Nabsys, a DNA technology startup, showed off today its solid-state gene sequencing machine at the Advances in Genome Biology and Technology conference in Marco Island, Florida. The company says that later this year it will begin selling its machine, which will allow researchers to determine the structural organization of long stretches of DNA. This differs from most existing sequencing methods, which read DNA in short snippets that are later stitched together by software. The new system will, at first, complement existing methods, but it could eventually offer cheaper and faster sequencing than other approaches.
Groups such as Oxford Nanopore (see “Nanopore Sequencing”), which introduced its technology a year ago at the same conference, and Gundlach’s lab are developing nanopore technologies as another method for getting long sequences, but so far no nanopore technology has made it to the market. These systems use a biological pore as the site of DNA analysis, which limits the speed at which DNA can be read.
Nabsys’s technology also passes DNA through a pore, but instead of the protein pore approach that Oxford Nanopore and others are taking, Nabsys uses a pore cut into a solid-state chip. According to the journal Biotechniques, Oxford Nanopore’s system can process DNA at a maximum rate of 400 bases per second. Nabsys claims its system can read up to a million nucleotides per second. Such speed could be critical in clinical settings, where fast diagnoses are needed to make treatment choices.
Because of the highly repetitive nature of human DNA and the relatively short length scales over which DNA sequencing platforms obtain information, assembling the data produced by these platforms is computationally intensive and results in contig lengths that are very short compared to the lengths of chromosomes. Complete genomes typically have required additional finishing to unambiguously place repeated or difficult regions. In contrast, Positional Sequencing as developed by Nabsys using nanoscale detectors and specific hybridization
probes will provide information over hundreds of kilobases and even megabases of contiguous sequence. Specifically, the platform locates, with sub-diffraction- limit resolution, the positions of oligonucleotide probes that have bound to long DNA fragments. This information can be assembled into contigs whose lengths approach the lengths of chromosomes. This information can used to automatically finish sequencing projects as well as correct misassemblies.
The limitations of short read sequencing are becoming more and more recognized. Long range sequence information such as that offered by Nabsys Positional Sequencing is essential for full genomic analysis. We have demonstrated a complementary relationship between short read sequencing and Nabsys mapping. The combination of these two low cost technologies produces sequence quality surpassing that of current standard practices.
We have demonstrated the ability to place short read contigs on a genome wide scaffold. This type of information is useful for discovering clinically relevant structural variants. We have also demonstrated the ability to detect and correct misassemblies in short read de novo sequence. These improvements point the way to a regime in which sequencing is not only fast and cheap but also correct and complete.
ABSTRACT – Even prior to the introduction of capillary DNA sequencers, nanopores were discussed as a low-cost, high-throughput substrate for sequencing. Since then, other next-generation sequencing technologies have been developed and achieved widespread use, but nanopores have lagged behind due to difficulties in generating usable sequence data. The practical and theoretical issues of translocation speed and signal detection encountered when attempting to sequence DNA with nanopores are discussed. Various methods that different laboratories have used to overcome difficulties in biologically based and solid-state nanopores are also presented. Different approaches designed to circumvent the overriding issue of detecting signals from individual bases in a time-resolved manner in nanopores are described. For example, genomic positional sequencing utilizes hybridization of short oligonucleotide probes to very long DNA templates and then detects these probes by variations in current blockade in solid-state nanodetectors. The positions of the probes relative to each other and relative to the ends of the DNA are determined by measuring the time between current blockade peaks. By assembling many such measurements, it is possible to overcome the problems encountered when attempting to sequence DNA at high speed in nanopores, providing the potential for true de novo sequencing of large genomes on a routine basis.