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MSKCC Medical Donation Program Data Access Committee

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Christine Iacobuzio-Donahue
iacobuzc@mskcc.org

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This DAC controls 13 datasets

Dataset ID	Description	Technology	Samples
EGAD00001003153	Sequencing of untreated pancreatic cancer metastases and primary tumor sections.	Illumina HiSeq 2000 Illumina HiSeq 2500	49
EGAD00001003200	Files from whole exome sequencing of 26 tumors and two matched normals from one melanoma patient. The 26 tumors include the untreated primary, cutaneous metastases and distant metastases to internal organs.	Illumina HiSeq 2500	28
EGAD00001003261	These are seven sequencing files form whole exome and whole genome of five tissue samples collected from one pancreatic cancer patient	HiSeq X Ten Illumina HiSeq 2500	5
EGAD00001004044	Files from whole exome sequencing of eight tumors from eight pancreatic cancer patients along with matched PanIN precursor lesion(s) and a matched normal tissue.	Illumina HiSeq 2000	28
EGAD00001004212	Files from whole exome sequencing of 14 tumors from two cancer patients (endometrial and lung cancer) along with a matched normal tissue per patient.	Illumina HiSeq 2000	16
EGAD00001005519	Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.	Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	252
EGAD00001005779	Files from DNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues. Sequencing files include those derived from whole exome sequencing as well as MSK-IMPACT sequencing.	Illumina HiSeq 2500	81
EGAD00001006410	Files from whole exome sequencing of matched normals and multiple tumors from 7 melanoma patients. The tumors include primary tumors and distant metastases.	Illumina HiSeq 2500	127
EGAD00001009735	Files from Tapestri snDNA-seq of archival tissue samples from 16 pancreatic ductal adenocarcinoma (PDAC) patients. Matched bulk sequencing (whole-exome, whole-genome, MSK-IMPACT) data are attached for a subset of the patients.	Illumina HiSeq 4000 Illumina NovaSeq 6000	46
EGAD00001011109	This study includes 542 of multi-region sampled whole exome sequencing data from 83 pancreatic cancer patients in 6 individual experiments : Kras wildtype, local recurrence, treatment-naive (MetomeV2), radiotherapy plus chemotherapy (Radome), chemotherapy-only group (Treatome) and Proj_B-100-478.	Illumina HiSeq 2500	706
EGAD00001011285	Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.	Illumina NovaSeq 6000	37
EGAD50000000354	Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).	Illumina HiSeq 2500	244
EGAD50000001936	This dataset comprises single-cell DNA sequencing data for selected pancreatic ductal adenocarcinoma (PDAC) autopsy samples. It employs a targeted gene panel to identify single nucleotide variants (SNVs) and copy number variations (CNVs) using the Mission Bio Tapestri platform. The samples encompass primary and metastatic tissue from selected PDAC patients. This dataset includes 74 sample-level BAM files and 24 patient-level H5 files, generated by the MissionBio pipeline.	Illumina NovaSeq 6000	98