Sequencing

Targeted RNA Sequencing Approaches

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Happiness is getting more of what you want, in RNA-Seq as in other things...
Happiness is getting more of what you want, in RNA-Seq as in other things…

There are several commercial methods for looking at 10’s or 100’s of gene expression levels via a high throughput TaqMan™ assay from Life Technologies / Thermo Fisher Scientific, a competitive offering from Roche, Douglas Scientific, or also Fluidigm. The limitation of these technologies however is the amount of multiplexing a single assay in a given volume, which regardless of the amount of miniaturization does limit the samples by genes evaluated throughput.

To perform RNA-Seq, one looks at all the particular RNA species present, dependent upon the up-front sample preparation. (To clarify, a miRNA experiment would purify small RNAs then go into cDNA synthesis and sequencing; mature polyA+ RNA can be purified and then cDNA made and sequenced etc.) But what about a targeted set of expressed genes to evaluate via NGS?

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Oxford Nanopore at AGBT 2014

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Borrowed from a Oxford Nanopore Video (without permission)
Borrowed from a Oxford Nanopore Video

A few attending the Advances in Genome Biology and Technology meeting in Marco Island Florida (February 12 – 15 2014) have blogged about a presentation from David Jaffe (Broad Institute), presenting the first data the next-generation sequencing community has publicly seen from Oxford Nanopore Technologies. For those not familiar with Oxford Nanopore (or ONT as I’ll refer to them), it was AGBT12 that they absolutely stunned the crowd in attendance with their announcements of both a GridION™ nanopore sequencing ‘module’, and a MinION™ USB-stick portable DNA sequencer that got a lot of press. They planned to commercialize ‘by the end of the year’ (that is, 2012), and since I was not there ‘in’ the meeting first-hand (I was supporting the meeting on-site at Marco Island for Life Technologies, just not as a conference attendee), I heard first-hand from several that year with interest.

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FDA Approval for the MiSeq

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For Research Use OnlyCongratulations are in order to the US Food and Drug Administration for approving the Illumina MiSeqDx™ system,  including two Cystic Fibrosis assays, and two additional approvals for the platform (the instrument and the reagents). This is the first next-generation sequencer approved by the FDA, an important milestone reflecting a sea-change in how genetics and genomics is revolutionizing healthcare. The genetics revolution has been taking place for some time now – here’s a handy FDA table of over 200 pharmacogenomic biomarkers in drug labeling – but with the advent of NGS the ability to determine multiple biomarker genes via a simple electronic query is only one of several promising applications with direct clinical impact and utility.

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Personal Genomics and the Future of Healthcare

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“The future is already here – it is just not very evenly distributed.” William Gibson, author of Neuromancer and the person who coined the term ‘cyberspace’. Way back in 2006 or so when I was working for Illumina, the personal genetics firm 23andMe launched their whole-genome genotyping service (called ‘Genetic Testing for Health, Disease and Ancestry’ … Read more

Update from BioNano Genomics at #ASHG2013

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BioNanoGenomics' chip, shown at ASHG Boston 2013
BioNanoGenomics‘ chip, shown at ASHG Boston 2013

Almost a year ago I wrote up this post about a startup called BioNano Genomics, which was hard at work launching a nanofluidic device and scanner called the Irys™. At February’s AGBT meeting in Marco Island (FL), they presented a scientific poster about the spider mite genome. Tetranychus urticae has a lot of interesting features, including being an important agricultural pest. Now I don’t have anything against entomology per-se, it is just that the capacity of a genetic analysis system will need to look at humans (at 3 gigabases for the haploid genome), rather than insects (T. urticae is on the order of 90 megabases, and today I learn that it is the smallest arthropod genome sequenced to-date).

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Next-Generation Sequencer GnuBIO

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GnuBIO next generation sequencer
The GnuBIO’s new sequencer at ASHG

There are two next-generation sequencing ‘platforms’ (i.e. systems) that are being prepared for commercial launch; one from QIAGEN (that I wrote about here and I was told at ASHG that they working hard to launch it in 2014), and another from GnuBIO. This technology came out of the same laboratory that RainDance Technologies’ emulsion droplets came out of (David Weitz’ ‘squishy physics’ laboratory), and it applies the microfluidic principle to sequencing chemistry on a picoliter scale.

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