GENERATION BIOTECH, LLC — Department of Health and Human Services SBIR Phase I: 172

Description

This project develops a platform independent target enrichment technology for the preparation of largekbDNA fragmentsThese are magnetically selected from genomic regions of interest and used directlywithout any intermediate amplification stepfor next generation sequencingNGSThis will allow the direct detection of methylated base information on several of the newer NGS systemsLarge DNA templates can currently be processed by several NGS platformsand even more powerful systems are being developedThe ability to utilize largecontiguous DNA segments as sequencing templates greatly assists in detecting and characterizing structural variantsobtaining accurate sequence information across complex and GC rich genomic lociconducting de novo sequence assemblyphasing long range haplotype informationand finding new or unexpected sequence elementssuch as viral integration sitesinversionsduplications and other types of chromosomal rearrangementsExisting methods for genomic enrichment are not able to provide a comprehensive characterization of complex genomic loci in an economical and flexible manner because they cannot provide the large size fragments that are required to successfully span confounding sequence elements and resolve persistent challenges at important lociWe will develop an efficient long read capture technology for small amounts of input DNA that resolves common sequencing and assembly problems that occur with most current amplificationor hybridizationbased enrichment technologiesThe benefits of this large fragment enrichment as carried out with capture primers with a very small footprintbaseswill extend to all types of NGS platformsincluding to those that rely on short read lengthsWe believe that we can significantly improve the ability of researchers and clinicians to obtain complete and accurate characterizations of complex genomic variations and regions of interest that are important for disease diagnosis and prognosis by NGSAnonymouspre existing samples for this project are provided by the NCI Over the past decadenext generation sequencingNGStechnology has transformed the field of geneticsenabling a better understanding of the genetic causes of diseaseThe application of this knowledge to companion diagnostics and companion therapeutics is now quickly transforming research and clinical practiceIn additionso called targeted DNA sequencing of selected genomic loci is more cost effective than whole genome sequencingWGSfacilitates higher sample throughput and optimized coverageeliminates ambiguities and improves accuracy by greatly reducing the complexity of the DNA to be sequencedCurrent methods for genomic targeting however remain a severely limiting factor for resolving complex genomic loci because they do not provide the large size fragments required to span confounding sequencesWe will fill this need with a large fragment enrichment methodRSEwhich will permit direct long read nextgeneration sequencing after enrichmentincluding the ability to detect methylation on several NGS systemsThis combination will significantly improve the ability of researchers and clinicians to obtain complete and accurate characterizations of complex genomic variations and regions in disease