A 20 year evolution of an NCI Cancer Center

Bioinformatics Shared Resource , and

Lessons Learned

Yate-Ching Yuan, Ph.D.

Director, Bioinformatics Core

Sorena Nadaf, MS, MMI

Senior Vice President

Chief Informatics Officer

Director, Center for Informatics & Digital Health Innovations

Laboratory

City of Hope Medical Center and Beckman Research Institute

October 3, 2018

City of Hope NCI Designated Comprehensive Cancer Center

Beckman Research Institute

Medical Center

Education & Training

11 Department

57 Professional series faculty

2 Clinical research professor

TGEN

32 Professional series faculty

2 Clinical research professor

18 Department

113 Professional series faculty

118 Research professor series

faculty

400+ Staff Scientist, Research

Associates, Visiting Scientists

Irell & Manella Graduate School of

Biological Science

88 Enrolled Ph.D. students

153 Graduated (over 24 years)

2 Enrolled MS students

Postdoctoral Training Office

160+ Enrolled postdocs

Graduate medical educations

20+ Departments/Divisions

33+ COH trainees

86+ Visiting Medical Students,

residents, fellows

Clinical Investigation Training Program

90+ Graduates (since 2007)

Center for Informatics

Admin. Team

HT Cores

Researchers

ITS

BIC Computing

BIC Methodology

Cyber Infrastructure

Cloud Computing resources

& Vendors

Yate-Ching Yuan, Ph.D. Bioinformatics Core Facility Director

Integrative Bioinformatics

Genomics

• NGS

• Microarray

• Molecular Biology

Proteomics

• Mass Spectrometry

• X-ray

• NMR

Cheminformatics

• Synthetic Chemistry

• HTS

• GMP

Imaging• HCS

• Microscopy

• Animal imaging

Bioinformatics

CBIS

Genomics• NGS

• microarray

• molecular biology

Proteomics• Mass Spectroscopy

• X-ray/NMR

• Compuer Modeling

Cheminformatics• Synthetic Chemistry

• HTS

• LIMS

Imaging• Digital Pathology

• small animal imaging

• microscopy

Bioinformatics

CBIS

IS&T Enabling Cost-effective Research

1998

• Establish Web

application GCG

w/ 140 suite of

sequence

analysis tools and

Laboratory

collaborative

database

• Setup first SUN

E450 server

2004

• Negotiate first

Affymetrix

microarray for

genome research

• Establish first

research web

portal using

CITRIX

• Establish MEM

LIMS system

2008

• Establish first

Next generation

sequencing

(NGS) Illumina

GA

• Setup Isilon 100

TB local storage

solution and HP

ScaleMP blade

clusers

• HP workstation

for visualization

2011

• Illumina HiSeq

2000,

HiScanHQ in

production

• Establishing

Cloud

infrastructure

w/ high

network

bandwidth

• GPGPU

computing

20182013

• Bruker

ultraflex

extreme

• Establish CBIS

LIMS for

pateint sample

and exp

tracking

• Establish

workflow for

Imaginfg Mass

Spectrum and

Mascot

protein

identification

and

annotation

2014

• Vectra

Automated

Multispectral

Imaging System

Establishing

Cloud

infrastructure w/

high network

bandwidth

• GPGPU

computing

NanoString

nCounter

IS&T Enabling Cost-effective Research

Current HPC Environment

Use Case !: Partek Flow OMIC analysis Cloud Solution

Use Case 2: Qiagen Genomics analysis Cloud Solution

Bioinformatics in-house BRAVO tools

– Genotype to Phenotype Mapping of Complex Traits

• Retrieve and data mining TCGA, NCBI, Ensembl, Oncomine, cBioportal, GTEX, & other public available patient

cohorts studies as needed

• 14 Diseases including human normal (for some disease) and tumor samples

• Including gene expression profiling from microarray and RNA-seq (mRNA & miRNA expression), methylation along

with on clinic pathological features (e.g. age, sex, race, stage, disease subtype, treatment, and outcomes, etc)

TCGA Pan Cancer cohorts Public Breast Cancer cohorts

Com m on m iRNA s in pub lic da ta and la b da ta

Differential Gene Expression Analysis

TCGA Ovarian Survival Analysis using 481 patients

miR-625-5p miR-1908 miR-3187-3p

Use Case 3: Chen SF, Liu Z, Chaurasiya S, Dellinger TH, Lu J, Wu X, Qin H,

Wang J, Fong Y, Yuan YC. Identification of core aberrantly expressed

microRNAs in serous ovarian carcinoma. Oncotarget. 2018 Apr 17;9(29):20451

CCSG Share Resource Pilot grant 3 cycles, 54 PIs/Collaborators, 16/26 shared core facilities participated

BIC

22 PIs

Translational Biomarker Discovery

5 IGC

7

CRISPER/

Viral Vector

1

Mass Spectroscopy

1

Animal Tumor Model

2

Analytical Cytometry

1Cytogenetics

1

Synthetic Chemistry

2

HTS

4

X-ray

1

Biostatistics

1

Pathology

5

Share Resource Pilot grant

(#) indicated jointly submitted

Jointly awarded

Bioinformatics Regional and Group Computer Hands-on Trainings

Total of 225 attendees for 2017 NCBI training workshop

City of Hope Bioinformatics Core Facility 2018 Publication Highlights

Thank You!