BluePippin users are generating longer reads from their Oxford Nanopore MinION sequencers, as demonstrated in a new app note from our colleagues at Nippon Genetics. The app note showcases a workflow used by Kazuharu Arakawa, an associate professor in the Institute for Advanced Biosciences at Keio University in Japan.
The app note describes an experiment performed on DNA extracted from the leg of a golden silk spider. Sample prep included size-selection with a BluePippin instrument to remove the shorter library fragments that would otherwise limit the amount of data produced by the MinION nanopore sequencer. As the app note points out, this step must be handled prior to library prep, during which electrophoresis-sensitive tethers are added.
According to Dr. Arakawa, “Size selection using BluePippin allowed us to remove short reads and perform effective sequence of long-chain DNA fragments, compared to using samples not size selected.”
If you’re in the Boston area, don’t miss this Friday’s one-day symposium on genomics and computational biology at the Broad Institute. Organized by the Genomic Exchange Community, this geXc (pronounced “jexy”) event will bring together speakers from academia and industry to offer updates on everything from the microbiome and data analysis to genome modeling and population studies.
Sage is proud to be a sponsor of geXc Boston. Our own Jun Zhou, a senior scientist, will be giving a talk about using the HLS-CATCH method for targeted, long-range sequencing of large genomic elements. The event is free to attend and includes giveaways of an Oxford Nanopore MinION and an Apple Watch. We hope to see you there!
Conference season is going strong. Next on our list: the annual meeting of the Association of Biomolecular Resource Facilities in Myrtle Beach, S.C. We never miss this conference — it’s a great event for tech-loving life science people like us. ABRF brings together hundreds of core lab managers from around the world to share novel protocols, results of instrument bake-offs, and best practices.
At ABRF, scientists offer a different perspective on tools than we get from individual researchers. Core labs have to run technologies at near-industrial capacity, with tons of effort going toward nailing down workflows and automation for the most consistent, reliable results possible. Many of the great advances in our area of interest, NGS sample prep, have come from the dedicated and methodical core lab scientists in this community. At this year’s conference, we’ll be attending many sessions in the genomics track, which will include presentations on single-cell sequencing, clinical NGS, CRISPR, and bioinformatics.
We’re also looking forward to the high-level talks. Amos Bairoch from the Swiss Institute of Bioinformatics will be honored with the 2018 ABRF Award Lecture for Outstanding Contributions to Biomolecular Technologies, a talk that promises to cover highlights from a remarkable career in protein analysis. There will be an interesting opening keynote address from Howard McLeod of the Moffitt Cancer Center entitled “Precision Medicine: Nice Start, But A Long Way to Go.”
If you’ll be attending ABRF, please stop by booth #103 in the exhibit hall to visit the Sage team. We’d be happy to learn about your core lab and help you determine whether our automated DNA size selection instruments could be of assistance. And don’t miss poster #128, “Faster DNA Size-Selection for Long-Read Sequencing,” for a sneak peek at the new High-Pass Plus cassette for shorter run times and larger input samples on our BluePippin system.
Long-read sequencing is steadily gaining traction as scientists realize its value for resolving regions of the genome that are intractable with short-read methods. From structural variants to repetitive or GC-rich regions, many clinically important stretches of the human genome just aren’t a good fit for traditional Illumina or Ion Torrent platforms.
That’s why we’re really pleased that The Jackson Laboratory for Genomic Medicine is hosting a new Long-Read Sequencing Workshop next week to help scientists understand protocols and strategies for using these tools. Held at the Farmington, Conn., location, the event features a who’s who of long-read pioneers presenting tutorial information about genome assembly, structural variant identification, variant phasing, and more. Attendees will also hear from scientists at PacBio, 10x Genomics, and other leading players in long-read and long-range technologies.
Long-read platforms offer unique sample preparation challenges, and our automated DNA size selection instruments have become a crowd favorite for maximizing the read lengths they generate. Sage is a proud sponsor of the workshop, and our CSO Chris Boles will also be giving a talk about Cas9-assisted sample prep strategies for long-read sequencing. We’re particularly looking forward to touring the new sequencing center and research facility.
We hope to see you there!
There’s a great new podcast interview with Stanford clinical geneticist and oncologist Hanlee Ji about targeting extremely large stretches of DNA by combining CRISPR methods, automated DNA purification with the SageHLS instrument, and 10x Genomics technology. The approach works with minute amounts of DNA, far less than is needed for long-read sequencing platforms, but can still resolve large and complex structural variations. (For readers who want a deeper dive, his lab also posted slides from an AGBT presentation of this work.)
As Ji described it, the method targets sub-megabase regions — as long as about 500 Kb — and his team has validated it with the BRCA1 gene, the MHC locus, and other examples. By getting large, intact DNA molecules, scientists can delineate structural variants, rearrangements, and more. The long-range information generated “would have been impossible” using short-read sequencing technology that requires fragmenting these large molecules, Ji noted. The protocol also makes it feasible to enrich for tumor DNA or other types of DNA that might get drowned out by normal DNA. “Our approach represents a solution to be able to pull that out, tease that information out, even when you have these complex mixtures and your event of interest is underrepresented compared to the normal genome,” he said.
Such information is clinically useful for everything from cancer to schizophrenia. As Ji pointed out, this method is a strong alternative to the FISH technology typically used for pediatric congenital disorders, finding somatic rearrangements in cancer, and more. His team’s work offers higher resolution and potentially lower cost to generate clinically relevant results.
The interview wraps up with a segment about precision medicine and its most promising applications in the oncology realm. Ji said he is particularly excited about personalized cancer vaccines and immunotherapy, and he stressed the importance of enrolling more patients in clinical trials. He also urged cancer centers to bank more samples than they do now, noting that samples considered unsuitable for use now could one day become important sources for population studies as technology continues to improve.