ARIMA GENOMICS, INC. — Department of Health and Human Services SBIR Phase II: 172

Description

Commercialization of a low cost user friendly DNA preparation kit that produces chromosome span contiguity from conventional short read sequencing for a wide range of applications Arima GenomicsProject Summary Abstract Overof Next Generation SequencingNGSis sequenced via Illumina short read sequencersThis is because of its cost effectiveness and faster turn around timesHowevershort read sequencing technologies lose critical contiguity information and are limited in assembling genomes de novo and reconstructing maternal and paternal haplotypes of diploid genomesContiguity information is valuable for understanding the genetics of human health and diseaseand therefore critical for advancing precision and personalized medicineLongread technologiese gPacific Biosciencesonly reach megabase scale chromosomal contiguitybut areX more expensive than Illumina short readlimiting its useRecent advances in DNA preparation can preserve long range information that is compatible with Illumina short read sequencingThesesyntheticlong readsor SLRmethods can improve short read technologies withlong range contiguity and short read economyHoweverthe maximal SLR contiguity is onlythe contiguity aMb average human chromosomeTo construct multi megabase contiguitySLR methods require genomic DNAgDNAfragments rtKbbut obtaining long gDNA fragments is challenging and this limits current SLR methodsArima Genomics has repurposed HiC technology as an SLR based DNA preparation kit that preserves chromosome span contiguity and haplotype phasing that is short read compatibleArima key technical innovation israther than using purified gDNAour method leverages the long contiguity information preserved naturally in thedimensionalDorganization of genomes in cellsasD information is long range informationBy capturingD genome informationArima s Contigo kit reconstructs chromosome span informationThe Contigo kit from Arima therefore has complete contiguity with short read economyThe Contigo kit is affordabledoes not require esoteric reagentsadditional skills or equipmentand is compatible with exiting short read workflowsto offer easy user adoptionIn additionContigo is the only kit to preserveD genomic information essential to interpreting non coding functional genomicsThe Contigo kit has the potential to serve as a new standard in next generation sequencing with broad applications in genotypingphasingallele specific gene expression and epigenetics on phased genomesstructural variation analysesmetagenomics andD genomicsIn this proposal we will commercialize the Contigo technology by improving sensitivity to wide range of cell inputs and uniformity in genome coverageand enablingwell compatibilityIn additionwe will design for manufacturereduce cost and improve sourcingassure robust performance in real world shipping and storage conditionsimprove user experienceand finallybenchmark performance of the Contigo kit with domain expertskey opinion leadersand power users to demonstrate commercial viability