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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:
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
