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Peter Mac Data Governance

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Maria Macheda
dac@petermac.org

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This DAC controls 11 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
EGAD00010002734	Tumor and matched normal DNA profiling by SNP array	Illumina Infinium OmniExpress-24 BeadChip array	48
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
EGAD50000001131	Tumour somatic variants (in VCF format) called from paired tumour-germline whole genome sequencing (using IDT library preparation system followed by sequencing on Illumina NovaSeq platform) of three high-grade serous ovarian tumour samples. The dataset comprises three VCF variant files.	Illumina NovaSeq 6000	3
EGAD50000001132	Tumour variants (in VCF format) from exome sequencing (using Agilent SureSelect and TWIST library preparation systems followed by sequencing on Illumina HiSeq and NovaSeq platforms) of 108 high-grade serous ovarian tumour samples. Germline variants from EGAD00001006030 for these individuals were used to call somatic and tumour-only variants separately, creating two VCF files per sample (except for one sample without paired germline data- somatic variant file only provided). The dataset comprises 215 VCF variant files.	Illumina HiSeq 2500 Illumina NovaSeq 6000	215
EGAD50000001846	Primary DCIS and recurrent DCIS/IBC (total n=82, ipsilateral n=78 and contralateral n=4) as well as non-recurrent DCIS (n=32) cases were identified through hospital databases from Royal Melbourne Hospital (RMH), Nottingham City Hospital (UK), the LifePool cohort and Peter MacCallum Cancer Centre (PMCC). All cases were micro-dissected from haematoxylin stained sections (range 4-20 sections) by manual micro-dissection to achieve >50% tumour tissue purity. DNA was extracted using the FFPE AllPrep kit (Qiagen, MD, USA). Depending on the success and timing of DNA extraction (Figure 1), cases were analysed by a targeted sequencing panel (n=46, samples pre-2020), whole exome sequencing (WES, n=67), or low-coverage whole genome sequencing (LCWGS). WES: DNA was processed by the Australian Genome Research Facility (AGRF) using the Twist Bioscience Human Comprehensive Exome v1 or v2 (Twist Bioscience HQ, South San Francisco, CA, USA) according to the Twist Target Enrichment Standard Hybridisation Protocol. Sequencing was performed on the Illumina NovaSeq 6000 with 150 bp paired-end reads for a median depth of 101.29x, range: 20.39-247x. Whole Genome Sequencing (WGS): Libraries for four paired samples with matched stromal DNA were made, processed and sequenced by AGRF using the IDT xGen Kit (USA) according to the manufacturer’s protocol, aiming to achieve 60x depth for tumour DNA and 30x for matched normal. File type: Paired-end FASTQ.	Illumina NovaSeq 6000 NextSeq 500	196