Long-Range Genomic Analysis

After a decade of DNA genomic sequencing being restricted to short reads, new technologies are making it possible for scientists to capture long-range genetic information that is too large to detect in small sequencing fragments. Capturing these larger DNA snippets facilitates the discovery and detection of clinically important elements such as structural variants, characterization of complex regions marked by repetitive DNA, and phasing of distant variants.

A number of long-range platforms exist, including single-molecule sequencing as well as optical mapping and other scaffolding approaches. All of these platforms share one common feature: the need for extremely large DNA fragments.

Unfortunately, many biology labs have long forgotten the methods for working with high molecular weight (HMW) DNA. After ten years of needing fragments of just a few hundred bases, few scientists know how to handle and process megabase-sized fragments.

The New SageHLS Platform for HMW DNA Extraction

That’s why Sage Science has released the new SageHLS platform. The HLS stands for HMW Library System. This automated sample prep device produces ultra-long DNA fragments to enable long-range genomic analysis. The SageHLS instrument relies on electrophoresis to isolate DNA from cells, generating fragments as long as 2 Mb. It can also be used with Cas9 and guide RNAs to purify whole genes of interest.

How does the SageHLS platform work?

1. Load cell suspensions, tissue samples, or bacterial cultures into specialized gel cassettes.
2. The SageHLS lyses the cells and applies electrophoresis to remove everything but the intact DNA.
3. The system incorporates an enzyme to lightly cleave the DNA into fragments that can move through the gel, and those fragments are sized and collected in six bins.

The result: Consistent collection of DNA fragments ranging from 200 Kb to 2 Mb. The SageHLS platform can yield up to 3 µg of DNA from input loads of about 10 µg of DNA, or about 1.5 million human cells.

DNA of this size and quantity is ideal for long-range genomics applications (including sequencing systems from PacBio and Oxford Nanopore), long-range linkage analysis approaches (such as Dovetail Genomics and 10x Genomics), and optical mapping methods (like Genomic Vision and Bionano Genomics).

Currently, scientists use the SageHLS platform with CATCH (Cas9-Assisted Targeting of Chromosome Segments) to purify whole genes. See results of experiments with E. coli genes and the human BRCA1 gene in this AGBT poster.

To learn more, check out the Sage Science website.

Further reading:

Q&A: How SageHLS Brings Back the ‘Lost Art’ of HMW DNA Prep