sept2016 newsample cancer_craig

COLO829 Datasets for COLO829David W. Craig, Ph.D.

Co-Director Institute for Translational Genomics

Professor, USC

USC Translational GenomicsKeck Medicine of USC

RESEARCH LAB OVERVIEWApplied Genomics, Bioinformatics For Precision

Medicine

Genetics of Inherited Disease

CENTER FOR RARE CHILDHOOD DISORDERS

Neurogenomics Precision Oncology & Genomics

Applied Bioinformatics Data Sharing And Privacy Genomic Technology

`

Rare Childhood Disorders

Multiple Myeloma Glioblastoma Breast Cancer Melanoma

Neuroblastoma Lung Cancer Childhood Cancer Rare Cancers General Oncology

PRECISION MEDICINE STUDIES

Collaborators

Trials

USC Translational GenomicsKeck Medicine of USC

PRECISION MEDICINE REQUIRES COORDINATED EXECUTIONFlexibility with regulatory compliance

Library Preps & Sequencing

Molecular characterization (Pathology)

High Performance Computing & Analysis

Multiple Institutions In coordination, executing in days

Utilizing a rapidly updating growing body of knowledge

Regulatory Bodies

Molecular grand rounds

Therapy selection and Pharmacology

Clinical protocol, consenting, enrollment

Clinical & Genomic Data Integration (Knowledge Mapping)

USC Translational GenomicsKeck Medicine of USC

REGULATION- Tumor/Normal Exome+

Sequencing CAP/CLIA FDA Requirements for

Trials

- RNA/Transcriptome

USC Translational GenomicsKeck Medicine of USC

1 Kb PTEN Deletion

USC Translational GenomicsKeck Medicine of USC

USC Translational GenomicsKeck Medicine of USC

COLO829Focal Amplification

BRAF+1

PTENCDK2NA

USC Translational GenomicsKeck Medicine of USC

METRICS

USC Translational GenomicsKeck Medicine of USC

OVERLAP IN CELL LINES & LINEAGES

USC Translational GenomicsKeck Medicine of USC

STRUCTURAL VARIANTS

USC Translational GenomicsKeck Medicine of USC

FEATURE 3: CGH SNP TILEDPolymorphic probes placed every 25kb for copy number and

LOH

1.2kb PTEN deletion

All C

hrom

osom

es C

OLO

829

Valid

ation

USC Translational GenomicsKeck Medicine of USC

DATA

- FASTQ, BAMs, and Small Indel VCFs- dbGAP

phs000932.v1.p1- EBI

EGAS00001001385- Email:

DavidWCr@usc.edu

AcknowledgementsLab

• Jessica Aldrich, M.S.• Ana Claasen• Daniel Enriquez• Tyler Izatt, M.S.• Rebecca Halperin, Ph.D.• Sara Nasser, Ph.D.• Megan Russell• Szabolcs Szelinger,

Ph.D.

CENTER FOR RARE CHILDHOOD DISORDERS

Collaborators (PIs)• John D. Carpten, Ph.D.

Irene Chemi Shukmei Wong

• Jeffrey M. Trent, Ph.D.• Sara Byron, Ph.D.• Winnie Liang, Ph.D.• Janine LoBello, D.O.• Vinodh Narrayanan, M.D.• Matthew J. Huentelman,

Ph.D.• Isabelle Schrauwen, Ph,D.

OrganizationsFamilies And Advocates