Cradle Genomics, Inc. — Department of Health and Human Services SBIR Phase I: NICHD

Description

The overall goal of this research is to provide a flexible prenatal genetic testing kit that can be expanded to detectany inheritable trait as early asand up toweeks of gestationfrom a safenoninvasive Pap smearStudiesshow that perinatal Pap tests pose no risk to mother or fetusand capture trophoblastlike cells that migrate fromtheplacentaintothereproductivetractTrophoblastretrievalandisolationfromthecervixTRICefficientlyisolates hundreds of fetal cells without limitations due to early gestational agematernal obesityor uteroplacentalinsufficiency disordersIn a recent Science Translational Medicine reportwe isolated sufficient genomic DNAfrom intact fetal cells obtained by TRIC atweeks of gestationnto definitively distinguish maternal andfetalDNAbytargetednextgenerationsequencingNGSofshortterminalrepeatsSTRsandsinglenucleotidepolymorphismsSNPsComparedtomassivelyparallelsequencingofcellfreefetalDNAfrommaternal serumwhich has a fetal fraction of onlyat weekof gestationDNA obtained by TRIC had afetal fraction ofcapable of providing nucleotidespecific haplotypingTRIC will be commercialized toidentify single gene and chromosome number disorders in a prenatal test from Pap smearsWe will develop acustom multiplex PCR platform to simultaneously amplify SNPs and STRs to identify fetal DNAas well as lociacross ChromosomeChrto detect trisomyDown syndromeThis platform will be expanded to otherchromosome number diseases in Phase IIWe will accomplish four milestonesPrimers will be designed andtested with human genomic DNA to amplify STRsSNPs and loci across Chrand ChrreferencesequencingPCR products by NGS to optimize their amplification and coamplification in singleplex and multiplex PCRDNAisolatedfromfetalandmaternalcellsisolatedbyTRICNaswellasthecorrespondingnewbornbloodspotsreferencewill be compared by targeted NGSWe expect amplicons to be generated for each setofprimersSTRandSNPhaplotypeswillbeidentifiedbasedonreaddistributionsintheNGSdatatodeterminetheproportionoffetalandmaternalDNAandcorrespondencetonewbornbloodspotDNANGSresults for Chrand Chrwill be compared to determine their relative ploidyDNA from patients carrying afetusatriskforTrisomyNwillbeanalyzedbytargetedNGStocompareSTRSNPandsequencesacrossChrandChrinfetalmaternalandnewbornbloodspotDNAWeexpecttodemonstrateuniqueidentities for fetal and maternal DNAidentical fetal and newborn haplotypesand concordance between Chrploidy of fetal and newborn DNAIt should be possible to detect Trisomyand mosaicismif presentWith anestimatedannualmarketpotentialof$billiontheenvisionedtechnologywillfillanexistinggapinclinicaldiagnostics by providing an earlysafe approach for prenatal genetic analysisOur initial commercial product willenable management of high risk pregnanciesand provide valuable information to physicians and patients in theprocess of establishing familiesspecifically impacting pregnancies at risk of having a child with TrisomyThis research provides major public health benefits by leveraging a safenoninvasive method to capture fetal cells that migrate into the reproductive tract from a Pap smear for development of genetic tests to identify women carrying a fetus with a chromosomal disorder such as Down SyndromeWe will build a DNA sequencing kit that can be commercialized to detect trisomyin fetuses as early asweeks of pregnancyAdvances emerging from the proposed research will generate new clinical tools for managing pregnancy complications to benefit the well being of mothers and their babies