January 15, 2013 (Vol. 33, No. 2)
Vicki Glaser Writer GEN
At the ASHG meeting in San Francisco Life Technologies announced the QuantStudio™ 3D Digital PCR System. This is a benchtop, scalable, chip-based instrument capable of generating up to 20,000 data points in one run. Also new from the company are the Ion AmpliSeq™ Community Panels, designed as a community-driven solution for sequencing of gene panels related to conditions ranging from cancer to inherited diseases, and based on the same technology used in the Ion AmpliSeq Ready-to-Use and Custom panels.
Pacific Biosciences presented the XL release, featuring new chemistry and software to enhance the company’s existing Single Molecule, Real-Time (SMRT®) DNA sequencing C2 chemistry for applications on the PacBio RS Analyzer that require long reads, such as de novo assembly. The XL release enables average read lengths of 5,000 bases and reads as long as 20,000 bases.
As Roche phases out production of its NimbleGen microarrays, the company signed an agreement with Agilent Technologies for continued product and service support that provides a path for NimbleGen users to transition to Agilent microarrays, which can be run on the NimbleGen MS 200 Microarray Scanner.
At ASHG, Roche featured its recently released Whole Exome Plus UTR sequence capture panels. The NimbleGen SeqCap EZ Exome + UTR library contains 2.1 million empirically optimized long oligonucleotides in solution, which includes 64 Mb of coding exons and miRNA regions and 32 Mb of untranslated regions (UTRs). Agilent introduced additions to its SureSelect Target Enrichment platform for NGS: the SureSelect Human All-Exon V5 and V5+UTRs.
Affymetrix partnered with Hamilton in the design and development of the Nimbus Target Preparation instrument for performing post-PCR clean-up of CytoScan® assay samples. Users can have the system perform individual stages of the target prep or do them all. The instrument can process either 25 samples (24 + 1 negative control) or 49 samples at a time.
At the ASHG meeting, Affymetrix also introduced the Axiom® miRNA Target Site Genotyping Arrays for analyzing genomic variation in microRNA and Axiom Biobank Genotyping Arrays, available in catalog and custom versions and designed for high-throughput analysis of large sample collections.
Thermo Fisher Scientific highlighted its NanoDrop Lite microvolume UV-Vis spectrophotometer capable of measuring nucleic acid concentration at 260 nm and purity using the 260/280 ratio.
The TargetRich™ targeted enrichment technology from Kailos Genetics offers a single-tube workflow, a two-step targeting process to avoid mismatches, and overlapping oligo patches to protect areas of interest from digestion. Based on the company’s Nested PatchPCR™ technology to enrich genomic regions of interest prior to NGS, TargetRich can simultaneously select multiple target regions across more than one sample. The process requires about an hour and a quarter of hands-on time.
Qiagen featured its GeneRead DNAseq Gene Panel System for PCR-based target enrichment for NGS. The system is designed to analyze a panel of disease-related genes and is compatible with the NGS platforms of the major manufacturers.
Otogenetics provides custom target resequencing services using NGS, employing its capture technology to capture targets of up to 24 million basepairs for deep coverage of scattered loci, or up to 5 million basepairs for deep coverage of an entire target.
DNA Genotek launched its GenoFIND™ genomic services optimized for oral fluid samples collected using the company’s Oragene® saliva collection devices. Services include project design consulting, logistics and coordination, automated nucleic acid extraction, whole genome and targeted sequencing, array-based SNP and expression profiling, custom assay development, and bioinformatic analysis.
Promega promoted workflows for its recently launched GoTaq® Probe real-time PCR systems, including applications for RNA analysis and biobanking. The system includes a 2X master mix optimized for hydrolysis probe assays that uses antibody-mediated hot-start chemistry and a 2-step or 1-step RT-PCR method.
Fluidigm’s C1™ Single-Cell Auto Prep System can isolate and examine single cells, grouping them according to unique genomes and transcriptomes, for use in whole transcriptome and variant discovery applications.
Simplifying Sample Prep
IntegenX introduced its directional mRNA kit for automated NGS library preparation on the Apollo 324™ system. The kit requires 500 picograms of mRNA starting material.
Hamilton Robotics, in collaboration with GE Healthcare, developed the easyPunch STARlet™ workstation, an automated system that integrates biological sample card punching (Whatman FTA™ and DMPK sample collection cards) for sample extraction and liquid handling in one workflow.
BIOO Scientific introduced the NEXTflex™ Pre-Capture Combo library preparation technology, designed to work in combination with the Roche NimbleGen v3 SeqCap EZ Exome and EZ Choice Library kits. The NEXTflex kit includes DNA barcode blockers and barcode adapters. Users have the option of pre-capture or post-capture pooling of samples.
New from Beckman Coulter is Solid Phase Reversible Immobilization (SPRI)-based chemistry for genomic DNA size selection for NGS fragment library preparation. The SPRIselect technology allows size distribution to be adjusted from 150–800 base pairs. Size selection can be performed manually or can be automated on a 96-well high-throughput platform. SPRIselect reagent kits are available in 5, 60, and 450 mL volumes.
New England Biolabs launched the NEBNext Ultra DNA (and RNA) Library Prep Kit for NGS is optimized for 5 ng–1 µg of input DNA, or as little as 10 ng of input RNA. Process optimization has allowed for elimination of clean-up steps, minimizing loss of sample and speeding up the workflow for library prep for Illumina NGS applications. The Q5® high-fidelity DNA polymerase was selected for even amplification across areas of high GC content.
Akonni introduced the TruTip® family of extraction products designed for use with the Hamilton Microlab® STAR line of liquid-handling workstations. Genomic DNA or RNA is extracted from fluid samples passed through a 5 mL pipette tip that contains an embedded, porous, solid-phase nucleic acid binding matrix. Extraction is achieved by chaotropic salt chemistry, and the entire process, including an automated heat incubation step requires less than an hour. For noninvasive prenatal diagnostics applications, TruTips can be used to extract circulating DNA and enrich for fetal DNA by adjusting the porosity of the matrix and controlling the flow rate. A 50 µL sample of DNA can be extracted and concentrated from a 5–10 mL plasma sample.
Bioinformatics and Cloud-Based Apps
Illumina showcased apps that will be available for its BaseSpace genomics cloud computing platform. For example, Golden Helix developed the GenomeBrowse™ cloud-enabled genomic visualization tool for analyzing DNAseq and RNAseq data. Users can access remote sample data and annotations. Partek’s Partek Flow® app provides a web-based environment for NGS data analysis, designed specifically for front-end alignment, enhanced quality control, RNA quantification, and variant detection.
A new company, Maverix Biomics, combined bioinformatics solutions designed for biologists, open-source algorithms, and cloud-based computing technology to create a software platform for NGS data analysis.
Signature Genomics demonstrated the upgraded Genoglyphix web-based data visualization software with an interactive browser for performing array-comparative genomic hybridization analysis.
Exiqon’s mIRSearch is a new web-based tool for identifying validated and predicted microRNAs that target specific gene transcripts. Gene names, sequence identifies, or key words can be used for searching.