What is the bioinformatics analysis service?
This service provides support from experimental design to analysis of data generated from high-throughput platforms, including microarray-based gene expression, copy number, single nucleotide polymorphism (SNP), methylation; and NGS platforms, such as ChIP Seq, cancer variants and RNA Seq, integrative TCGA analysis, single cell RNA Seq, analysis of immunogenomic markers, immune/stroma cell deconvolution, neoantigen prediction, analysis of microbiota composition, taxonomy, and metabolic pathways, integration of microbiome data with transcriptomics data. We can also provide guidance with large consortia data such as from TCGA, 1000 genomes and ENCODE.
Who is the contact person?
For project requests and questions, please email or call Uma Chandran (chandran@pitt.edu; 412-648-9326) or Riyue Bao (baor@upmc.edu; 412-623-0021).
Do you work with the Cancer Genomics Facility (CGF) or the Genomics Research Core (GRC)?
We work very closely with the CGF, which is a UPMC Hillman Cancer Center shared resource. GRC is an independent facility on the Oakland campus for non-cancer studies. CBS supports primarily cancer studies.
Do you work with non-Hillman investigators?
CBS supports cancer studies, and the Genomics Analysis Core (GAC) supports non-cancer studies. Please contact Uma Chandran for your non-cancer data analysis needs.
Can you help us download and store TCGA data?
Local infrastructure for regulatory compliant storage and analysis of TCGA data is provided through the Pittsburgh Genome Resource Repository (PGRR). Please see the PGRR website for details or contact Uma Chandran for assistance.
Do you provide computing and storage for 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, the Center for Research Computing (CRC) provides computing and storage for University of Pittsburgh researchers. For additional details, please see CRC link below. DBMI has contracted with the Pittsburgh Supercomputing Center for storage and analysis of data involving CBS projects.
Useful links
https://crc.pitt.edu/
https://www.psc.edu/
http://www.hscrf.pitt.edu/ngs
https://www.genomicsanalysis.pitt.edu/
