Gene Expression

Element Biosciences AVITI™ Sequencing System

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A new approach to next-generation sequencing, a little-known company unwraps an instrument that competes directly with the Illumina NextSeq 2000 with a third more of the throughput at half the consumables price For a technology that started in 2005 with the first 454 / Roche FLX next-generation sequencing (NGS) platform, followed in 2007 with the … Read more

The age of mRNA isoform discovery at #AGBT19

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Single-cell isoforms from long-reads take the stage at the Advances for Genome Biology and Technology, along with structural variation and better reference genomes. Underlying all these advances is better long-read technology from Pacific Biosciences and Oxford Nanopore. Thinking a little further about the overarching theme of this year’s Advances in Genome Biology and Technology conference … Read more

The early days of spatial genomics at #AGBT19

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Illustration of Nanostring's GeoMx Digital Spatial Profiling technology

At #AGBT19 there is a palpable movement from dissociated single cells to single cells in situ Every year at the Advances of Genome Biology and Technology you can see what the future holds. When long-read sequencing was introduced in 2011, people here at AGBT19 are still talking about that Pacific Biosciences fireworks display on the … Read more

NanoString’s Digital Spatial Profiling Microscope at #AGBT18

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Now that another year has passed it is great to see the NanoString Digital Spatial profiling microscope near its commercial launch. The platform will be in early access to select customers in the fourth quarter of 2018, and full commercial launch in the first half of 2019. For those interested in accessing the technology, they … Read more

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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The new QuantStudio 3D™ digital PCR instrument

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QuantStudio 3D Digital PCR System
The QuantStudio 3D, image courtesy of Life Technologies.

You may (or may not) have heard about digital PCR, which is set to be the next application set to explode in the gene expression market. But Life Technologies has a continuing investment in genetic analysis, and this new instrument, the QuantStudio 3D, demonstrates it.

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The Fluidigm C1™ Single Cell Auto Prep System

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The Fluidigm C1 single cell microfluidic chamber showing a capture
The Fluidigm C1 IFC chip, borrowed from Fluidigm’s Spec Sheet

Every human being came from a single cell. While that fact may not be so obvious in our day-to-day routine, the power of a single cell is observed with the burst of research activity in stem cells and induced pluripotent stem cells (and also see the Nobel Prize winner for 2012 in Physiology or Medicine, Shinya Yamanaka, who discovered the reprogramming process). In cancer research, the concept of cancer stem cells has developed into a major effort into identifying and characterizing circulating tumor cells (“CTC’s”) by which metastatses occurs. This was a major topic of discussion at the Spring 2013 AACR meeting in Washington DC, as well as a recent Next Generation Dx meeting (also in Washington DC). In many other areas of human disease biology, the inherently heterogeneous nature of tissues in general point to the need to analyze biology at a much finer resolution.

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Single molecule in-situ RNA startup Advanced Cell Diagnostics

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Biopsy of skin sample courtesy of euthman via Flickr
Biopsy of skin sample courtesy of euthman via Flickr

FFPE (Formalin-fixed paraffin embedded) tissues are standard preparations in the clinical world. It has been estimated that there are millions of FFPE samples stored in countless hospital laboratories and research pathology groups, all part of a standard operating procedure among pathologists and other hospital personnel. These tissue samples are embedded in paraffin blocks for indefinite room-temperature storage and are easily handled, and standard staining and microscopy techniques can then be employed to determine cancer stage, for example.

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Readlengths do matter in Next Generation Sequencing

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Notebook cover from AGBT 2009 (c) Dale Yuzuki

Recently I was asked about how important readlengths are, in the context of where MiSeq and Ion Torrent PGM currently stand in the marketplace. As the 454 advertisement used to say until recently, ‘Length Matters’. Given a number of recent announcements from Ion Torrent and the other folks in San Diego, let’s assess where we are.

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Virtual Research from a Million Datasets

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Image courtesy of <a href=”http://www.flickr.com/photos/jurvetson/”>jervetson</a> via Flickr.

Way back in 1997 a company launched one of the first commercial expression microarrays. The company was Affymetrix, the technology was micro-lithography, and the excitement around this new technology was palpable in the days before even the Human Genome Project had been completed.

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NanoString and Focused Gene Expression

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Image courtesy of <a href=”http://www.flickr.com/photos/libertasacademica/”>Libertas Academica</a> via Flickr

NanoString is a startup company that has commercialized a product called the nCounter™ system. It is able to take an RNA sample and look at the expression level of up to 800 genes per sample, and recent news indicates that it is in current preparation for an IPO.

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