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Description
This dataset contains summary data visualizations and clinical data of rectal cancer tumoroids based on massively parallel sequencing using the custom, Food and Drug Administration (FDA)-cleared tumor-profiling panel MSK Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT). The clinical data includes mutation count, information about mutated genes, Gene Panel, Impact TMB Score, Institute Source, MSI Score MSI Type, Sample coverage, Somatic Status, Specimen Preservation Type, Therapy Prior to derivation Tissue Site, Tissue site of derivation, and Tumor Purity,. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.
Subject of Study
Homo sapiens
Subject(s)
DNA Mutational Analysis
Rectal Neoplasms
Rectal Neoplasms/genetics
OncoTree Cancer Type(s)
Bowel
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.

Downloaded SEG files (tab-delimited segmented data text files that list loci and associated numeric values) can be viewed by downloading and installing the Integrative Genomics Viewer desktop application.
Associated Publications
Ganesh K, Wu C, O’Rourke K, et al. A rectal cancer organoid platform to study individual responses to chemoradiation. Nature Medicine. 2019; 25(10):1607-1614.
Data Type
Genomic
Software Used
FACETS

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing

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
552 KB
Data Catalog Record Updated
2021-11-09