Observations from American Association for Cancer Research 2018 #AACR18

It is something of a tradition for me to give some reviews of notable presentations from past AACR conferences. For example, here’s one that I did while at SeraCare for #AACR16, here’s one from #AACR15, and another one here from #AACR14. (Briefly looking for highlights from 2017, well it looks like something is remiss!) I’ve had … Read more

Preview of Association for Molecular Pathology 2017 #AMP2017

With over 2000 clinical laboratory professionals in molecular diagnostics and pathology, plenty of technology and offerings on display. This year the Association for Molecular Pathology takes place in Salt Lake City Utah, and promises an abundance of new technology as well as the new accompanying science around diagnostic testing. Since this is a molecular pathology … Read more

Formulatrix Constellation Digital PCR

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

SeraCare Precision Oncology

Seracare precision medicine ngs control reference material seraseq mutation mix
The Seraseq Solid Tumor Mutation Mix-I (AF20), the first product from SeraCare’s Precision Medicine Group

This post is about Seracare’s new direction for Precision Medicine (in particular Precision Oncology), and the launch of a new product the Seraseq Solid Tumor Mutation Mix-I (AF20). But I’ll start first with a story from my days at Illumina.

It was ten years ago this week that I last launched a product. It was the Illumina Infinium Human-1 Genotyping BeadChip, and it took months of hard work, many core-team meetings, plenty of long days and many hallway discussions about the finest details of the product. Long days and many meetings go together: how can you get the things you commit to in a meeting ever done if you go to many meetings?

And in case anyone is wondering, yes that is the job of a Product Manager – you get to work hard and work closely with a team from across different areas of the company (research, manufacturing, quality, support, and engineering) and you get to experience many ups-and-downs, and learn things about yourself and others through this experience that you carry with you. These may be hard days, but they are good ones.

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Complete human diplotypes & Google X Life Sciences podcast

Theral Timpson produces a weekly podcast at Mendelspod.com, and in his latest edition he interviews me about Google X Life Sciences (I wrote about them before here), long-read sequencing (in particular Pacific Biosciences) which then I’m able to discuss the value of complete human diploid sequencing, and my involvement with the Behind the Bench blog. … Read more

The Core Competency of Google is not Life Sciences

What does Google X have to offer in life science diagnostic development? I’ve picked up a phrase, ‘it’s a narrow world’, from somewhere in my travels. Way back in my laboratory manager days in Santa Monica California at the John Wayne Cancer Institute (‘laboratory manager’ sounds so much better than ‘laboratory technician’), I met a … Read more

Nabsys single molecule mapping technology

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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FDA Approval for the MiSeq

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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Single molecule in-situ RNA startup Advanced Cell Diagnostics

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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Single molecule mapping OpGen making slow progress

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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