Optical Mapping

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 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

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

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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Single molecule mapping OpGen making slow progress

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Photo of an OpGen mapping card

In contrast to BioNano Genomics, who is starting commercialization with early access customers now and full commercial launch in the Spring of 2013, OpGen launched the Argus™ Optical Mapping system in the summer of 2010. Their customers use this system for microbial strain mapping, mainly for infectious disease research or finishing reference bacterial strains.

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BioNano Genomics explores Copy Number Variation

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The Irys system in the BioNano Genomics booth. Note the small chips in the lower right corner, about 3″ square, with three input/output ports to accommodate three samples.

ASHG 2012 in San Francisco is finally over! The exhibit booths get torn down, the equipment gets packed up and shipped to storage, and hundreds of foot-weary front-line soldiers get back to their normal routines, whether in sales, marketing, product development, R&D or product management.

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BioNano Genomics, OpGen and Copy Number Variation

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Image courtesy Flickr user <a href=”http://www.flickr.com/photos/48677280@N00/”>karen2754</a>.

A few weeks ago this paper appeared in Nature Biotechnology, “Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly”. It was the first publication of a startup company in San Diego called BioNano Genomics.

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