Beyond Nanopores: News and Notes from AGBT

February 19, 2012

By Bio-IT World Staff 

February 20, 2012 | Oxford Nanopore may have stolen the show at the Advances in Genome Biology and Technology (AGBT) meeting* last week (see, Oxford Strikes First in DNA Sequencing Nanopore Wars), but they weren’t the only company showcasing advances in next generation technologies.  

The BioTeam announced the availability of BioTeam MiniLIMS for Ion Torrent Personal Genome Machine (PGM). MiniLIMS is a powerful Web-based Laboratory Information Management System (LIMS) built for scientists who want a cost-effective solution that is fast, simple and flexible.  MiniLIMS will be available for direct purchase through Life Technologies WebStore after March 15, 2012. Among MiniLIMS’ core capabilities are: simplified data entry; automatic loading of PGM data; and powerful report generation. Create custom reports to see the state of your experiments at any time; there are pages that show the history of all data in the system. To see the most recent screenshots of MiniLIMS for PGM visit: http://biote.am/73 

The New York Genome Center (NYGC; see, “New York Genome Center Unveiled in Manhattan”) and Illumina announced a large-scale whole genome sequencing project with the Feinstein Institute for Medical Research to understand the genetic basis of Alzheimer’s disease. Whole genome sequencing efforts will begin with 130 Alzheimer’s patient samples, for whom there is detailed clinical data and brain pathology available. Over a four-year period, up to 1,000 genomes of patients with Alzheimer’s disease will be sequenced and compared to the genomes of a control group of elderly individuals. All data resulting from this project will be made freely available to the scientific community. The Feinstein Institute is part of the North Shore-LIJ Health System, an Institutional Founding Member of NYGC, which has a strategic collaboration with Illumina.  

OpGen demonstrated a new application for whole human chromosome mapping that improves the completeness of human genomes and enables thorough analysis of a wide spectrum of structural variations. The company also presented preliminary results from a comparative genomics study using the company’s Whole Genome Mapping technology and Genome-Builder tool suite to efficiently and accurately order and orient large sequence scaffolds on a human genome de novo sequence project. The findings also demonstrate the ability to effectively construct complete high density physical maps of human chromosome arms and have detected structural variations between human individuals.  

Nabsys demonstrated what is reportedly the first direct electronic re-sequencing and mapping of DNA. Nabsys' positional sequencing platform uniquely reveals information about both the identity and location of DNA sequences through direct electrical detection of probes bound to single molecules that may be as large as hundreds of kilobases in length. "The data we are presenting at AGBT,” said Barrett Bready, chief executive officer of Nabsys, “demonstrate what is possible with purely solid-state detection. These data provide insights into how the Nabsys positional sequencing platform, once scaled, has the potential to set new performance standards and open new markets for DNA sequence analysis." 

Ingenuity announced the general availability of Ingenuity Variant Analysis, a web application designed to help researchers studying human disease rapidly identify causal variants from human resequencing data. Researchers can quickly and reliably take a list of millions of variants down to the most compelling set of variants for follow-up study and analysis. Ingenuity Variant Analysis supports individual whole genome or exome studies with thousands of samples without deleting data sets. Ingenuity Variant Analysis streamlines the annotation and prioritizing of all variants through rich biological interpretation and analysis. Its unique combination of filtering, analytics, and richly annotated content allows researchers to identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and the researcher’s own knowledge of disease biology. 

* Advances in Genome Biology and Technology (AGBT), February 15-18, Marco Island, Fla.