BASEPAIR INC — Department of Health and Human Services SBIR Phase I: NICHD

Description

PROJECT SUMMARYSince its inceptionyears agoin vitro fertilizationIVFhas resulted in the birth of more thanmillion babies in the United Statesand has revolutionized the field of reproductive medicineUnfortunatelythe success rate of IVF is still exceedingly lowespecially for women andgtyears oldwith onlyof implanted embryos resulting in pregnancyThis is partly due to the cytological method used for pre implantation screeningwhich cannot detect the most common genetic defect during IVFaneuploidyi echromosomal copy number variationAneuploidy is linked to higher rates of miscarriageand occurs more often in women andgtyears of agethusaneuploidy has been a frequent target for genetic screening to improve IVF outcomesPre implantation genetic testing for aneuploidyPGT Arefers to a variety of techniques aimed at detecting changes in chromosomal copy numberwith the goal of identifying high quality euploid embryos for implantationRecent advances in next generation sequencingNGStechnologies have made it possible to screen embryos at higher levels of precisionand across a wider range of genetic defectsincluding mosaicismtriploidy and single nucleotide polymorphismsSNPsDespite these remarkable advancesthere are still significant challenges with PGT A sequencingIndeedthe most commonly implemented software for PGT Ai eBlueFuseare bundled with specific sequencing platformsi eVeriSeqand are only designed to test for aneuploidyFurthermoreexisting pipelines are not user friendly or customizablewhich is a serious obstacle prohibiting the use of NGS by cliniciansembryologistsA more accessible bioinformatics platform is desperately needed that will bridge the gap between PGT A sequencing and IVF outcomesBasepairis an innovator in efficientuser friendlyweb based NGS analysis systemswith fully automated ChIPRNAATACand DNA Seq bioinformatics pipelines available onlineHereBasepair will deliver PiNDAthe first fully integrated software solution for comprehensive PGT A analysisIn Aimwe will develop modules to test for specific chromosomal abnormalitiesincluding mosaicism and triploidyand validate each model with training data derived from somatic cell lines with known chromosomal aberrationsIn Aimwe will integrate our modules into the PiNDA software systemcreating a user friendlyweb based interface that will perform full data analysisraw data to full summary reportin andltminuteswith no manual input requiredFinal data will be accessible via Basepair s online portalfacilitating rapid data transfer from embryologists to physiciansand supporting the integration of NGS tests in IVFOur innovative bioinformatics platform will accelerate NGS analysis for IVFimproving rates of pregnancy and advancing research in the success of IVF procedures PROJECT NARRATIVEIn vitro fertilizationIVFmethods have begun to leverage next generation sequencing technologies for pre implantation genetic testing of aneuploidyPGT Aexpanding the array of chromosomal abnormalities that can be accurately detectedHoweverthe vast majority of software can only distinguish one type of genetic defecti eaneuploidyare difficult to useand are tied to distinct sequencing platformslimiting the clinical utility of resulting analysesBasepairIncis a pioneer in user friendlyweb based bioinformatics pipelinesproviding comprehensive services for a wide range of sequencing projectsHereBasepair will develop an inclusive suite of software for PGT Acompatible with sequencing data from multiple platformsThis product will be of high value to the field and will help bridge the gap between advances in DNA sequencing and IVF technology