A Physician s Perspective J. E. Froelich, D.O., FACOFP dist. Disclosure Not presently on any pharmaceutical speaker s bureaus CardioDx Research and development company, Palo Alto, California. Have a commercially available product (ChorusCAD ) that utilizes gene expression testing to stratify cardiovascular risk (plaque burden) Speaker has participated in post marketing clinical studies of the CardioDx product Has spoken for CardioDx in the past for compensation Human Genome Project 1
Human Genome Project (HGP) An international research effort to sequence and map all of the genes of Homo sapiens (the human genome) Completed p in April 2003 One of Mankind s greatest feats of exploration and science in history Created an ability to read nature's complete genetic blueprint for building a human being DNA DNA A A gene is a length of DNA that encodes information Genomic DNA consists of two antiparallel and reverse complementary strands, each having 5' and 3' ends. The two strands may be labeled the "template strand," which serves as a blueprint and the "coding strand" 2
DNA DNA template strand serves as a blueprint for the production of an RNA transcript Coding strand is the DNA version of the transcript sequence. The production of RNA copies of the DNA is called transcription, and is performed in the nucleus by RNA polymerase which adds nucleotides to a growing RNA strand This RNA is complementary to the template DNA strand Gene Expression Gene expression: the process by which information from a gene is used to synthesize a functional gene product These products are usually (unique) proteins The process of gene expression is used by all known life including bacteria and some viruses - to generate the macromolecular machinery for life. Gene Expression Process by which genetic code, stored in DNA, is reproduced then "interpreted Gene expression is the most fundamental level at which the genotype gives rise to the phenotype, i.e. observable trait 3
Gene Expression Several steps occur in the gene expression process including the transcription, RNA splicing, translation, and post-translational translational modification of protein The process of transcription begins when mrna interacts with DNA through RNA Polymerase (RNAP) and uses the DNA template to produces mrna Transcription and Translation Genes are expressed through active processes by being transcribed onto RNA, and then that RNA being translated into protein. Transcription and Translation 4
Gene Expression Testing Gene Expression testing (GET) is the measurement of specific gene activity through mrna levels DNA (gene) is static: a library of information RNA is fluid: the expression of a variable; status at a given point in time GET is measurement of protein creation, immediate and highly specific Gene Expression Testing Examples of present use: Specific cancer tumor activity level Discovery of cancer s presence and cell type Quantitation of tumor activity it Monitoring of cancer cell activity post treatment Quantitation of atheroma activity in the coronary arteries - total plaque burden in obstructive CAD GET (Genomics): A New Era in Medicine Oncotype DX Genomic test estimates the likelihood of breast cancer recurrence by expression profile of 70 genes MammaPrint test categorizes women into a high versus low risk for breast Ca recurrence by the expression profile of 21 genes 5
GET (Genomics): A New Era in Medicine Afirma tissue test by Veracyte Determine if a fine needle aspiration Bx is benign or suspicious for thyroid cancer expression of 142 genes AlloMap Molecular Expression Blood test for probability of acute cellular rejection (ACR) of heart tissue during transplant panel of 20 gene expression assays GET (Genomics): A New Era in Medicine EarlyCDT EarlyCDT -Lung by IDL Blood test evaluates 7 autobodies Predicts lung cancer presence ColonSentry blood test by IDL predicts the presence of colon cancer by measuring the expression of 7 gene biomarkers Could replace screening colonoscopy GET (Genomics): A New Era in Medicine CorusCAD by CardioDx Predicts obstructive CAD Peripheral blood test Evaluates the expression profile of 23 genes Test results have nearly linier relationship to level of coronary artery obstruction Could replace Nuclear Stress Test 6
Completion of the Human Genome Project heralds a new era in medical science Genomic data will exponentially improve our ability to diagnose and treat heart disease, cancer, and a myriad of chronic diseases Opportunity exists to replace invasive diagnostic tests with genomic tests that can be performed without risk or significant stress to patients Gene expression data were used to develop predictive models that accurately classified unknown aortas as having minimal or severe disease with over 90% accuracy. JACC; Vol. 48, Issue2; 18 Jul 2006 7
Quantitation of obstructive CAD through GET using venous blood CorusCAD blood test Evaluates expression profile of 23 genes Relationship to disease is linier Could replace Nuclear EST More accurate than Stress Nuc GET CAD Score Proportional to Disease Severity 4 Gene Expression Links to Atherosclerosis Gene expression test reflects cellular and molecular processes involved in: Innate and adaptive immune responses to LDL oxidation and other inflammatory processes Inflammatory cell migration into atherosclerotic plaque Cellular apoptosis and necrosis 8
Lifetime Risk for Cardiovascular Event vs. Current Likelihood of Obstructive CAD Gene Expression Test (GET) CV Risk Factors for CAD Hypertension, high cholesterol, Measures gene activity through mrna family history, smoking, etc. levels for each individual Genetic Factors Information on obstructive CAD status An individual DNA signature at a given point in time Constant over lifetime An algorithm that measures Genetic variation yields traits expression levels of 23 genes indicative of obstructive CAD Long-term risk for major cardiovascular event. Informs on, for example, the chance of having a heart attack. Current status of obstructive CAD Informs on the likelihood that a patient's symptoms are due to obstructive CAD. GET CAD Score Increases with Coronary Stenosis as Assessed by CTA 30 Relationship between GET CAD and CTA Determined Stenosis* Score Average Corus CAD 25 20 15 10 5 0 None Minimal Mild Moderate Severe Occluded n=117 n=60 n=35 n=11 n=11 n=3 Global p<0.0001 * positive cases is defined as coronary stenosis of 70% by site-read CTA (severe and occluded) Gene Expression Patient Report Graph: Depicts the relationship between test score and likelihood of obstructive CAD 36 68% 9
GET CAD Validation Data Published in Annals of Internal Medicine October 2010 10 Rosenberg and colleagues study lies at the vanguard of clinical genetics in cardiovascular care. -Excerpt from AIM editorial, Donna Arnett Ph.D., M.S.P.H. Cancer detection identification, classification, differentiation of cell type Invaluable insight into tumorigenesis, diagnosis, prognosis and follow-up of therapeutic interventions. Cancer 46 W/M smoker 40pk-yr Auto body / painter Chronic Cough, sputum am only No recent wt change; notes fatigue Both parents had cancer: Fa lung @56; mother breast at 48. CXR neg 5 months ago 10
Alzheimer's Ds Monitoring and quantitation of proteins associated with Alzheimer's disease Identification of early cognitive impairment d/t AlzD and differentiation Alzheimer's Ds 71 yr W/F Healthy lifestyle FmHx: Fa memory changes noticed @72, Memory Unit @76, died @77. Exercises her mind: Sudoku, word search, crossword puzzles Car incident - Terrified Profiling cervical dysplastic changes and HPV activity Infertility research 11
Pathologies of obesity Regulation of metabolism in obesity and particular obesity- associated diseases Level Level of health Underactive children Present fat/muscle ratio Nutritional status Muscle recruitment/fitness Brain activity/inactivity/fitness Toxins present from inactivity Gene Expression A Physicians Perspective J. E. Froelich, D.O., FACOFP 12