Chris Boles is Chief Scientific Officer of Sage Science, where he’s been helping the R&D team develop the new SageHLS (that’s short for HMW Library System), a platform designed to rapidly purify high molecular weight DNA directly from samples. We caught up with him to learn more about it.
Q: What’s so important about having high molecular weight DNA?
A: Working with extremely long DNA has become a lost art in the life science community. Back in the early days of the Human Genome Project, every lab had to think about this as they worked with recombinant BACs, fosmids, Southern blots, and so on. But beginning with PCR in the early ’90s and continuing with short-read NGS since the early 2000s, life scientists have had the tools to do amazing things without the need for HMW DNA. Now, researchers are tackling repetitive genomic regions, long-range structural variation, and long-range phasing, and the need for high-quality, high molecular weight DNA has resurfaced.
Q: What are some of the long-range technologies that the SageHLS platform could be used with?
A: Really any system that requires DNA that is hundreds of kilobases to megabases in size. These include long-read sequencing platforms like PacBio or Oxford Nanopore, optical mapping technologies such as those from Bionano Genomics or Genomic Vision, and other long-range linkage analysis methods like the ones from 10x Genomics or Dovetail Genomics. The SageHLS can improve input DNA quality and size for all of these systems.
Q: What kind of sample prep is required before loading the SageHLS?
A: In general, very little. We have focused initially on sample types that 1) are important for biomedical research, and 2) work well in SageHLS. These include white blood cells from whole blood, tissue culture cells, or bacterial cultures. For these sample types, only a few brief centrifugation steps are necessary to wash the cells and resuspend them in an isotonic gel loading buffer. The cassette reagents do the hard work of lysis and purification without mixing or shearing the HMW DNA.
Q: How does the new system work?
A: Users load their samples into a gel. Then the platform automatically performs cell lysis and contaminant removal. This happens very quickly, leaving megabase-sized DNA stuck in the agarose. Next, the DNA is lightly cleaved with a non-specific nuclease and retrieved from the gel through an automated elution process.
Q: What kind of results have you gotten from the SageHLS internally?
A: From mammalian WBC and tissue culture cells, we routinely obtain DNA ranging in size from 200 kilobases to 2 megabases. From input cell loads containing about 10 ug of DNA (about 1.5 million human cells), we recover 1 to 3 ug of DNA of this size, which is sufficient for even DNA-hungry applications like optical mapping.
Q: You’re already working on new uses for the SageHLS platform. Can you give us a sneak peek?
A: There are several improvements that should happen fairly quickly after launch. Next up is a process we call HLS-CATCH, which uses CRISPR/Cas9 technology to excise and isolate a genomic fragment of interest in a targeted fashion. We’re also working on several methods for making NGS libraries directly in the HLS cassettes so that we can integrate DNA extraction directly with NGS library construction. It will be interesting to learn from customers what else they want to do with the system.