PacBio: Long Read Sequencing Capability for Whole Genome Sequencing

Abstract

The advancement in cameras and computation ability has allowed the sequencing industry to make revolutionary progress. One of the latest sequencing technologies, called “Third generation sequencing”, relies on the reading of long, continuous fragments of DNA. The long, continuous sequencing of DNA fragments allows for less reliance on post-sequencing analytics and fewer restrictions when identifying difficult-to-assemble regions of the genome. In order to optimize the workflow and make the technology available for research efforts, The Broad Institute’s Genomics Platform added ‘Long Read’ Sequencing to its repertoire of genomic services. Pacific Biosciences released the Sequel II instrument in early 2019 along with a higher output protocol and sequencing chip (8M SMRT Cell) that was reported to produce up to 8 times as much data as the original Sequel I instrument. The new workflow claimed to provide higher output, Q50 accuracy, uniform coverage, and a reduction in GC bias content. This claim was tested by comparing this new instrumentation to the previous Pacific Biosciences version as well as a second-generation sequencing equivalent. Size selection and fragmentation optimizations, as well as other process improvements were undertaken to optimize the lab workflow. Ultimately, it was found that new product is faster and simply more cost-effective than its previous version. With the sinking costs and increased output, it was found to be feasible to move the Pacific Biosciences technology into a more mainstream whole human genome application, which provides an innovative way to identify genomic error, such as variants and mutations, within the population.