PacBio Users: Size Selection Is Essential for Generating Excellent Results

The Sage Science team was delighted to attend and co-sponsor PacBio’s annual East Coast user group meeting in Baltimore last week, particularly since there was a half-day session devoted to our favorite subject: sample prep.

There were plenty of customer presentations during the sample prep workshop, and it was great to see so many PacBio users deploying BluePippin, PippinHT, or SageELF in their sequencing workflows. Melissa Laird Smith from the Icahn School of Medicine at Mount Sinai may have put it best when she told attendees that the two most important components for PacBio sample prep are upfront quality control and size selection. The QC step, of course, evaluates sample quality and quantity to ensure that long-read sequencing is viable. Size selection allows users to really make use of their PacBio platforms by eliminating shorter fragments and letting the sequencer focus on the longest fragments available. Those are often used as seed reads to anchor assemblies, making them critical for achieving optimal contiguity. Smith said her team uses BluePippin or PippinHT to select either 10 kb – 50 kb or 20 kb – 50 kb ranges, depending on the sample.

Sonny Mark, a field application scientist manager at PacBio, also took the opportunity to introduce attendees to the SageHLS extraction and purification instrument we launched earlier this year. Designed expressly for the kind of high molecular weight DNA that single-molecule systems require, the SageHLS platform should be a nice fit for long-read sequencing pipelines. Users simply load their samples (up to four at a time) and the instrument extracts or purifies DNA fragments as long as 2 Mb. The fragments are automatically sorted by size into six collection bins. We anticipate that this product will work well for scientists studying structural rearrangements, copy number variation, haplotype phasing, and other applications for which HMW DNA is advantageous.

During the rest of the user group meeting, we thoroughly enjoyed learning about so many impressive results users have generated with their PacBio systems, from reference-grade genome assemblies to in-depth annotations. Congratulations to everyone who contributed!

This entry was posted in Blog and tagged , , , , . Bookmark the permalink.

Comments are closed.