016345	RNA-Seq data generated from tumour samples from patients from the operable cohorts of the LUD2015-005 Oesophageal cancer study (NCT02735239, EudraCT 2015-005298-19).	Illumina NovaSeq 6000	85
EGAD00001016793	Whole genome sequencing (WGS) generated from the operable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19). WGS data was generated with the aim to assess previously reported (e.g. tumour mutational burden) and novel predictive genomic markers for immunochemotherapy treatment in this setting. Using these data, mutation and copy number profiles were generated for the LUD2015-005 study, which were assessed for correlation with patient outcomes from this trial.	Illumina NovaSeq 6000 Illumina NovaSeq X	118
EGAD00001016815	single cell RNA sequencing from primary tumour biopsies of 16 patients from the operable cohorts of the LUD2015-005 oesophagleal cancer study (NCT02735239, EudraCT 2015-005298-19).	NextSeq 2000	1