Rapid sample preparation method for high molecular weight DNA from tumor tissues suitable for structural variant analysis

Summary Claremont BioSolutionsLLCCBIOThe introduction of long read sequencing and mapping applications is set to change the field of cancer research by allowing unparalleled insight into the complex structure of tumor genomesWith the ability to sequence large spans of DNA that aress of kb in size these technologies will offer more accurate de novo assemblyresolve highly repetitive regionsand allow identification of large structural variants in tumor genomesAs cancer researchers move to these platforms they will face new hurdles as effective sample preparation of ultra long DNAandgtkbremains a limiting stepCurrent methods of DNA extractionincluding spin column and magnetic bead applicationssignificantly shear ultra long DNAOlderalbeit effectiveagarose plug digestion techniques are difficulttime consuming and highly variableNew commercial products have been introduced that can isolate ultra long DNA but are restricted in use to bacteriatissue culture cellsor fresh blood cellsand are not usable with clinically relevant solid tumor tissue samplesTo overcome this challengeClaremont BioSolutions is developing a prototype technology that combines gentle and rapid tissue dissociation with a novel binding matrix to isolate high quality high quantity ultra long DNA in andltminutesThe method reduces DNA shearing and tangling and is compatible with small quantities of solid tissueIn Aimwe shall use the combined approach to demonstrate isolation of ultra long DNAandgtkbfrom matched normal and tumor tissue samples and analyze length and qualityIn Aimwe shall validate compatibility of the isolated ultra long DNA with third generation long read sequencing and mapping technologies and analyze the sequence data to demonstrate improved long read sequencing over existing DNA extraction methodsUltimatelythe goal will be to integrate this miniature technology into an automated platform to provide a rapidcost effectiveand reproducible method to isolate DNA from solid tissues for improved downstream analysis of tumor samples Narrative Claremont BioSolutionsLLCCBIOSolid tissue samples offer a wealth of untapped information relevant to cancer and genetic diseasesExtracting high quality ultra long DNA from solid tissue samples for downstream long read genomic applications is often difficultlabor intensive and highly variableThis project will apply a new technology to allow rapid isolation of ultra long DNA from tissue samples to improve complex structural variant detection using long read technologies