Standardized Comparison of Different DNA Sequencing Platforms

Abstract

Next-generation sequencing (NGS) has largely been implemented for clinical testing in many laboratories and offers a wide variety of applications ranging from targeted oncology panels to metagenomic sequencing for bacterial classification to population-based whole genome sequencing. Most laboratories operate NGS platforms that use short-read (SR) sequencing chemistry that sequences short fragments of DNA (reads) that are up to a few hundreds of base pairs in length. The reads are then reassembled to a reference genome assembly to detect genetic alterations such as single nucleotide variations (SNVs) or insertion/deletions (INDELs). Third-generation sequencing technology has emerged that sequences long reads (LR) that are several thousands of base pairs in length that can also detect larger structural alterations (e.g., translocations, inversions, duplications). An advantage of LR sequencing is the ability to resolve difficult-to-sequence regions of the genome where large stretches of repetitive sequences are present that can be challenging to align to the correct portion of the reference genome. A large comprehensive comparison of SR and LR technology, within the context of clinical laboratory testing, had not been undertaken until recently.

Topics & Concepts