Development of an information rich assay for C ORF as a test for ALS and FTD

Project Summary The long term goal of this project is to develop validate and commercialize an assay for improved analysis of C orf a gene on chromosome that is linked to frontotemporal dementia FTD and amyotrophic lateral sclerosis ALS Expansion of a guanine and cytosine rich hexanucleotide repeat GGGGCC in the non coding region of C orf is associated with of familial ALS The expansion also appears in of familial frontotemporal dementia FTD cases as well as of sporadic ALS and of sporadic FTD The C orf region is difficult to size accurately because most expansions in affected individuals are andgt repeats in length Currently testing typically relies on homebrew PCR based assays for accurate sizing of andlt repeats or separately Southern blot analysis for crude sizing of andgt repeats We have developed a solution to enable high throughput reliable sensitive and accurate sizing of the repeat region for both short andlt repeats up to repeats and long expansions to at least repeats in a reflex assay The proposed assay offers a solution to these technical challenges based on the repeat primed assay platform AmplideX FMR PCR that Asuragen has developed and successfully commercialized for fragile X syndrome a CGG triplet repeat disorder We will continue to leverage andgt years of experience in optimizing high performance diagnostic assays for GC rich repeat sequences to develop an accurate and robust diagnostic test for C orf Funding for this Phase II will support the efforts necessary to complete the development of the test The specific aims of this proposal are Aim Integrate a novel engineered PCR polymerase system to achieve extreme processivity and reliable amplification of andgt hexanucleotide repeats Aim Develop and integrate a set of controls and standards in an optimized workflow that supports C orf testing Aim Develop a data analysis pipeline and reporting tools within a user friendly application that allows rapid and accurate identification C orf repeat number Aim Evaluate an assay system that integrates the workflow and controls Aims and with the analysis software Aim Validate the integrated system with cell lines and retrospective clinical samples The development of an improved information rich assay for C orf will be useful as a screening and diagnostic test for ALS and FTD as well as a clinical research tool to identify intermediate and or expanded repeat sizes that are potentially relevant to other forms of age onset neurodegeneration In addition this assay can further the understanding of known and novel genotype phenotype associations and enable opportunities for targeted therapeutics and clinical trials Project Narrative We are developing a test to improve diagnosis and screening for genetic alterations that are linked to neurodegenerative diseases Alterations in the gene C ORF are associated with frontotemporal dementia FTD and amyotrophic lateral sclerosis ALS The test will be useful as a clinical research tool to support opportunities for emerging therapeutic options