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Genomics Cores

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 UPMC Hillman Cancer Center Started in 2004

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Genomics Cores

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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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