A recently shared preprint demonstrates the effectiveness of size-selection for nanopore sequencing, relying on the PippinHT automated DNA sizing platform for high-throughput pipelines.
“Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing” comes from lead author Mircea Cretu Stancu and collaborators at University Medical Center Utrecht, the University of Torino, and other institutions. In it, the scientists report results from using an Oxford Nanopore MinION to sequence the genomes of two patients with congenital abnormalities, with a focus on structural variant (SV) detection. “Long-read sequencing is breaking ground for the discovery of SVs at an unprecedented scale and depth,” they write. The team used the PippinHT system to size-select DNA libraries for the second patient prior to sequencing.
The effort, which produced the first known whole human diploid genome assemblies using the MinION, was a success. “We were able to extract all known de novo breakpoint junctions for Patient1, even at relatively low coverage,” the scientists report. For the second patient, the sequence data revealed more complexity for many breakpoint junctions. “We observed that 33.3% of the high confidence set of SVs observed in the Nanopore data could not be found in matching Illumina sequencing data, despite the use of six different variant calling methods,” they add.
The authors note that “these results highlight the feasibility to sequence clinical human samples in real-time on a low-cost device.”