Uma Chandran MSIS Ph D Research Associate Professor

Uma Chandran, MSIS, Ph. D Research Associate Professor, DBMI Training Program Core Faculty Co-Director, Cancer Bioinformatics Services Director, Genomics Analysis Core email: chandran@pitt. edu phone: 412 -648 -9326

Genomics Cores • Cancer Bioinformatics Services (CBS) – https: //hillmanresearch. upmc. edu/research/facilities/c ancer-bioinformatics/personnel/ – For the UPMC Hillman Cancer Center – Started in 2004 – 2 bioinformatics analysts • Genomics Analysis Core (GAC) – https: //www. genomicsanalysis. pitt. edu/ – 60 projects in since 2016 – Collaborate with HSLS and high performance computing facilities including PSC and CRC – 3 bioinformatics analysts, 2 Ph. D consultants

Core’s Aims Data Analysis • RNA Seq, WES, WGS, ATAC Seq, single cell RNA Seq, TCGA, GEO mining, integrative analysis • Best practices for rigor and reproducibility – Git. Hub, SLACK, Workflow tools, containerization technology • Genomics data analysis with rigor and reproducibility High Performance Computing (HPC) for genomics • Collaborate with PSC, CRC – 2 PB storage, 500 K SUs • Evaluate Cloud solutions – NIH STRIDES GCP, Azure, AWS • Serve on PSC and CRC advisory committees Teaching • Command-line workshops through CRC • Mentor Hillman Summer Academy students Support team science projects • Pittsburgh Genome Resource Repository (PGRR) – local regulatory compliant infrastructure for over 2 PB of TCGA data • Data Coordination Center (DCC) for BCRF funded AURORA project on breast cancer • Pa. CURE – BD 4 BH

CBS

GAC

Data Analysis – Selected projects WES and WGS - somatic variant analysis • • Lung cancer brain mets Head and neck cancer response to therapy Soft tissue sarcomas Mesothelioma WES Germline variant analysis • Pediatric sepsis Gene expression – RNA seq and microarray • • • microarray analysis of LSD 1 and LSD 2 KO in breast cancer cell lines Androgen resistant prostate cancer cell lines De Novo transcriptome of opossum kidney Influenza vaccine study Gene expression in transplant rejection ATAC Seq • Chromatin accessibility in neural stem cells after glucocorticoid treatment Single Cell RNA Seq • T cell diversity in response to therapy Custom integrative analysis • Melanoma: correlative analysis with immune markers in dendritic cell vaccine Custom pipelines • HIV mutation detection, integration site detection and Co. VID – SARS 2 genomics

Grant funding, Collaborators, Challenges Grants • • • NCI – Cancer Center Support Grant School of Medicine – Genomics Analysis Core USAID – Urvi Parikh NIH and NCI - R 01 to Drs Wang, De. Franco, Metes, Mellors Analysis Contracts Collaborators • University of Pittsburgh faculty who use core’s services • Consortium collaborators – Drs. Perou, Mardis, and Laird • CRC, PSC, HSLC, Pitt IT Challenges • Request for services is growing and we are at capacity • Training, staffing, professional development