A novel NIPT assay based on single cell sequencing

Non invasive pre natal screeningNIPTby sequencing of cell free fetal DNAcffDNAisolated from maternal blood has resulted in significant benefitsthe screening is saferelatively low costand greatly reduces the number of invasive amniocentesis and chorionic villus samplingCVSproceduresCurrent NIPT screens have a very high negative predictive valueandgtbut have a relatively low positive predictive valuethere is a high likelihoodandgtin some casesof a false positive resultThereforea follow up invasive test is required to confirm positive NIPT screensFurthermorelow sensitivity limits NIPT screening to trisomies that are more easily measured from the low levels of circulating fetal DNA in maternal bloodA test that can simultaneously detect trisomies as well as subchromosomal abnormalitieswithout the need for follow up testingwould represent a significant advance of the current standard of careThis project proposes to develop a cell based NIPT test that provides a true diagnosis of trisomies without the need for follow up amniocentesis or CVSFurthermorethe test would have sufficient gains in sensitivity and specificity to allow detection of rare subchromosomal genetic disordersresulting in a significant advance in terms of the current non invasive screening capabilitiesThe workflow of the test takes advantage of several technologies that we have pioneeredrare cell isolationsingle cell manipulation analysisand single cell sequencingInitial proof of concept experiments have demonstrated that model cells representing fetal trophoblasts can be isolated and detectedand we have demonstrated the ability to isolate and analyze individual cells via NGS from an enrichedheterogeneous mixtureThe proposed workflow comprises a cell isolation systemlibrary prep kits for sequencing single cells on commercially available sequencersand bioinformatics software for analysisSuccessful execution of this project will result in a complete workflow for genetic analysis of cffDNA samplesresulting in a true in vitro diagnostic test that can detect not only trisomies but other rare subchromosomal genetic disorderswithout requiring an invasive follow up analysisThe development of this capability will represent a substantial advance in the current standard of care and will also serve as a platform for development of another rare cell testing This application proposes the development and validation of a non invasive prenatal test for aneuploidies and subchromosomal abnormalities by isolating and sequencing individual fetal cells from maternal bloodIf successfulthis approach will allow diagnosis of fetal abnormalities without the need for follow up invasive testing such as amniocentesisThis will lower risk of pregnancy loss and improve the standard of care