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 Genomics 7. Project Summary/Abstract Over 90% of Next-Generation Sequencing (NGS) is sequenced via Illumina short-read sequencers. This is because of its cost-effectiveness and faster turn-around times. However, short-read sequencing technologies lose critical contiguity information and are limited in assembling genomes de novo and reconstructing maternal and paternal haplotypes of diploid genomes. Contiguity information is valuable for understanding the genetics of human health and disease, and therefore critical for advancing precision and personalized medicine. Long- read technologies (e.g. Pacific Biosciences) only reach megabase-scale chromosomal contiguity, but are 5-7X more expensive than Illumina short-read, limiting its use. Recent advances in DNA preparation can preserve long-range information that is compatible with Illumina short-read sequencing. These ?synthetic? long-reads (or SLR) methods can improve short-read technologies with, long-range contiguity and short-read economy. However, the maximal SLR contiguity is only 1-5% the contiguity a 100Mb average human chromosome. To construct multi-megabase contiguity, SLR methods require genomic DNA (gDNA) fragments >100-150Kb, but obtaining long gDNA fragments is challenging and this limits current SLR methods. Arima Genomics has repurposed HiC technology as an SLR-based DNA preparation kit that preserves chromosome-span contiguity and haplotype phasing that is short-read compatible. Arima key technical innovation is, rather than using purified gDNA, our method leverages the long-contiguity information preserved naturally in the 3-dimensional (3D) organization of genomes in cells, as 3D information is long-range information. By capturing 3D genome information, Arima's Contigo kit reconstructs chromosome-span information. The Contigo kit from Arima therefore has complete contiguity with short-read economy. The Contigo kit is affordable, does not require esoteric reagents, additional skills or equipment, and is compatible with exiting short-read workflows, to offer easy user adoption. In addition, Contigo is the only kit to preserve 3D genomic information essential to interpreting non-coding functional genomics. The Contigo kit has the potential to serve as a new standard in next-generation sequencing with broad applications in genotyping, phasing, allele-specific gene expression and epigenetics on phased genomes, structural variation analyses, metagenomics and 3D genomics. In this proposal we will commercialize the Contigo technology by improving sensitivity to wide range of cell-inputs and uniformity in genome coverage, and enabling 96-well compatibility. In addition, we will design for manufacture, reduce cost and improve sourcing, assure robust performance in real-world shipping and storage conditions, improve user-experience, and finally, benchmark performance of the Contigo kit with domain experts, key opinion leaders, and power users to demonstrate commercial viability.
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 Genomics 8. Project Narrative Next-generation short-read sequencing (e.g. Illumina) has advantages of price, speed, accuracy, and broad adoption. With short-read sequencing, however, a key principle in genomics is severely limited: contiguity, a measure of fully-linked DNA sequence. Contiguity in the context of haplotype phasing and de novo assembly is critical for genomic medicine. Several companies have attempted to improve contiguity with long-read or synthetic long-read technologies by increasing read-length, or bar-coding, or reconstituting artificial chromatin. These methods are limited to 1-5% of the actual contiguity of a human chromosome, require specialized and expensive equipment, and are technically demanding. Arima has overcome these deficiencies with our easy- to-use and inexpensive Contigo DNA preparation kit that applies an improved HiC technology to achieve chromosome-span contiguity at a fraction of price of competing technologies and as a result the Contigo kit maximizes contiguity, convenience, and economy with compatibility to Illumina workflows.
