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(Precision) Medicine 9/23/2014 Disclosures Personalized (Precision) I am an employed by Promega Corporation, a Madison Medicine based international biotechnology company Promega does not market any of the products mentioned in Wisconsin Association of Physician Assistants this presentation, although we do provide components to some of the manufacturers of these diagnostic assays October 10, 2014 Ashley G. Anderson Jr., MD, MS Chief Medical Officer Promega Corporation Objectives Promega Corporation Look into the future, and appreciate the growing role, and limitless potential, of molecular diagnostics Understand the term “personalized medicine” Be motivated to read, learn, and become an early adopter of precision diagnostics Appreciate that these bill be big changes, but they may not come fast. 1 9/23/2014 Personalized medicine Precision medicine “The molecular methods that make personalized medicine The tests themselves are not necessarily “personalized.” possible include testing for variations in genes, gene expression, They are standardized like most other tests proteins and metabolites as well as new treatments that target molecular mechanisms. Test results are correlated with clinical The results from these tests are increasingly more predictive factorsfactors--suchsuch as disease state, prediction of futurfuturee disease states, of disease states drug response, and treatment prognosisprognosis--toto help physiciansphysicians Certain tests are more predictive of responses to specific individualize treatment for each patient” therapies Personalized Medicine Coalition The net result is a more precise method of assessing disease and response to therapy Key developments in medicine Sterility Antibiotics Eradication of smallpox, and vaccines for polio, diphtheria, rubella, chicken pox, hep A&B Blood banking and transfusion Insulin Medical imaging advances Heart surgery Minimally invasive surgery 2 9/23/2014 Physical exam /radiographic studies Blood chemistry Biomarkers A objectively measurable indicator of a biologic state or condition Physical exam Pulse, respiration, blood pressure Clinical chemistry Radiology finding Precision medicine is the identification of more sensitive and specific biomarkers. 3 9/23/2014 A brief review of the genome Basic DNA structure DNA is composed of 3 billion base pairs, AA--TT or C--GGC Short sequences of DNA represent genes, each of which may code for one or more proteins Each gene is located on one of the 23 paired chromosomes The genetic information on an entire genome can be placed on one DVD DNA toto RNA toto proteins Genes & alleles Gene = A stretch of DNA that codes for a polypeptide or RNA chain that has a function in an organism Gene = “A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions or other functional sequence regions” An “allele” is an area of variation in a gene responsible for variation in some trait. Everyone has a gene for eye color, but different alleles for the specific color. An allele is a variant of, or within a gene. 4 9/23/2014 Genes as biomarkers Loci and chromosome rregionsegions Locus = It is not a gene, but refers to a map position. “A •• There are 20,00020,000--25,00025,000 protein encoding genes locus is a point in the genome, identified by a marker, which can be mapped by some means. It could, for example, be an •• But it’s not all about genetics. anonymous nonnon--codingcoding DNA segment •• EpigeneticsEpigenetics--BaseBase pairs, genes are “turned on/turned off ” by Chromosome region : a genomic region which has been “epigenetic” factors associated with a specific syndrome or phenotype, •• So, is your genetic anatomy your destiny? Only partly. particularly when there is a possibility that several genes within it may be involved in the phonotype Molecular biomarkers Biomarker that gives an indication of risk Diagnostic biomarkersbiomarkers--makemake the diagnosis of a specificspecific disease Drug development and Prognostic biomarkersbiomarkers--showshow progression of disease therapeutics Therapeutic predictive biomarkersbiomarkers--showshow the probableprobable effect of a specific treatment on a patient. 