Companies

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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Formulatrix and an inexpensive digital PCR for NGS library quantitation

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Formulatrix Digital PCR Plate
Underside of the Formulatrix Digital PCR Plate

The American Society for Human Genetics 2013 Annual Meeting was held this week in Boston. Starting from Tuesday and going through Saturday, there are ancillary meetings both before and after (and Life Technologies had an Ion World event the two days prior). As one of the two ‘main event’ trade-show exhibits for the genomics tool-providers (the other being the Advances in Genome Biology and Technology in Marco Island FL every February), you can learn a lot by walking around and talking to different vendors.

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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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The next NGS platform – the QIAGEN GeneReader™

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The QIAGEN GeneReader at AACR (April 2013)
The QIAGEN GeneReader at AACR (April 2013)

Earlier this year at the February AGBT Conference, a person from QIAGEN came over to the Ion Torrent suite and asked me a few questions about the Ion Proton and in particular the upcoming Ion Chef unit. (The Ion Chef for those not familiar with it can replace the OneTouch 2 automated template preparation instrument with another one that will not only perform the emulsion PCR but also enrich the ion sphere particles, and load the chips as well.)

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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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Moleculo and Haplotype Phasing

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A picture of a robot toy (sorry, my kids do not have a toy that looks like the ‘Moleculo Man’ of Conan OBrien from 2001…)

A few weeks ago at the J.P. Morgan Healthcare Summit in San Francisco, Illumina announced that they acquired a startup company called Moleculo that provides virtual long reads of 8 to 10kb. Single molecule sequencing will provide long reads (Pacific Bioscience’s RS will now go out to 5kb, although the platform is hampered by poor accuracy), and I’ve written before about last summer’s accomplishment by Complete Genomics in publishing their Long Fragment Read technology of phased reads on the order of 100kb. (And do take a look there to see why haplotype phasing is important.)

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Is there room for 90 providers of genomics software?

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Image courtesy Libertas Academica via Flickr.

“Let a hundred flowers bloom, let a hundred schools of thought contend”, Mao once said during the Revolutionary Days of 1957. Now in the middle of a genomics revolution, it feels that way in the market for genomics software to analyze next-generation sequencing data. New companies are being formed, large software and hardware firms are expanding into the life sciences, and others are offering in addition to software options the implementation of a cloud-based service.

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The end in sight for Complete Genomics by merging with BGI

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Complete Genomics was started in 2005 with the promise of setting up a whole-genome sequencing service for millions of human genomes at a very low cost. Launching a service in 2009 at $5,000 per individual sample, Complete Genomics went public under the symbol GNOM in November of 2010 at $7.69/share, reaching a high of $17.42 in June 2011 before returning to it’s IPO price in Sept 2011, and then declining to the $2 to $4 range.

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Direct To Consumer Genomics – A Long Way To Go

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Image courtesy Libertas Academica via Flickr.

Once upon a time, when I was working for one of my prior employers (you can guess which one it was as the company name started with an ‘I’), the offer was made to have 23andMe to do whole-genome genotyping of myself and my immediate family. It being 2007 or so, the cost was not unreasonable in terms of the ’employee discount’ (23andMe used the company’s equipment and microarrays to do the genotyping) and after thinking about it for a few minutes, I decided to decline the offer.

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Sequencing the Immune Repertoire (T-Cell Receptor genes)

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Image courtesy <a href=”http://en.wikipedia.org/wiki/T-cell_receptor”>Wikipedia</a>

Immunology is a fascinating subject. Immense in its complexity, debilitating when the immune system malfunctions, our ability to fend off bacterial and viral infection, cancers of different types, and other foreign invaders is a remarkable biological capability.

The NIH estimates 24M Americans are affected with an autoimmune disorder, but that number rises to 50M when the definition is expanded from a list of 24 disorders to over 100 by the American Autoimmune Related Disease organization. It is the second highest form of chronic illness, arthritis being the most familiar to many.

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