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.
Director: Quackenbush, John, Ph.D.
Phone: (617) 582-8163
Role: Lab Manager
Phone: (617) 632-3035
Role: Program Administrator
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Location of Core: Dana-Farber Cancer Institute, Smith Building, Room 822, Boston, MA 02115
- Automated Microarray Pipeline
- Fluidigm Access Array System
- Illumina HiSeq 2000
- MultiExperiment Viewer
- DNA and RNA sequencing services
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
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
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.
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
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