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Peter Mac Data Governance

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Gareth Jones
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This DAC controls 7 datasets

Dataset ID	Description	Technology	Samples
EGAD00001011817	Plasma samples from patients with melanoma (stage II/III/IV) and breast cancer (stage IV) as well as healthy individuals were subjected to low-coverage whole-genome sequencing (less than 10x average depth). This dataset contains raw fastq files from 39 breast cancer, 127 melanoma and 42 healthy control plasma samples.	Illumina NovaSeq 6000	208
EGAD50000000138	The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 100 plasma samples from patients with lung cancer undergoing treatment in the OSCILLATE trial. After 150 bp paired-end sequencing, reads were aligned to the human genome reference with the AVENIO Oncology Analysis Software. These files are the sorted non-deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.	NextSeq 500	100
EGAD50000000206	These are 28 targeted exome sequencing fastq files (tumour and germline) generated from ovarian cancer samples which had been exposed to PARP inhibitors, for the described project.	NextSeq 500	28
EGAD50000000364	Single nuclei RNAseq data from 14 HGSOC primary tumour samples	Illumina NovaSeq 6000	14
EGAD50000000804	Plasma samples from healthy individuals were subjected to low-coverage whole-genome sequencing (less than 10x average depth). This dataset contains raw fastq files from 18 healthy control plasma samples.	Illumina NovaSeq 6000	18
EGAD50000000810	Plasma samples from patients with breast cancer (stage IV) who had confirmed BRCA mutations were subjected to low-coverage whole-genome sequencing This dataset contains raw fastq files from 6 breast cancer plasma samples.	Illumina NovaSeq 6000	6
EGAD50000000811	This data set contains the fastq files from whole-genome sequencing of temporally matched tumour (fresh frozen biopsies), blood germline and plasma samples collected from a BRCA1-mutant breast cancer patient to directly compare mutation signature analysis using gold-standard tumour-germline paired variant calling with a novel ctDNA-based method (MisMatchFinder).	Illumina NovaSeq 6000	3