BaseSpace Cohort Analyzer Update

BaseSpace Cohort Analyzer enables users to apply complex genomic data in novel ways across the entire drug discovery and development process. Pharmaceutical and biotechnology organizations can incorporate data analysis and interpretation into biomarker discovery, translational research, and clinical trials.

We are writing to summarize recent changes to BaseSpace Cohort Analyzer and to share our plans for 2017.

2016 Highlights

Last year our main focus was on enabling you to upload basic cancer data in a quick, easy, automated and secure manner. We implemented the following features:

User upload of somatic and copy number variation data

Users can simply create a Variant Call Format (VCF) file in BaseSpace Sequence Hub, or with other software, and drag and drop the files into a secure site for automated ingestion. This functionality is enabled for panels, exomes and whole genome sequencing (WGS) of somatic mutation data and copy number variation (CNV).

Access control

Your administrators can now assign permissions to private studies uploaded into BaseSpace Cohort Analyzer to allow certain users to see one study but not another.

TCGA Update

We recently started a major update of The Cancer Genome Atlas (TCGA), for which we are bringing in thousands of new samples for somatic mutations, CNVs and more, which will be finalized in the coming months.

Novel Cancer Outlier Algorithm (Patent Application & AACR)

We developed an improved algorithm for Cancer Outlier Profile Analysis, which was recently released as a new app. We have a pending patent application and will present our method at this year’s American Association for Cancer Research (AACR) conference.

Try our new Cancer Outlier Profile Analysis that helps identify genes in which a subset of subjects show “outliers,” e.g. unpregulated genes like fusion genes or amplified oncogenes such as ERBB2 in breast cancer.

2017 Roadmap

This year we are expanding the ability to upload hundreds of clinical attributes, as well as enabling user upload of RNA-seq data. We will also continue to bring in more TCGA and other public data and increase ways to get input and feedback directly from you. Please note that this roadmap is representative of our current development plan, which may evolve and change over time.

For now, if you have any questions or suggestions, contact us at

We look forward to an exciting year ahead and to hearing from you!

BaseSpace Cohort Analyzer Team

For Research Use Only. Not for use in diagnostic procedures.

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