End-to-end sequencing

The latest sequencing technologies include automation tools that make the process faster and more accurate.

Life Technologies has announced the first end-to-end sequencing solution for exon-level copy number variation (CNV) analysis, which combines the Ion Reporter CNV data analysis workflow, the Ion AmpliSeq Exome kit and the Ion Proton system.

Inherited and de novo CNVs of chromosomal regions, in which large regions (>1kb of the genome) are duplicated or deleted, are associated with many diseases, including cancer, autism, and schizophrenia. Until now, the primary CNV analysis methods — microarrays and fluorescence in situ hybridisation — have had poor dynamic range, limited breakpoint resolution, lower genomic coverage, and can only detect known single nucleotide polymorphisms (SNPs).

"The launch of the industry's first solution for whole human exome CNV analysis using Ion AmpliSeq Exome is another example of how Ion Torrent is delivering turnkey solutions to enable sequencing for all," said Ion Torrent's vice president of marketing, Maneesh Jain. "The Ion AmpliSeq Exome kit and Ion Reporter software provide an integrated solution for detecting SNPs, indels and high-resolution copy number variation."

The Ion Reporter software CNV data analysis workflow vastly simplifies and automates all of the steps for a priori identification and interpretation of CNVs, SNPs, and insertions/deletions (indels) so virtually anyone can quickly understand the implications of their exome data with the same sensitivity as microarray data.

Users simply choose the predefined Ion Reporter software CNV data analysis workflow, run the sample and receive a list of mutations, including copy number variants ranging in size from exon level up to aneuploidies, and associated annotations drawn from dozens of public databases — all in a single day.

Life Technologies has also launched the Ion AmpliSeq Exome certified service provider programme, a global organisation of some of the world's providers that will sequence and analyse human exomes in as little as two days. Sequencing requires just 50 ng of DNA and is very competitively priced, making exome sequencing accessible to any researcher.

Until now, exome sequencing through a service provider has cost US$1000 (€727) or more, taken six to eight weeks and required as much as three micrograms of DNA. Using the Ion AmpliSeq Exome kit, the Ion Proton sequencer, and the Ion Reporter software, service providers can sequence two exomes in a single run - from DNA to results in just two days. This eliminates the need to batch samples just to make the price of exome sequencing affordable.

In addition to being faster and more affordable, Life Technologies says the Ion AmpliSeq Exome kit delivers the most uniform sequencing coverage in the industry, with up to 98 per cent of bases covered at 10x, and up to 95 per cent covered at 20x, for a single exome.

"The Ion AmpliSeq Exome kit dramatically reduces the time and the cost required to sequence a human exome," said Stephen Scherer, senior scientist at The Hospital for Sick Children, Toronto, Canada, and director of The Centre for Applied Genomics at the hospital. "With the Ion Proton sequencer, we can capture and sequence the exome in just two days, so there's no need to batch projects together in a run to keep costs down. This is important to customers dealing with clinical research samples who often need their sequence data as quickly as possible."

"Ion AmpliSeq Exome certified service provider programme makes fast, affordable and high-quality exome sequencing available to any researcher," said Jain. "The low amount of required input DNA and the turnkey analysis-to-annotated-results solution provided by Ion Reporter software make this an ideal solution for clinical researchers."

Sequence alignment

DNASTAR has released Lasergene 11.2, its primary focus to incorporate new sequence alignment methods and tools in the MegAlign Pro application.

Lasergene, which has been the most published sequence analysis software in peer reviewed journals for each of the past 28 years, already included a large number of sequence alignment methods. With the release of Lasergene 11.2, DNASTAR now additionally supports Clustal Omega, Mauve, a fully integrated Muscle alignment algorithm, and enhanced phylogenetic trees.

Tom Schwei, vice president and general manager of DNASTAR, commented, “Lasergene 11.2 introduces significant new capability in DNA and protein sequence alignments. We will continue to develop our software’s capabilities in each of these areas with additional software upgrades beginning early next year. We are very pleased to respond to the needs of the market by maintaining our longstanding tradition of supporting life scientists with continually improving, outstanding, easy to use software.”

