Mixed cfDNA (MSKCC, 2020): IMPACT sequencing of 229 cell-free DNA (cfDNA) and associated tumor samples with matched normal

UID: 10573

Publisher(s): Memorial Sloan Kettering Cancer Center

Description: This dataset contains the summary data visualizations and clinical data of IMPACT sequencing of 229 cell-free DNA (cfDNA) and associated tumor samples with matched normal from 118 patients. Clinical data includes: Cancer Type, Number of Samples Per Patient, Mutation Count, Fraction Genome Altered, Sex, Primary/Metastasis Sample Type, Collaboration Id, Gene Panel, Oncotree Code, Tumor/cfDNA Sample Class, Tissue Site. The plaintext components of the dataset can be downloaded as a tar file. The clinical data can be downloaded as a tsv file. The dataset includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Adenocarcinoma, NOS
Bladder Urothelial Carcinoma
Bladder Squamous Cell Carcinoma
Mixed Germ Cell Tumor
Breast Invasive Carcinoma, NOS
Combined Small Cell Lung Carcinoma
Cancer of Unknown Primary
Breast Invasive Ductal Carcinoma
Lung Adenocarcinoma
Lung Squamous Cell Carcinoma
Mixed Germ Cell Tumor
Neuroendocrine Tumor, NOS
Ovarian Germ Cell Tumor
Prostate Adenocarcinoma
Papillary Renal Cell Carcinoma
Prostate Neuroendocrine Carcinoma
Small Cell Bladder Cancer
Seminoma
Cutaneous Melanoma
Choriocarcinoma
Yolk Sac Tumor
Urachal Adenocarcinoma
Urethral Adenocarcinoma
Urethral Urothelial Carcinoma
Upper Tract Urothelial Carcinoma

Access via cBioPortal
Access Restrictions: Free to All
Access Instructions: This cBioPortal for Cancer Genomics dataset is publicly available for viewing in tables or, for copy-number segments, via integrated IGV application. The data is also available for download in its entirety as a tarball or as individual TSV (tab separated value) or SEG files. Some features are only available by logging in with a Google or Microsoft account. These features include storing your virtual studies and groups which allows you to access your studies and groups from any computer, and to allow cBioPortal to remember your study view charts preferences for each study (i.e. order of the charts, type of charts and visibility). Login is optional and not required to access any of the other features of cBioPortal.
Data Type: Genomic
Software Used: Integrative Genomics Viewer (IGV)
High-performance visualization tool for interactive exploration of large, integrated genomic datasets.

OncoTree
Open-source ontology that was developed at Memorial Sloan Kettering Cancer Center (MSK) for standardizing cancer type diagnosis from a clinical perspective by assigning each diagnosis a unique OncoTree code.
Dataset Format(s): TSV, TAR, SEG
Data Tool(s): MSK-IMPACT
Dataset Size: 370 KB (TAR), 40 KB (TSV), 645 (SEG)

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