5 9/23/2014 Personalized medicine pparadigmaradigm One dose fits all vs. personalized medicine Personalized medicine approach Future *Drugs targeted at small Evidence-based patient populations Medicine *Genomic profiles determine patient segmentation and therapy Improved therapeutic Genomic outcomes with fewer adverse Diagnosis events paradigm Current state *Blockbuster drugs targeted at broad patent diagnoses *Approximately 50% or more Today of patients to not have desired ‘Trial and error therapeutic outcomes medicine’ *Significant adverse events Diagnostic Broad Narrow- Targeted Population-based Patient specific Therapeutics Source: Personalized Medicine©2009 Future Medicine, Ltd Warfarin sensitivity Molecular diagnostics Genetic analysis Antithrombotic effects of warfarinwarfarin——narrownarrow therapeutic index 2 Million people are placed on warfarin annually in the US. Some individuals are highly sensitive to warfarin Risk of adverse drug events (bleeding) approaches 9.5%, mostly in the first month of therapy. Cost approaches $18.5M/10,000 patients/5 years Many of these individual have polymorphisms in CYP2C9 and/or VKORC1 genetic loci Cancer Infectious disease So…we should be testing for these allelic variants, but few institutions are. Why? 6 9/23/2014 Sequencing the human genome Next gen sequencing Began in 19901990--2003.2003. The sequence of last chromosomechromosome was Definition: published in Nature in 2006. Goal was to determine the Developed approximately 5 years ago sequence of chemical base pairs that make up human DNA, Low cost sequencingsequencing--approachingapproaching the $1000 genome and identify and map all the genes Very rapid results at significant cost reductions Human Genome Project (HGP) = $3 Billion dollar project Ion Torrent Illumina (Solexa) sequencing Celera Corporation, using some data from the HGP, sequenced the genome for $300M with commercial Exome sequencingsequencing--lookinglooking only at the protein encodencodinging genes in aspirations, which caused controversy the genome Select for the subset of genes that encode proteins (180,000), or 1% Very slow, painstaking, expensive of the genome or 30 million base pairs Mutations in these are much more likely to have severe consequences Next generation ssequencingequencing Next generation ssequencingequencing 7 9/23/2014 Genome WWideide Association The $1000 dollar genome Study (GWAS) Collect genomic information Analyze information for common genetic variants (alleles) in different individuals to see if they are associated with a trait. Perform “SNP analysis” to determine the SNPs associated with the disease. SNP= sequence variation within population consisting of a single nucleotide (A,T,C or G) different in individuals First GWA study was performed in 2005, for macular degeneration. Found 2 SNPs with altered allele frequency as contrasted with controls. Genetic testing Carrier screeningscreening--screensscreens for one copy of a gene mutationmutation PrePre--implantationimplantation genetic diagnosis (PGD) Avoids selective pregnancy termination Sex discrimination? Ethical issues? Forensic testing Crime Paternity 8 9/23/2014 Prenatal genomic sscreeningcreening (PGS) Circulating fetal DNA (cfDNA) fragments are harvested from the maternal blood stream Costs range from $200$200--$2500$2500 (or more) Multiple companies, notably Sequenom, Illumina False positive rates for detection of trisomies 21 and 18 Illumina’s Verifi test has false positive rate of only 0.03% were significantly less than other methods of screening (0.03%) (Test is very specific) What are the implications of a diagnosis, and how might this impact parent’s decisions Use of cfDNA detected all cases of aneuploidy (100% sensitivity) DNA Deletions in chromosome 22 associated with DeGeorge Synd Molecular diagnostics Genetic analysis Cancer Infectious disease 9 9/23/2014 Phenotype to Breast cancer phenotype + genotype Myriad Bracanalysis® assay for BRCA1 and BRCA2 gene mutations Patients with either mutation have up to an 87% chance of developing breast cancer, and a 44% chance of developing ovarian cancer prior to age 7070 Benefits: Increased surveillance for test positive individuals Enhanced customization Earlier diagnosis and treatment for specific individuals Cost = $4000.00 and tumors Competitors tried to offer for less resulting in legal action ultimately confirming Myriad’s right to “own” genes Companion diagnostics Herceptin® (trastuzumab) Companion diagnostics are assays (a test or Monoclonal antibody that interferes with the Her2/neu measurement) intended to assist physicians in making receptor treatment decisions for their patients. They do so by HercepTest™ elucidating the efficacy and/or safety of a specific drug Approved by FDA in 2010 as companion diagnostic or class of drugs for a targeted patient group or subub-- groups. Identify tumors with over expression of HER2 protein Immunohistochemistry test Types of diagnostics Dako Corporation manufactures test, while Genentech Test developed after drug comes to market manufactures the therapeutic Test developed in conjunction with drug Numerous other companies now have companion diagnostic assays for HER2 (Ventana, LTI, Abbott, Biogenex) 10 9/23/2014 HER2 Oncotype DX Tests surgical samples from breast CA patients for 21 genes to predict probability of recurrence. Genomic HealthHealth--RedwoodRedwood
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