No Nanopores but AGBT 2013 Showcases Plenty of New NGS Technology

By Bio-IT World Staff 

February 25, 2013 | The 2013 Advances in Genome Biology and Technology conference—likened by one participant as “the bastard child of a Gordon Conference and a Las Vegas Porn Convention"—may have lacked the show-stopping presentation of an Oxford Nanopore this year, but there was plenty to admire on the new technology front.

Nabsys, which has been growing steadily since Bio-IT World first profiled the Providence, RI, company in 2010, demonstrated its pre-beta instrument at AGBT. The electronic, solid-state, single-molecule sequencing platform, “finds the locations electronically of probes that have been bound to very elongated molecules,” says Barrett Bready, Nabsys CEO, speaking to Bio-IT World from a Florida beach on the eve of the conference.

“By employing electronic detection rather than optical detection you have no problems with the wavelength of light; you’re able to get much more information content… and do a lot more in terms of assembling genomes,” he says. 

Nabsys filled all 100 slots for demonstrations at AGBT. “[Early users will get the opportunity to] see data generated live,” Bready said. “Unlike other technologies, you don’t have to run the technology and look at it later. Here you get real-time histograms, real-time analysis of what’s going through the detectors, which is a very cool thing. It’s a technology that’s interesting to watch!” Bready hoped to get feedback on the workflow and user interface from AGBT attendees before the product formally launches later this year.

Keith Robison (Omics! Omics!) gives his first impressions of the Nabsys instrument here.

Bina Technologies announced the Bina Genomic Analysis Platform and unveiled the Bina Box. “It’s an optimized, on-premises hardware and software solution that sits alongside the sequencers,” says Mark Sutherland, senior VP business development. The reason for an on-premises solution, he says, is that the files streaming off sequencers amount to 0.5 TB data. As researchers sequence multiple genomes per day, “this quickly becomes a big data problem,” Sutherland says.

The Bina Box handles assembly and alignment of raw reads and variant calling. The variant calls are then uploaded to the cloud for comparative analysis, disease-association studies, aggregation, mining, and other downstream analyses.

Bina was founded by Narges Bani Asadi, an electrical engineer from Stanford University. She points to innovations in multiple areas, including algorithms, statistical analysis, and systems software, as well as “how you parallelize and scale the computation across many compute nodes and how you minimize the data latency and i/o latency.”

“This solution brings the price down several fold to around $200/sample for full analysis,” says Sutherland, including the alignment and whole-genome assembly, variant calling, and evaluation of structural information. Bina will face stern competition from the likes of DNAnexus and Seven Bridges Genomics.

Although tracking new sequencing technologies from companies such as Nabsys and Oxford Nanopore, Goldman Sacchs analyst Isaac Ro says his firm is taking “greater interest in how the bioinformatics market is developing with a growing number of companies in attendance at AGBT that garnered positive feedback and/or showed interesting new solutions for the NGS market (Bina, DNAnexus, Personalis, Real Time Genomics).”

Real Time Genomics (see, Computer Scientists’ Solution to a Biologists’ Problem) introduced its genome analytics platform to enable rapid, accurate interpretation of genomes in the study of early childhood disease. The platform will provide biomedical and clinical researchers with the ability to robustly detect de novo variants in childhood disease, perhaps for the first time.

“Our ability to accurately detect de novo variants is an important R&D milestone and confirmed to us and our collaborators that the platform was ready for use in human disease applications,” says CEO Steve Lombardi. “We believe that childhood disease is the optimum early application of our technology.”

The platform can be imbedded locally into existing infrastructure, accessed on-demand in Amazon’s public cloud, or offered as a professional service by staff scientists. The company announced there will be both annual subscription pricing as well as pay-per-use pricing. Read more.

Agilent Technologies expanded its portfolio of target-enrichment products with the introduction of HaloPlex exome kits and SureCall software. The new additions are designed to complement Agilent's Web-based SureDesign and custom HaloPlex gene panels to provide a complete, integrated workflow. Press Release 

QIAGEN is rebranding the IBS clinical sequencer it acquired last year as GeneReader. It dubs the instrument as a "transformational NGS benchtop sequencer,” featuring a carousel capable of analyzing up to 20 samples in parallel. The instrument is part of QIAGEN’s NGS workflow, which also includes QIAcube for fully automated nucleic acid isolation and purification, as well as library preparation; GeneRead DNAseq Target Enrichment gene panels; and a dedicated QIAGEN software solution for user-friendly and automated result analysis. Read more.

The Ion Torrent platform was showcased in several talks, including a presentation from Dagan Wells (University of Oxford) on screening IVF embryos prior to implantation to detect potential chromosomal aneuploidies. And Agnes Viale (Sloan-Kettering Cancer Center) showed data demonstrating on the identification of novel mutations in two genes (FLT3 and TET2) associated with acute myeloid leukemia using RNA-sequencing from as little as 2 ng DNA.

Among the best received talks, as judged by an army of bloggers and commentators on social media, was Pacific Biosciences co-founder and chief scientific officer Jonas Korlach. “Everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology,” enthused Duke University’s Brian Krueger at the LabSpaces blog. One of the key takeaways was the claim that PacBio can supply all the reads necessary to produce highly accurate consensus assemblies using a Hierarchical Genome Assembly (HGAP), following the publication last year in Nature Biotechnology of a powerful hybrid long-read/short-read assembly approach blending PacBio reads with second-generation Illumina reads. An upgrade is promised for later this year that will double throughput.

Another strong talk was from Harvard University researcher Sunney Xie, who discussed his group’s single-cell genome sequencing technique, published last December in Science. Cold Spring Harbor Laboratory’s Gholson Lyon commented that it was “the most interesting talk” at AGBT and “technically cool.”