Single Molecule

The world’s first complete chromosome sequence at #AGBT19

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The full x-chromosome map

NGHRI’s Dr. Adam Phillippy presents a remarkable dataset – the telomere-to-telomere assembly of a complete human X chromosome When the completion of the Human Genome Project was announced on June 6, 2002, President Bill Clinton said the following: We are here to celebrate the completion of the first survey of the entire human genome. Without … Read more

The next leap in Personalized Medicine will be advances in sensor technology like Cardea

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Can a graphene biosensor company like Cardea Biosciences play a role in making P4 medicine (predictive, preventive, personalized and participatory medicine) a reality? Lee Hood’s vision for P4 medicine It was about six years ago I attended a Personalized Healthcare conference at Virginia Commonwealth University in Richmond Virginia, where Leroy Hood of the Institute of … Read more

Two Pore Guys single-molecule diagnostic platform update

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Two Pore Guys Artist Rendition, kindly provided by 2PG

Two Pore Guys (2PG) has come a long way in a little over 18 months Background of Two Pore Guys At the recent Next Generation Diagnostics Conference in Washington DC (#NGDx18) Two Pore Guys had a nice exhibit where I had the privilege of meeting Tyler Shropshire Ph.D., their Sr. Scientific Manager of R&D. It … Read more

Bionano Genomics’ New DLS Saphyr Technology at #AGBT18

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It has been almost five years since I wrote this post about Bionano Genomics and OpGen, and tools to look at structural variation. At that time OpGen was mapping bacterial genomes and Bionano Genomics would do insect genomes (about 100x as large), and the open question at that time was whether these technologies could scale … Read more

NanoString’s Hyb & Seq Single Molecule Sequencer at #AGBT18

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Background Back in 1989 in Belgrade Yugoslavia, Radoje Drmanac had an idea that would shape the next decade of genetic analysis, which was being able to sequence megabases of DNA information by a collection of 11-mers to 20-mers. Doing the mathematical calculations, this paper lays out what kind of DNA oligonucleotides would be needed to … Read more

Formulatrix Constellation Digital PCR

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Summary: A new digital PCR instrument with two different sample throughput formats (24 and 96), many more partitions, and more colors to enable multiplexing The digital PCR market continues growing, as it finds its continued utility for absolute quantitation of nucleic acids for a multitude of applications, from rare virus detection in infectious disease to … Read more

Nabsys single molecule mapping technology

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Close-up of Nabsys ChipAnother interesting single-molecule technology is a company out of Providence (RI) called Nabsys. For several years I had heard the name involved in developing single-molecule sequencing technology, and this technology will start its initial product around genomic mapping, rather than sequencing.

For background on genomic mapping and CNV analysis along with the competitive landscape, here are  prior pieces written previously called BioNano Genomics, Opgen and Copy Number Variation, and an update on BioNano from last Fall’s ASHG meeting. So while BioNano Genomics and OpGen both use optical mapping of single molecules, Nabsys uses electrical detection. (Cue the optical vs. digital detection methodology of Ion Torrent here).

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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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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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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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