Nanopore sequencing detects structural variants in cancer

BioRxiv : the Preprint Server for Biology
Alexis L NorrisWinston Timp

Abstract

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrat...Continue Reading

Related Concepts

SMAD4
Tumor Suppressor Genes
Membrane
Pancreatic Carcinoma
Cyclin-Dependent Kinase Inhibitor p16
Synaptic Vesicles
Malignant Neoplasm of Pancreas
Gene Deletion
Nucleic Acid Sequencing
Particle Count and Size Analyzer

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