Sequencing

A 2022 NGS Cost and Throughput Comparison

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Cost and Throughput calculations for NGS systems

With Singular Genomics announcing the new G4 system at the end of 2021, and Element Biosciences announcing the AVITI system in March 2022, here is a look at the existing state-of-the-art systems in a single graphic After spending some time in Los Angeles this week visiting a few existing and potential customers for Olink Proteomics, … Read more

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

Agilent Magnis NGS Prep System library automation – a pleasant surprise at #AGBT19

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Agilent's Magnis NGS Library Prep system at #AGBT19

Automation may seem a straightforward task, for those who have not tackled it before As an attendee of Advances in Genome Biology and Technology (#AGBT19) there are plenty of new things to check out, and while it may not be as cutting edge as spatial genomics or mRNA isoform discovery from long single-molecule reads, liquid … Read more

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

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

Highlights from the #AGBT18 Advances in Genome Biology and Technology Orlando Florida

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I have had the privilege of attending this conference every year (except for one) for over 10 years, and this year has a few memorable experiences, presentations, conversations and introductions. Companies come and go; the mix of attendees is of course different every year; and I’ve had enough change in my own professional affiliation that … Read more

SeraCare Precision Oncology

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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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WaferGen SmartChip TE™ – a PCR-based approach to target enrichment

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A WaferGen chip, finger and photo courtesy Dale Yuzuki
A WaferGen chip, photo courtesy Dale Yuzuki

WaferGen is a California Bay-Area company that originally developed an idea similar to BioTrove, which was to create a solid substrate with nanoliter-sized wells for high throughput real-time PCR. WaferGen’s SmartChip™ has 5,184 wells (that’s a 54 multiple of 96), while BioTrove’s OpenArray™ has 3,072 (that’s a 32 multiple of 96). The concept is that each well contains a real-time assay master mix and the sample of interest, and a flexible format of sample number / real-time targets (either gene expression or end-point genotyping) can be performed in a single run.

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Some clarifications about Ion Torrent PII and NextSeq 500

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Yesterday’s Ion Torrent Proton PII™ and Illumina NextSeq 500™ post certainly got a reaction from several quarters, including detailed pricing information about the 1x75bp format for the high-throughput configuration on the consumables. Instead of making edits to the original here are some clarifying points, as it is clear that Illumina is making a break from … Read more

The upcoming Proton PII and the NextSeq 500

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Record PI runs with a 20.5GB at the top, from the Ion Community site
Record PI runs with a 20.5GB at the top, from the Ion Community site

There has been a lot of publicity around the NextSeq 500 from Illumina, and it appears to have been designed to compete directly against Ion Torrent’s upcoming PII chip. Thanks to a visit to upstate New York last week, I met Dr. Sridar Chittur who told me how important it was to put current information out on this blog, and if I can put out the disclaimers up-front it would be very helpful for those thinking about what benchtop system to purchase over the next several months.

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