Point of care genotyping assays, and algorithm for warfarin dosing

DESCRIPTION (provided by applicant): On August 16, 2007, the FDA updated the label for warfarin to include information in the precautions section to remind physicians that people with variations in the CYP2C9 and VKORC1genes may require a lower initial d ose of the drug (see http://www.fda.gov/cder/drug/infopage/warfarin/default.htm). Unfortunately, the FDA did not provide specific guidance to physicians on how to use this genotyping information. Soon after the announcement for an altered label for warfari n, the FDA cleared a genotyping test for the most common mutations influencing patients' responses to warfarin (i.e., Nanosphere's Verigene warfarin test FDA 510(k) # K070804). Unfortunately, this new diagnostic device did not include instructions on how t o use the genetic information to prescribe warfarin. In addition, the cleared warfarin test requires large quantities of highly purified DNA (2 5g), and uses costly instrumentation (such that high test volumes will be required to justify the reagent lease) . As FDA has not yet cleared a nucleic acid extraction method for use with the Verigene warfarin test, only large clinics with laboratories capable of complying with the Laboratory Accreditation Program Molecular Pathology Checklist, developed by the Colle ge of American Pathologists, will adopt the Verigene warfarin test. We believe the lack of information of how to use the genotyping data, and the complexity of the DNA extraction required to perform the genetic test will limit its utility. We propose to de velop a low-cost, instrument free genotyping system that does not require large quantities of extensively purified DNA, and that includes a web-based computational tool that integrates genetic, and physical factors to offer an individualized predictive mod el for warfarin dose. The genetic test will use BioHelix's proprietary helicase dependent amplification (HDA), as well as a disposable lateral flow device designed to prevent laboratory contamination with amplicons. The HDA reagents will be formulated as a Ready-to-go IsoAmp dry reagent formulation with extended stability at room temperature. We have found that crude buccal swabs can be used to perform HDA genotyping tests; therefore no DNA extraction will be required. As lateral flow tests widely used in CLIA waived and moderate complexity assays, we believe coagulation will prefer this detection format to using complex instrumentation. In Phase I, we will develop 3 genotyping assays for the CYP2C9*2 (a.k.a. 3,608 CgtT or R149C), the CYP2C9*3 (a.k.a. 4 2,614 AgtC or I359L), and the 1,639 GgtAVKORC1 loci using ARMS technology. We will also implement design control for our product development process, and secure ISO 13485 certification for BioHelix. Trimgen (Sparks, MD) will manufacture BuccalQuick DNA e xtraction kits under GMP. BioHelix will manufacture bulk enzymes required for HDA. GE Healthcare will manufacture the Ready-to-go IsoAmp warfarin dry reagents under GMP. The amplicon containment, lateral flow device will be manufactured under GMP by Ximed ica. Finally, we will validate the 3 warfarin assays at PGX laboratories using 50 samples and compare the performance of the Ready-to-go IsoAmp warfarin assays to DNA sequencing and warfarin genotyping assays validated at PGX laboratories. In Phase II, we perform a retrospective, multi-site clinical study aimed at validating the assays using the Verigene warfarin test as a predicate device, and PGXL technology's algorithm with ~500 patients on consistent dosing of Coumadin for 3 months. This study will inc lude a warfarin dosing algorithm. We believe we can offer genetic typing test for warfarin with a moderate degree of complexity with a link to a web-based computational tool for individualized predictive modeling of warfarin dosing for between 15 and 2 0/locus. Narrative In patients with atrial fibrillation (AF), the uneven and arrhythmic pumping of the heart's two upper chambers results in pools of blood in