Even Orlando’s sky-high humidity can’t get us down during a fast-paced AGBT meeting where size selection and HMW DNA have been front and center since the opening session.
Last night we enjoyed a plenary talk from Ami Bhatt, a scientist and clinician at Stanford who presented exciting data from studies of microbial communities, both in patient populations and in samples from the ocean floor. Her primary challenge, that metagenomics alone cannot link taxonomy to function, was largely addressed with a combination of 10x Genomics technology, size-selected HMW DNA, and a custom assembler from her lab called Athena designed specifically for de novo metagenomics. Read cloud sequencing, as the pipeline is known, outperformed other workflows and produced useful data that made it possible for Bhatt’s team to understand which microbes were in a sample and what they were doing. Preprints describing much of this work are available here and here.
Today, GiWon Shin from Stanford continued the emphasis on size selection and HMW DNA. A scientist in Hanjee Li’s lab, Shin presented a method developed for targeting nearly megabase-size regions for analysis with the 10x Genomics platform. Targeting is handled with customized Cas9 guides, and DNA extraction from intact cells is performed using the SageHLS instrument. Barcoding reads allows the scientists to phase and assemble data. Shin presented results from evaluations of this process targeting BRCA1, the MHC locus, and 38 candidate structural variants. The Sage team collaborated with the Li lab on this project for the HLS-CATCH method, and you can dive into the data on this page.
AGBT is still in full swing, and we can’t wait to hear more great science in the days to come! If you’re at the meeting, be sure to stop by suite #1765 to meet the Sage Science team and learn more about HLS-CATCH.