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Comprehensive Cancer Bioinformatics Services at UPMC Hillman Cancer Center

Providing cancer bioinformatics services since 2004. Offering genomics data analysis, infrastructure support, and various projects related to cancer and genomics research.

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Comprehensive Cancer Bioinformatics Services at UPMC Hillman Cancer Center

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  1. Uma Chandran, MSIS, PhDResearch Associate Professor, DBMITraining Program Core FacultyDirector, Cancer Bioinformatics ServicesDirector, Genomics Analysis Core

  2. Genomics Cores • Cancer Bionformatics Services (CBS) • For the UPMC Hillman Cancer Center • Started in 2004 • Cancer Center Support Grant (CCSG) – rated exceptional • 2 Master’s level analysts • Co-authors on 40 + publications • Genomics Analysis Core • 2 analysts • 24 projects in since 2016 • 4 publications • Partnered with HSLS and high performance computing facilities including PSC and CRC

  3. Objectives • Genomics Data analysis • Microarray, NGS from all platforms and applications, integrative analysis, TCGA, GEO • Infrastructure • Hardware and software, storage solutions NGS • Support for DBMI’s data science portfolio – PACURE, BD2K • Genomics analysis, integrating genotype with phenotype

  4. Projects • Cancer Bioinformatics Services • Melanoma: correlative analysis with immune markers in dendritic cell vaccine • Lung Cancer : somatic variant analysis in brain mets • Head and Neck Cancer: somatic variant analysis and RNA Seq analysis of tumor specimens • Cholangiocarcinoma: somatic variant analysis • Mesothelioma: integrative RNA seq and Exome seq variant analysis • Breast: microarray analysis of LSD1 and LSD2 KO, • Genomics Analysis Core • Transcriptome during monkey gonadal development – RNA and miRSeq • Variants with severity of diseases in pediatric sepsis – WES Seq • De Novo transcriptome of opossum kidney – RNA Seq • Differences between lizard and salamander tail regeneration – RNA Seq • Influenza vaccine study – RNA Seq • HIV mutational analysis • Chromatin changes in B-cells following transplantation – ATAC Seq • Infrastructure • Pittsburgh Genome Resource Repository (PGRR) • Support for BD4BH, PACURE

  5. Grant funding, Collaborators, Challenges • Grants • NCI – Cancer Center Support Grant • School of Medicine – Genomics Analysis Core • NCI - Skin SPORE • USAID – Urvi Parikh • NIH and NCI - R01 to Drs Wang, Pollack, Plant, Locker, Carcillo, Weisz • Other sources of grant funding for Stabile, Ferris, Dacic • Collaborators • University of Pittsburgh faculty who use core’s services • Graduate students from DBMI, Graduate School of Public Health, undergraduate joint program in Computer Science and Biology, UPCI summer academy students • Challenges • Request for services is growing and we are at capacity • Training, staffing

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