Is it really possible to detect somatic structural variants accurately from a single sequencing read? A new protocol from scientists at the Albert Einstein College of Medicine in New York and Voronezh State University in Russia was designed to do just that.
In the Nature Methods paper entitled “Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing,” lead author Wilber Quispe-Tintaya, senior author Alexander Maslov, and collaborators describe a method called Structural Variant Search (SVS).
“The key feature of SVS is its ability to definitively call [a structural variant] using a single sequencing read that spans the breakpoint, without the need for multiple supporting reads,” the scientists report. The workflow relies on preparing a chimera-free library and on a new algorithm that calls structural variants without using consensus data. The variant caller uses a split-read method for identifying potential structural variants, filters out artifacts, and then separates somatic from germline variants.
They demonstrate the workflow on a cell line known to harbor integration events from human papillomavirus. SVS called 20 integration sites; 17 had previously been reported, and two of the three novel findings were confirmed by PCR testing. “Most likely these two HPV integration sites had not been detected previously because of their low abundance, underscoring the unique capability of SVS to detect low-frequency [structural variants],” the authors note.
The team’s library prep procedure included size-selection on a PippinHT instrument, after which the samples were sequenced using the Ion Torrent Proton platform.