High Efficiency Nucleic Acid Extraction From FFPE Samples Using Bulk Lateral Ultrasonic Wave Transducer

DESCRIPTION provided by applicant Genetic analysis is a driving force behind andquot Personalized Medicineandquot and has become an essential tool in advancing all areas of biology medicine and behavioral biology A significant amount of genomic and proteomic information is stored in archived formalin fixed paraffin embedded FFPE samples throughout the world FFPE tissue preparation emerged over years ago as a method for long term tissue preservation These samples are usually retrievable with clinical pathology histories and therefore represent a treasure trove for the retrospective study of human disease Protein expression in pathological specimens by immunohistochemical IHC detection is well established and currently part of the diagnostic routine In contrast an analysis using DNA and RNA extracted from FFPE tissue remains difficult because chemical crosslinks dehydrated tissue and the paraffin matrix of FFPE preserved samples present significant challenges for the robust extraction of good quality DNA Furthermore many methods for extracting nucleic acid from FFPE tissue particularly those that are highly manual are not standardized protocols Much variation exists between methods e g proteinase enzyme digestion time and incubation temperature In addition these manual protocols are time consuming and require the use of hazardous and flammable materials like xylene and ethanol for deparaffinization As a result these isolation protocols have often been incompatible with high throughput formats Researchers and diagnostic institutions and companies are constantly searching for more efficient time saving and less costly ways to extract data from the nucleic acids stored in FFPE samples The primary goal of this proposal is to show proof of principle that the Bulk Lateral Ultransonic BLU tm energy from the Microsonic Systems Inc transducer can be used to obtain high quality DNA from archived FFPE tissue samples Since our transducer that produces BLU waves has a very small footprint is scalable and automation friendly our long term goal is to develop high throughput capabilities for this fast growing application After having attained promising preliminary data we propose to extend these studies for optimization of the BLU energy protocol for DNA extraction from FFPE samples More specifically we plan to optimize Bulk Lateral Ultrasonic BLU energy parameters and DNA extraction protocol using FFPE engineered cell lines as Reference Standards and evaluate and validate the optimized BLU energy FFPE DNA extraction protocol across FFPE samples from various human tissue types including kidney brain liver heart and uterus PUBLIC HEALTH RELEVANCE This project will improve the efficiency of high quality DNA extraction from the millions of archived formalin fixed paraffin embedded FFPE tissue samples by speeding up the process and eliminating the use of hazardous and flammable materials like xylene for deparaffinization This makes the process more compatible with high throughput formats providing the industry with more efficient access to an invaluable repository of information for genetic analysis These samples can be analyzed for a wealth of applications including biomarker discovery drug development and cancer research