University of Pittsburgh Cancer Institute (UPCI)

CCSG Acknowledgement

Required CCSG Acknowledgement

The NCI requires that publications acknowledge the UPCI CCSG support, and they are tracking compliance. If a UPCI CCSG-supported Shared Resource provided data used in your publication, please include the following statement in the acknowledgment section of your publication(s):

"This project used the UPCI [insert name(s) of shared resource(s)] that [is/are] supported in part by award P30CA047904."

Shared Resource Directors: Please make sure to include this statement on all of your order forms, contracts, etc. as a reminder to your users to acknowledge the UPCI CCSG support.

Bioinformatics Data Analysis FAQs

What is the bioinformatics analysis service?

This service provides data analysis support for all high throughput genomic platforms. In addition, support is also provided for tissue microarray (TMA) analysis, and advanced integrative integrative analysis between different platforms. We can also provide guidance with large consortia data such as from TCGA, 1000 genomes and ENCODE. CBS also has the expertise to perform analysis of Next Gen Sequencing data, particularly cancer variant analysis, ChIP Seq and RNA Seq.

We also provide consultation and assistance with analysis tools such as Ingenuity, Meta Core and other tools licensed through the Health Science Library System (HSLS).

Who is the contact person?

For analysis requests and questions, please contact Uma Chandran at or Phone number: 412-648-9326.

What are your fees?

Our fees are either on an hourly basis or through grant support. The hourly rate is $84/hour; the scope of the study and the estimated number of hours required to complete a study will be determined upon discussion with the investigator. Generally, preliminary analysis of a small-scale microarray expression study and generation of differential gene expression lists takes about 10 hours. If investigators wish to perform analysis independently, but would like assistance with tools, we can provide such assistance on an hourly basis.

Do you work with the Cancer Genomics Facility (CGF) or the GPCL cores?

We work very closely with the CGF, which is a UPCI shared resource. GPCL is an independent facility on the Oakland campus. Our facility supports primarily cancer studies.

Will you work with non-UPCI investigators?

Our facility supports mainly cancer studies, and the majority of the investigators we work with are UPCI members. However, our work load permitting, we will consider requests from non-UPCI investigators, especially for short consults.

Which platforms are supported?

Our group supports analysis of Affymetrix chips including SNP and expression arrays, Illumina expression, microRNA and methylation arrays, Agilent arrays, other microRNA platforms, and TMAs. We support NGS studies from the most commonly used platforms such as Illumina, Ion Torrent and SoLiD.

Do you perform proteomic analysis?

We can provide some preliminary analysis of proteomic data. For advanced informatics support, please contact Dr. Nathan Yates.

Do you expect to be a co-author on publications?

Determination about co-authorship is based upon discussion with investigators and varies from study to study.

Can you help us analyze TCGA data?

We have performed analysis of TCGA breast and ovarian cancer data. We have analyzed each of the individual platforms, including copy number, expression and microRNA analysis and have also performed integrative analysis.

Can you analyze ENCODE and 1000 genomes data?

Although we have not worked extensively on these datasets, we do have the technical resources to provide support for these data.

Can you help us download and store TCGA data?

Each investigator has to acquire IRB approval for protected TCGA data or be included in the common Data Use Agreement (DUA) from DBMI. Please refer to the TCGA website for details. There are ongoing efforts to provide storage and analysis resources for TCGA data.

Do you provide Next Gen Sequencing (NGS) analysis?

We do not provide storage media for NGS data. It is up to each investigator to purchase hard drives and store their data. However, DBMI is currently evaluating and developing campus-wide infrastructure for storage, archiving and analysis of NGS data.