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Center for Cancer Computational Biology (DFCI)

Director: Quackenbush, John, Ph.D.

Location: Dana-Farber Cancer Institute, Smith Building, Room 822, Boston, MA 02115


The Center for Cancer Computational Biology at Dana-Farber Cancer Institute provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research.





  • GeneChip Oncology Database ( Database )

    "Cancer gene expression database is a collection of publicly available microarray expression data on Affymetrix GeneChip Arrays related to human cancers.

    Currently only datasets with available raw data (Affymetrix .CEL files) are processed. All processed datasets were subjected to extensive manual curation, uniform processing and consistent quality control.

    You can browse the experiments in our collection, perform statistical analysis, and download processed data; or to search gene expression profiles using Entrez gene symbol, Unigene ID, or Affymetrix probeset ID."

  • GeneSigDB ( Database )

    "The Gene Signature DataBase is a searchable database of fully traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed."


  • Fluidigm Access Array System ( Next generation sequencer )

    "The Access Array System is the first high-throughput, target-enrichment system designed to work with all of the major next-generation sequencing instruments. The Access Array System enables the user to enrich multiple unique targets (such as exons) from a large number of samples, all at one time. The system combines the cost and throughput benefits of microfluidics with the proven performance and flexibility of PCR.

    Target Enrichment
    Sample Barcoding for Multiplexed Sequencing
    Sequencing Library Prep Using Amplicon Tagging

    Custom designed primer sets amplify (and tag) PCR products for sequencing. Simply provide Fluidigm with your regions of interest for the human genome."

  • Illumina HiSeq 2000 ( Next generation sequencer )

    "The HiSeq 2000 system makes it possible for labs to take on the largest and most complex sequencing studies at the lowest cost. The ability to process larger numbers of samples and to decode larger and more complex genomes means that virtually any sequencing project is now within reach."

  • MiSeq ( Next generation sequencer )

    "MiSeq is the only fully integrated personal sequencer, delivering a streamlined solution that takes you from rapid sample prep through automated data analysis and storage in the BaseSpace cloud. Sequencing doesn’t get any easier than this."


  • DNA and RNA sequencing services ( Material analysis service )

    "The CCCB offers a wide range of services to assist in the design, implementation, and analysis of Next-Gen sequencing projects. We are currently sequencing samples on the Illumina HiSeq2000 platform. We offer standard and custom run configurations to support DNA and RNA applications, and a variety of options are available for sample preparation.

    Samples are run on a first-come, first-served basis, and in batches of 7 or 8. You are welcome to submit fewer than 7 samples, but we will need to pair you with another group with a similar run configuration, which requires scheduling coordination."

  • General computing services ( Support service )

    "In support of our research and analytical service programs, the CCCB and our associated Computational Biology and Functional Genomics Laboratory are composed of a diverse mix of individuals with skills across the scientific/computational spectrum including biologists, programmers, bioinformaticians, and database and systems administrators. Likewise, we maintain an extensive scientific computing infrastructure that includes a high performance compute cluster, large capacity data storage arrays, and high availability clustered Oracle database systems.

    Drawing from this varied expertise and infrastructure, the CCCB will offer limited support for more general scientific computing needs. Some examples of the types of services we can provide are as follows:

    * Web development and hosting.
    * Clinical data modeling and warehousing.
    * Relational database design, implementation, and support.
    * Custom software development.
    * Systems administration and support."

  • Microarray and other genomic data analysis ( Data analysis service )

    "We offer a analytical services for genomic and other 'omic data including: gene expression, copy number variation, ChIP-chip/ChIP-seq, SNP, and next generation DNA sequencing data.

    Some examples of the type of questions we can work with investigators to answer are as follows:

    * Identify novel gene signatures, and validate them using our large in-house cancer gene expression profile database.
    * Discover which biological pathways are differentially expressed.
    * Identify pattern of chromosomal abnormalities and loss of heterogeneity in aCGH data from SNP arrays.
    * Discover promoters or regulators of gene expression.
    * Build network models of gene expression, protein-protein interaction and literature data to uncover new biological connections.
    * Integration of high-dimensional clinical and demographic information with ‘omic data.
    * Multi-platform analysis e.g. Affymetrix, Illumina, and DASL data."

  • MiSeq ( Material analysis service )

    In response to growing demand in rapid turn-around sequencing applications such as microbial sequencing, amplicon sequencing, ChIPSeq, small RNA Sequencing, and targeted re-sequencing, the CCCB is proudly to offer the Illumina MiSeq System starting from April 8th, 2013. We offer the following sequencing configurations: Single End 50 bp, Paired End 150 bp, and Paired End 250 bp


  • Automated Microarray Pipeline ( Software )

    "AMP is used to perform normalization and quality control measures on microarray experiments."

  • MultiExperiment Viewer ( Software )

    "MultiExperiment Viewer (MeV) is a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes."

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Last updated: 2015-11-19T14:15:06.066-05:00

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