“What I Do”
Bryan Betz PhD
Clinical Assistant Professor
Technical Director
Molecular Diagnostics Laboratory
Molecular Diagnostics / Molecular Pathology
Application of molecular biology techniques and knowledge to clinical
laboratory diagnosis
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Infectious disease
Inherited disease
Hematopathology
Solid Tumors
Identity Testing
Forensics
Pharmacogenomics
Is and will continue to revolutionize the way in which diseases are
diagnosed and therapeutics are employed
Molecular Pathology
A Universal Discipline of Laboratory Medicine
INFECTIOUS
DISEASE
FORENSICS
HEMATO
PATHOLOGY
Molecular
Pathology
IDENTITY
TESTING
SOLID
TUMORS
GENETIC
DISEASE
Molecular Diagnostics is a Rapidly Expanding Field
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Molecular diagnostics is the fastest
growing segment of the diagnostics
industry
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~$34 billion world-wide market
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6-8% annual growth
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New discoveries and technology
platforms are leading to the
development of more and
increasingly sophisticated tests
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DNA sequencing
Expression microarrays
Array CGH
Detection technology/test platforms
Majority of the innovation and
discovery takes place in Universities
UM Molecular Diagnostics Test Volume and TAT
Jan 2002 – Dec 2009
Applications of Molecular Diagnostics in Clinical
Laboratory Medicine
Infectious Disease
- Qualitative and quantitative detection
- Microbial identification
- Drug resistance
Genetics (inherited disease)
- Diagnosis of:
Single gene disorders
Complex polygenic disorders
Chromosomal disorders
Oncology – Solid Tumor and Hematologic
- Diagnosis
- Prognosis
- Predict response to therapy
- Monitor residual disease
Identity Testing
- Determining familial relationships
- Bone marrow engraftment analysis
- GVHD monitoring
- Laboratory specimen identification
- Forensics
Pharmacogenomics
- Drug metabolism
- Determine drug dosage
UM Molecular Diagnostics Test Menu
Hematologic Malignancies
Solid Tumors
Quantitative BCR/ABL
BCR/ABL1 Kinase Mutation Analysis
FLT3 Gene Mutation
NPM1 Mutation
CEBPA Mutation
KIT D816V Mutation
t(15;17) PML/RARA Translocation
t(14;18) IGH/BCL2 Translocation
B Cell (IGH) Gene Rearrangement
T Cell Gamma (TRG) Gene Rearrangement
JAK2 V617F Mutation Detection
JAK2 Exon 12 Mutations (March 2010)
PAX/FOXO1 Translocation, Alveolar Rhabdomyosarcoma
EWSR1/WT1 Translocation, DSRT
EWS/FLI1, EWS/ERG Translocations, Ewing Sarcoma
SYT/SSX Translocation, Synovial Sarcoma
EWS/ATF1 Translocation, Clear Cell Sarcoma
Microsatellite Instability Analysis
KRAS Mutation
BRAF V600E Mutation
KIT Mutation in GIST
KIT Mutation in Melanoma
HER2 FISH, Breast cancer
UroVysion FISH, Bladder cancer
Genetics/Pharacogenomics
Cystic Fibrosis Carrier Screening
Apolipoprotein E Genotyping
Hereditary Hemochromatosis Mutation Detection
Factor V Leiden Mutation Detection
Methylenetetrahydrofolate Reductase C677T Mutation
Prothrombin 20210 Mutation
UGT1A1 Promoter Genotyping
Warfarin Sensitivity Analysis
Identity Testing
Bone Marrow Transplant Engraftment Analysis
My Day to Day Activities
Clinical
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Direct the development, validation, and implementation of new
molecular tests
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Technical oversight and trouble shooting of existing tests
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Maintain quality control and quality assurance standards
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Daily review of test data
Teaching
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MGP fellows and block E residents
Research/Academic
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Novel molecular diagnostic tests and technologies
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Collaborations with AP and HP faculty
New Tests Since July 2007
Hematologic Malignancies
Solid Tumor
Quantitative BCR/ABL
BCR/ABL1 Kinase Mutation Analysis
FLT3 Gene Mutation
NPM1 Mutation
CEBPA Mutation
KIT D816V Mutation
t(15;17) PML/RARA Translocation
t(14;18) IGH/BCL2 Translocation
B Cell (IGH) Gene Rearrangement
T Cell Gamma (TRG) Gene Rearrangement
JAK2 V617F Mutation Detection
JAK2 Exon 12 Mutations (March 2010)
PAX/FOXO1 Translocation, Alveolar Rhabdomyosarcoma
EWSR1/WT1 Translocation, DSRT
EWS/FLI1, EWS/ERG Translocations, Ewing Sarcoma
SYT/SSX Translocation, Synovial Sarcoma
EWS/ATF1 Translocation, Clear Cell Sarcoma
Microsatellite Instability Analysis
KRAS Mutation
BRAF V600E Mutation
KIT Mutation in GIST
KIT Mutation in Melanoma
HER2 FISH, Breast cancer
UroVysion FISH, Bladder cancer
Genetics/Pharacogenomics
Cystic Fibrosis Carrier Screening
Apolipoprotein E Genotyping
Hereditary Hemochromatosis Mutation Detection
Factor V Leiden Mutation Detection
Methylenetetrahydrofolate Reductase C677T Mutation
Prothrombin 20210 Mutation
UGT1A1 Promoter Genotyping
Warfarin Sensitivity Analysis
Identity Testing
Bone Marrow Transplant Engraftment Analysis
Molecular Diagnostics - Oncology
Diagnosis
Prognosis
Predict response to therapy
Monitor residual disease
Diagnosis – Ewing Sarcoma
Extract
RNA
Reverse
transcription
EWSR1/FLI1
cDNA
EWSR1
primer
FLI1
primer
PCR
~ 1 billion copies of target cDNA
PCR products
Detection
Capillary electrophoresis
EWSR1/FLI1 (Type 1)
GAPDH control
Molecular Diagnostics - Oncology
Diagnosis
Prognosis
Predict response to therapy
Monitor residual disease
Prognosis - Normal Karyotype AML
CEBPAmut
NPM1mutFLT3-ITDneg
Other genotypes
Schlenk RF et al. NEJM 358(18):1909, 2008
Prognostic Molecular Testing in AML – The UM Experience
90
80
Tests per Month
70
60
Total
FLT3
KIT
NPM1
CEBPA
50
40
30
20
10
0
Jan-04
2004
Jan-05
2005
Jan-06
2006
Jan-07
2007
Jan-08
2008
Jan-09
2009
Molecular Diagnostics - Oncology
Diagnosis
Prognosis
Predict response to therapy
Monitor residual disease
Predict Response to Therapy: KIT Mutations in Melanoma
(4 wk)
Hodi FS et al., 2008 J Clin Oncol 26(12):2046
Molecular Diagnostics - Oncology
Diagnosis
Prognosis
Predict response to therapy
Monitor residual disease
Monitoring Residual Disease – UroVysion FISH
Normal Urothelial Cell
CEP 3
LSI 9p21
CEP 7
CEP 17
Malignant Urothelial Cell
Monitoring Residual Disease – UroVysion FISH
Case 4
History of CIS (bladder), Post Resection
Recurrence of CIS, BCG therapy, Monitoring
Cystoscopy - Negative
FISH - Positive
Thanks!