In the genetics department at Albert Einstein College of Medicine, Research Assistant Professor Alex Maslov is working to understand structural variants associated with aging and cancer. Using human and mouse cells, he deploys whole genome sequencing to make these links. In one current project, his lab is investigating whether chemotherapy causes somatic mutations in non-tumor tissue. For these studies, his team relies on Pippin automated DNA sizing instruments from Sage Science.
Maslov began with Pippin Prep, which he uses primarily for library preparation before Ion Torrent sequencing. “We were extremely happy with it because it’s very precise and reproducible, and doesn’t take much effort,” he says. But between his lab and the core facility led by Shahina Maqbool, demand quickly surpassed the Pippin Prep’s capacity.
That’s when Maslov got his PippinHT. In addition to solving the capacity issue, he says, the PippinHT delivers results more quickly, taking just 20 minutes per run. Reproducibility of sizing is very important to Maslov, who uses split reads to detect structural variants in Ion Torrent data. Any variability between samples changes the sensitivity of structural variant detection and makes results less reliable. “What we like about PippinHT is that it’s extremely reproducible. All 12 samples come out as identical,” he says. “When you do size selection on a gel, you can never do it precisely from one sample to another.”
The PippinHT was installed at the core lab, where it’s used by other scientists for Illumina sequencing, both for DNA and RNA projects. “For RNA library preparation, it’s even more critical,” says Maslov. “They need to distinguish library fragments from adapter-dimers, and in the case of microRNAs, the difference might only be 20 base pairs.”
Bringing in either Pippin instrument is an investment, but Maslov says that ultimately the tools help scientists save money. “With Ion Torrent, if you use fragments that are too small, you’re not getting the full output of sequencing. If you use fragments that are too long, you can lose whole runs,” he says. These kinds of mistakes in size selection can be quite costly, but they can be avoided with precise, automated sizing. “My advice to other scientists is: do not hesitate,” Maslov says. “Pippin works.”