Review: SMRT Sequencing ‘Is Revolutionizing’ Clinical Applications
Wednesday, February 7, 2018
A new review in Nucleic Acids Research offers a sweeping look at clinical uses for SMRT Sequencing, concluding:
“The myth that SMRT sequencing is too error prone to be diagnostically useful is being expunged and replaced by evidence that it offers advantages over short-read sequencers.”
The authors continued, “Just as second-generation platforms stepped beyond Sanger sequencing and enabled a revolution in genomics medicine, third-generation single molecule sequencing platforms will likely be the next genetic diagnostic revolution.”
“Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics” written by Simon Ardui, Joris Vermeesch, and Matthew Hestand at KU Leuven and Adam Ameur at Uppsala University, offers a great overview of how SMRT Sequencing is being used in clinically relevant applications ranging from cancer to reproductive medicine and more. The paper notes that SMRT Sequencing offers tremendous benefits because it resolves many problems with short-read platforms — “limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles.” In addition, SMRT Sequencing has “higher consensus accuracies and can detect epigenetic modifications from native DNA,” Ardui et al write.
“SMRT sequencing is opening up new diagnostic avenues, such as the ability to determine tandem repeat lengths, interruptions, and even epigenetics in a single test at base pair resolution,” the scientists report. “Long read sequencing is already considered the gold standard for some applications, such as for HLA genotyping for tissue transplants.”
The review walks through many of those applications, offering prominent examples for each. Resolving tandem repeats, for example, is already important for Fragile X syndrome, spinocerebellar ataxia, and other repeat expansion disorders. “Replacing Southern Blots with faster and more direct SMRT sequencing will greatly enhance … repeat disorder diagnostics,” the scientists note. They also cover examples such as distinguishing pseudogenes, needed for CYP2D6 analysis for drug metabolism studies; identifying fusion genes to guide therapy selection for cancer patients; and infectious disease analysis; among many others.
Looking ahead, the review cites data indicating that whole transcriptome and whole genome sequencing on the PacBio system will soon see regular clinical utility. Regarding the Iso-Seq method, “as costs drop and throughput increases, unbiased PacBio expression and isoform detection will become routine in the near future,” the scientists write. They also note that “SMRT sequencing is greatly expanding the utility of WGS, permitting a factor greater in assembly completeness … even nearing reference genome contig sizes and including diploid aware assemblies.”