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

Genomics Cores Cancer Bionformatics Services (CBS) For the 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 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 16 projects in 2015-2016 with 2 publications Partnered with HSLS – trained Sri Chaparala Jacob Waldman Anish Chakka Raghu Avula Rahil Sethi

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 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 Melanoma: correlative analysis with immune markers in dendritic cell vaccine Lung Cancer : variants in brain mets Head and Neck Cancer: variant analysis Breast : microarray analysis of LSD1 and LSD2 KO, Genomics Analysis Core 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 Influenza vaccine study – RNA Seq HIV mutational analysis Infrastructure Pittsburgh Genome Resource Repository (PGRR) 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 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 Incorporate methods developed by DBMI faculty Develop teaching curriculum Develop cloud computing