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

2. 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 with 2 publications
Partnered with HSLS – trained Sri Chaparala
Jacob Waldman
Anish Chakka
Raghu Avula
Rahil Sethi

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 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

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
Incorporate methods developed by DBMI faculty
Develop teaching curriculum
Develop cloud computing