In a related development, DNASTAR has also announced that Dalhousie Medicine New Brunswick (DMNB) has entered into an agreement supporting an enterprise-wide site license of DNASTAR Lasergene software for genome sequence assembly and analysis. The license provides access to the DNASTAR software for all faculty, staff and students of DMNB.

Keith Brunt, assistant professor at DMNB, explained: “Until we entered into this agreement, we didn’t have much experience with DNASTAR or their Lasergene software. The more time we spent using the software and the more we learned about its capabilities, the more impressed we were with it. By signing this agreement, we provide access to outstanding software for all of our scientists, faculty, staff and students at a very reasonable cost. This software will help in the training of a new generation of physicians and is a step toward patient-tailored therapy. This agreement will help support the future success and growth of our programme.”

And Spectronics Corporation has introduced a high quality, inexpensive ultraviolet (UV) crosslinker that makes it possible to identify and analyse trace amounts of DNA/RNA with far greater sensitivity, accuracy and speed than with conventional analysis.

The Select XLE-Series UV crosslinker covalently binds nucleic acids to membranes in under 30 seconds — 240 times faster than vacuum-oven baking (Fig. 1). It has a novel true-UV-monitoring circuitry that safeguards valuable test results from washouts, even when the tubes age.

Researchers also rely on this versatile instrument for eliminating PCR contamination, nicking ethidium-bromide-stained DNA in agarose gels, gene mapping for creating cleavage-inhibiting thymine dimers, RecA mutation screening in E.coli, UV sterilisation and miscellaneous UV-dosage applications.

In another launch, Spectronics describes its Spectrolinker XL-1000 UV crosslinker as possibly being the biotech researcher's most versatile instrument. The company says its ease of use and unmatched accuracy make the Spectrolinker ideal for many applications including crosslinking of DNA and RNA, DNA, gene mapping, RecA mutation screening and testing, UV-induced polymerisation and UV intensity monitoring.

For researchers, other benefits include the XL-1000's ‘smart’ microprocessor controller and novel, true UV-monitoring circuitry, which allows users to obtain error-free results faster, safer and more accurately than previously possible. The Spectrolinker ensures reliable crosslinking in a very quick time by covalently binding nucleic acids to membranes in less than 30 seconds.

The UV-monitoring circuitry guarantees that the set dosage is always delivered, protecting important test results from washout damage. The company adds that the Spectrolinker greatly increases the visibility of samples on autoradiograms, which results in superior analysis and extra-sharp, extremely clear, publication-quality photodocumentation.

Free software toolkit from Lab7 Systems

Lab7 Systems has released a free software toolkit and new service offerings for the next-generation DNA sequencing (NGS) bioinformatics community, along with the latest beta version of its Lab7 Dashboard. 

BioBuilds is a reference collection of Open Source bioinformatics tools for genomics, pre-built for Linux and Mac OS X platforms. It eliminates the need for users to maintain and build their own versions of these tools. By providing binaries, BioBuilds also enables users easily to reproduce results by removing version dependencies on underlying software, since all tools in BioBuilds will be pre-built for those binaries.

“Open Source software is important for bioinformatics,” said Chris Mueller, Lab7 Systems’ president and cto. “However, building and maintaining Open Source tools can be a time consuming process. We maintain internal builds of many analytical tools and we feel that making our builds freely available is a good way to give back to the genomics community.”

BioBuilds is being released in conjunction with the second Public Beta of the Lab7 Dashboard, the company’s comprehensive software platform for managing sequencing projects, workflows, and pipelines. This release includes the Production Pipeline Engine, a complete sequence analysis pipeline management and report generation system. The Production Pipeline Engine allows users to easily port existing analysis pipelines into a managed, production-ready environment. All BioBuilds tools are made readily available in the Lab7 Dashboard, even though the platform is not expressly required to run the tools.

Lab7 Systems has also launched its SeqSigma and DashO3 optimisation processes, integral components of the company’s larger suite of custom services.

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