Fast and automated DNA and RNA extraction from formalin-fixed, paraffin-embedded tissue

DESCRIPTION provided by applicant Sample preparation is the essential first step to all genomics and transcriptomics and yet is a primary source of analysis variability and manually intensive Formalin fixed paraffin embedded FFPE samples are routinely collected and hundreds of millions are archived in tissue banks worldwide These samples are cross referenced with long term follow up patient data crucial to development of therapeutics and biomarker discovery However DNA and RNA are currently extracted from FFPE samples using sample preparation techniques which are difficult to automate and accelerate such as wax removal centrifugation multiple buffer exchanges and heated enzyme digestion Purigen Biosystems proposes a novel system to automate and improve the efficiency of RNA and DNA extraction from FFPE samples Purigen will develop a protocol and buffer chemistries as well as a novel injection molded microfluidic chip with eight parallel sample processing channels Purigen will also modify its existing benchtop system to automate an electric field based method for the extraction of DNA and RNA from FFPE tissue This method is uniquely faster significantly less manually intensive and has great potential to achieve higher quality analyses of FFPE tissue Purigen will use isotachophoresis ITP to simultaneously collect purify and focus extracted RNA and DNA quantify total extracted nucleic acid on chip via in line ITP aided labeling with an intercalating fluorescent dye and deliver downstream to eight parallel output reservoirs compatible with robotic pipetting Purigen will demonstrate the chip and modified system on andgt FFPE samples from colon breast liver and lung tissues including parallel comparison analyses with traditional methods and quantification of total versus amplifiable yield Work will include at least runs of fully automated NA extraction for eight samples in parallel in andlt min using Purigenandapos s modified benchtop system and will demonstrate amplifiable NA yields greater than existing FFPE kits PUBLIC HEALTH RELEVANCE For over years hundreds of millions of tissue samples many suspected tumors have been collected and stored in vast so called andquot biobanksandquot worldwide These samples are preserved using a technique known as formalin fixed paraffin embedded FFPE tissue preparation FFPE samples are cross referenced with unique long term follow up patient data The DNA and RNA in these samples therefore hold many possibilities for developing cancer treatments and discovering new disease markers However the DNA and RNA are currently extracted from these samples using decades old sample preparation techniques which are difficult to automate and accelerate Proposed here is a new electric field based method of automating the extraction of DNA and RNA from FFPE tissue This method is faster significantly less manually intensive and has great potential to achieve higher quality analyses of all FFPE tissue The system proposed will leverage low cost injection molded plastic chips and a touch pad controlled automated benchtop device