Genomics Cores

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

2. Genomics Cores Soumya Luthra Jacob Waldman Anish Chakka Rahil Sethi • 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 Raghu Avula

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. Current projects • Cancer Bioinformatics Services • 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 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 • 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

5. 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