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

2. Genomics Cores 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
Soumya Luthra
Jacob Waldman
Anish Chakka
Rahil Sethi
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 Genomics Analysis Core
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 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
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