A new review in Nucleic Acids Research offers a sweeping look at human sequencing applications for SMRT Sequencing, finding that “[t]he myth that SMRT sequencing is too error prone … is being expunged and replaced by evidence that it offers advantages over short-read sequencers.”
The authors conclude with a prediction about the ultimate potential for SMRT Sequencing and other “third-generation” platforms: “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 to study a variety of clinically relevant conditions ranging from cancer to Mendelian disorders 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 … 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,” the authors continue.
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. “Unfortunately, sequencing those DNA elements is difficult with short-read platforms because the reads are too short to span most tandem repeats,” the scientists note, indicating that in the future SMRT Sequencing can be used to replace more “labour intensive and inaccurate methods” such as Southern blots for such applications. They also cover examples such as distinguishing pseudogenes, needed for CYP2D6 analysis for drug metabolism studies; identifying fusion genes relevant to therapy selection in cancer samples; 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 use in human sequencing applications. 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.”
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