One area that's ripe for disruption is Next Generation Sequencing (a high throughput derivative of Sanger sequencing)
Illumina produces devices called sequencers, which are glorified microfluidics + imaging devices, which uses base pair chemistry to build the dna complementary strands of single stranded dna fragments one base by one using special dna bases that have washable fluorescent die and are blocking (so that the complementary strand grows by one base). Once the correct dna base is stuck to the single strands on the glass device, a picture of the glass device is taken by shining laser and using a CCD imager. The Nature of DNA makes sure that the correct complementary base gets stuck. 4 TIFF files are generated with billions of tiny dots one for each base A,C,G and T. The fluorescent die is washed, and the last added ddna base is deblocked and the cycle repeats. The whole software suite (image processing of TIFF files) and hardware specs (fluid chemistry, etc) is unfortunately closed source :(
I think it's more accurate to say that NGS is still in the midst of disrupting biology in general. Illumina has been consistently dropping sequencing prices for the last 7 years. Oxford Nanopore is a very promising technology as well that could completely disrupt the space.
I wouldn't say the the industry is ripe to be disrupted by software though. The cheapness of sequencing enables the development of new software for analysis, which in turn enables more sequencing.
The next frontier in NGS is long read SMRT (Single Molecule Real Time - PacBio) combined with Oxford Nanopore's technology. That is, very long reads combined with massively parallel transcription that doesn't rely on light emission. Illumina-based tech is not going to be part of the equation.
Illumina is really only related to traditional Sanger sequencing in that its sequencing by synthesis.
There is no way that this is going to be the case. It's much more likely to be a combination of Illumina and ONT or ONT alone. PacBio is far too expensive and low throughput to be a challenger outside of niche applications (like genome assembly).
I'm extremely skeptical that ONT's sequencing will become cost effective. Library preps for long range correlation + Illumina will likely dominate; why not get high fidelity + long range off the same instrument and reagents? Dovetail and 10X are two companies doing this right now.
That or a different nanopore tech. After all the time they've spent and the missed promises of ONT's CEO it doesn't look like the current generation will deliver.
I would much rather have ONT backed by Pacbio than ONT backed by Illumina. ONT is well suited for doing WES quickly, with better fidelity than Illumina and PacBio is much better for supplemental data to do genome assembly using reads from a short read system
What evidence do you have for ONT having better fidelity than Illumina in any application? Illumina's error rates are typically <= 1% while on "good" reads ONT has error rates cited at 15% and overall is even worse[1]. I agree that PacBio is better for genome assembly, but for many cases we do not need to do assembly. Resequencing workflows with alignment and variant calling are pretty good.
Comments
One area that's ripe for disruption is Next Generation Sequencing (a high throughput derivative of Sanger sequencing)
Illumina produces devices called sequencers, which are glorified microfluidics + imaging devices, which uses base pair chemistry to build the dna complementary strands of single stranded dna fragments one base by one using special dna bases that have washable fluorescent die and are blocking (so that the complementary strand grows by one base). Once the correct dna base is stuck to the single strands on the glass device, a picture of the glass device is taken by shining laser and using a CCD imager. The Nature of DNA makes sure that the correct complementary base gets stuck. 4 TIFF files are generated with billions of tiny dots one for each base A,C,G and T. The fluorescent die is washed, and the last added ddna base is deblocked and the cycle repeats. The whole software suite (image processing of TIFF files) and hardware specs (fluid chemistry, etc) is unfortunately closed source :(
I think it's more accurate to say that NGS is still in the midst of disrupting biology in general. Illumina has been consistently dropping sequencing prices for the last 7 years. Oxford Nanopore is a very promising technology as well that could completely disrupt the space.
I wouldn't say the the industry is ripe to be disrupted by software though. The cheapness of sequencing enables the development of new software for analysis, which in turn enables more sequencing.
The next frontier in NGS is long read SMRT (Single Molecule Real Time - PacBio) combined with Oxford Nanopore's technology. That is, very long reads combined with massively parallel transcription that doesn't rely on light emission. Illumina-based tech is not going to be part of the equation.
Illumina is really only related to traditional Sanger sequencing in that its sequencing by synthesis.
There is no way that this is going to be the case. It's much more likely to be a combination of Illumina and ONT or ONT alone. PacBio is far too expensive and low throughput to be a challenger outside of niche applications (like genome assembly).
I'm extremely skeptical that ONT's sequencing will become cost effective. Library preps for long range correlation + Illumina will likely dominate; why not get high fidelity + long range off the same instrument and reagents? Dovetail and 10X are two companies doing this right now.
That or a different nanopore tech. After all the time they've spent and the missed promises of ONT's CEO it doesn't look like the current generation will deliver.
I would much rather have ONT backed by Pacbio than ONT backed by Illumina. ONT is well suited for doing WES quickly, with better fidelity than Illumina and PacBio is much better for supplemental data to do genome assembly using reads from a short read system
What evidence do you have for ONT having better fidelity than Illumina in any application? Illumina's error rates are typically <= 1% while on "good" reads ONT has error rates cited at 15% and overall is even worse[1]. I agree that PacBio is better for genome assembly, but for many cases we do not need to do assembly. Resequencing workflows with alignment and variant calling are pretty good.
1. http://www.sciencedirect.com/science/article/pii/S2214753515...