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NextSeq Opens the Door to True Systems Biology Experiments

Abizar Lakdawalla, Ph.D.
| Jan 17, 2014

The introduction of the NextSeq 500 next-generation DNA sequencer expands the overall utility of NGS by providing a unique combination of price, throughput and accuracy to address a whole slew of experiments that were difficult to do before, due to either the high cost of generating data or needing enough samples to commit to a high output run. The NextSeq 500 with 120 Gb of fills a gap between the 15 Gb output of a MiSeq and the 1800 Gb output of HiSeq XTen.

The ability to sequence about 400 million clones in a single run on the NextSeq (think the human genome project sequenced less than 40 M clones) at a cost of a few thousand dollars, allows us to do experiments that were out of reach before.

The spectrum of applications that can be performed on the different Illumina sequencers is shown in the table below. The table compares the specifications of the sequencers and provides the approximate number of samples that can be sequenced on a single run for different applications. MiSeq and NextSeq provide the option of lower output runs, which are not shown in the table below.

The 400 M single reads (800 M paired read) capability on NextSeq enables sequencing  in a single run about 16 full exomes, gene expression profiling on about 20 samples or comprehensive ChIP-Seq analysis. It becomes easier to take a systems biology approach, for example to evaluate the impact of genomic variation on transcriptional factor binding and gene expression (Figure 1).

The effect of a gene knockout or knockdown can also be studied by sequence the coding and non-coding transcriptome to detect gene expression changes, differences in splicing isoforms, and potentially fusion events to enunciate on- and off-target effects of the knockdown.

Similarly, by NextSeq sequencing  of the mRNA and microRNA associated with the Argonaute complex (CLIP-Seq) and comparing this data with sequence data of RNA that is in the process of being translated (RiboSeq) would provide an effective overview of the mRNA undergoing cleavage as well as the impact of the siRNA on protein synthesis. More than enough data to get started on a compelling Ph.D. thesis.

Access to a box like the NextSeq during my academic days would have been a godsend. I would have been able to replace the large number of denaturing gradient gels and blots, arrays, real-time PCR and capillary electrophoresis-based sequencing with a few NextSeq runs. Progress!