Uma Chandran, MSIS, PhD Research Associate Professor, DBMI Training Program Core Faculty Co-director, Cancer Bioinformatics Services Director, Genomics Analysis Core

Genomics Cores Cancer Bionformatics Services (CBS) For the University of Pittsburgh Cancer Institute (UPCI) Started in 2004 Cancer Center Support Grant (CCSG) – rated exceptional 3 Master’s level analysts Co-authors on 40 + publications Genomics Analysis Core Newly formed core for the School of Medicine to meet the increasing demand for NGS support Two master’s level analyst and a third to be added Soumya Luthra Jacob Waldman Anish Chakka Rahil Sethi Raghu Avula

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

Current projects Cancer Bioinformatics Services Genomics Analysis Core Utilized by all CCSG disease specific programs GBM : CN analysis of pediatric and adult glioblastoma and re-analysis of adult TCGA. Melanoma : somatic variants associated with patients who develop colitis after Ipilumimab therapy, immunogenic signatures in a neo-adjuvant setting; 32 gene panel in archival tissue blocks for phase III national trials of the ECOG-ACRIN Lung Cancer : somatic variants in gefitinib resistance in lung cancer cell lines and characterization of variants in primary tissue versus xenografts, primary versus brain mets Mesothelioma : Somatic variants in pleural versus thoracic cancers Breast : microarray analysis of LSD1 and LSD2 KO, gene expression in pre versus post-menopausal women, estrogen response signature in different tissues Genomics Analysis Core Role of glucocorticoids in hypothalamic and cortical neuronal stem cells – RNA Seq Transcriptome during monkey gonadal development – RNA and miR Seq 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 Transcriptome of rat liver models of cirrohosis Infrastructure Pittsburgh Genome Resource Repository (PGRR) Pittsburgh Supercomputing Center (PSC) through XSEDE award Evaluating Cloud models Support for BD4BH PACURE

Grant funding, Collaborators, Challenges Grants NCI – Cancer Center Support Grant School of Medicine – Genomics Analysis Core NCI - Skin SPORE NIH and NCI - R01 to Drs Wang, Pollack, Plant, Locker, Carcillo, Weisz Other sources of grant funding for Drs. DeFranco, Stabile, Choudhry Collaborators University of Pittsburgh faculty mentioned above DBMI faculty Rebecca Johnson, Xinghua Lu, Greg Cooper 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 Fee for service pipeline model ($150/analysis?) versus collaborative model How to build infrastructure to meet increasing demand Training, staffing Incorporate methods developed by DBMI faculty