Mapping Eukaryotic Genomes Using Solid-State, Electronic Nanodetectors
February 21, 2014
Short-read sequencing has been plagued with difficulties in assembling complex genomes due to the highly repetitive and non-random nature of most DNA sequences. Most genomes are aligned to a reference rather than assembled de novo because extreme methodological measures are needed for even the simplest prokaryotic genomes. As different technologies have moved read lengths from hundreds of bases into the range of several kilobases, true de novoassembly for microbial genomes has become more feasible though even reads of 10 kb are not sufficient for some species. Eukaryotic genomes are even more complex and riddled with extensive repeats that make routine de novo assembly an impossibility with short reads, even up to 20 kb.
In order to span the more extensive repeats present in eukaryotes, much longer read lengths are necessary. Solid-state, electronic nanodetectors can generate the information needed with mapping information from single molecules of hundreds of kilobases. DNA is translocated through nanochannels at more than 1,000,000 bp/sec and detected electronically. These molecules can be tagged at specific locations and those locations mapped at much higher resolution than is possible with optical methods. Reads are mapped with high efficiency and used to generate accurate reference maps for eukaryotic genomes. Examples of assemblies generated with a few hours of data collection will be shown. Currently, the instrument has 8 modules, each with a single nanodetector chip. The technology is highly scalable with the potential for much higher throughput by placing multiple detectors on each semiconductor-based chip, making analysis of large, complex genomes like human and plants feasible in the future.