SBIR Phase I Award for development of Novel Genomic Technology
GENOMEWEB ARTICLE ON CLARETBIO-SINGULAR GENOMICS CO-MARKETING PARTNERSHIP
UC Santa Cruz Spinout ClaretBio Pursues NGS Sample Prep Market With Focus on cfDNA, FFPE
The firm is commercializing technology to analyze degraded DNA developed by the paleogenomics lab at the University of California, Santa Cruz.
GENOMEWEB ARTICLE ON NHGRI AWARD AND CLARETBIO PRODUCTS
UC Santa Cruz Spinout ClaretBio Pursues NGS Sample Prep Market With Focus on cfDNA, FFPE
The firm is commercializing technology to analyze degraded DNA developed by the paleogenomics lab at the University of California, Santa Cruz.
NHGRI SBIR Phase I Award
XACTLY Methodology Publication
Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5′ and 3′) of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80–90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
We are hiring > Computational Biologist
SRSLY Methodology Publication
Background
Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.
Results
Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.
Conclusions
SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
