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Uncovered: 1000 New Microbial Genomes

JUNE 12, 2017 Joint Genome Institute
The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what’s on Earth because they have only recently had the tools to deeply explore what is just underfoot. Now scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, have taken a decisive step forward in uncovering the planet’s microbial diversity. In a paper published June 12, 2017 in Nature Biotechnology, DOE JGI’s Prokaryotic Super Program head Nikos Kyrpides and his team of researchers report the release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes—the single largest release to date.

With the release of high quality genomic information from the 1,003 reference genomes, DOE JGI is providing a wealth of new sequences that will be invaluable to scientists interested in experiments such as characterizing biotechnologically relevant secondary metabolites or studying enzymes that work under specific conditions, Seshadri said. And because Kyrpides’ research team sequenced type strains that are readily available from culture collections, scientists can perform follow-up experiments with them in the lab, she added.

Source: Joint Genome Institute



GATC to be part of Eurofins Group

Constance, Germany, June 2nd, 2017: GATC, one of the leading sequencing provider will be a part of the Eurofins Group as of July 2017 to create the leading company in the worldwide sequencing market.

Eurofins Scientific (EUFI.PA), a global leader in bio-analytical testing, announces that it has signed an agreement to acquire GATC Biotech AG (“GATC”), one of Europe´s specialists in DNA sequencing. The transaction is expected to close in July, subject to the fulfilment of customary closing conditions.

Founded in 1990, GATC has achieved a strong recognition for DNA and RNA sequencing, as well as bioinformatics in Europe. The company employs 140 staff across 2 sites, and serves over 10,000 institutional and academic customers, generating annual revenues of about EUR 20m. As one of the larger players in Custom and Next Generation Sequencing, GATC has built a reputation for innovative, internally-developed applications, as well as industry-leading turn-around time (TAT). The acquisition should therefore further reinforce Eurofins' footprint in DNA sequencing, and strengthen the Group's technological platform supporting its genetic testing innovations.

Source: GATC



Roche launches AVENIO ctDNA Analysis Kits for Oncology Research

Basel, 08 May 2017 
Roche (SIX: RO, ROG; OTCQX:RHHBY) today announced the global commercial launch of the AVENIO circulating tumor DNA (ctDNA) Analysis Kits, a portfolio of three next-generation sequencing (NGS) liquid biopsy assay kits for oncology research: the AVENIO ctDNA Targeted Kit, Expanded Kit and Surveillance Kit. The kits include all reagents, bioinformatics and software to make ctDNA testing accessible to all NGS laboratories.

“We are pleased to introduce these state-of-the-art AVENIO ctDNA Analysis Kits1,2,3 that combine the convenience of liquid biopsy with the power of next generation sequencing,” said Roland Diggelmann, Chief Executive Officer, Roche Diagnostics. “Roche believes the AVENIO ctDNA assays can help researchers around the world advance personalized oncology by enabling them to carry out their own testing.”

The AVENIO ctDNA Analysis Kits are aligned with NCCN guidelines to support oncology research4. The kits detect all four mutation classes with high sensitivity3. With three different kits available, researchers can profile the genomic complexities of different cancer stages and tumor types, obtaining results in five days.
“As a cancer researcher, I see a tremendous advantage to using the AVENIO ctDNA Analysis Kits”, said Peter Meldgaard, MD, PhD, Associate Professor of Oncology at Aarhus University in Denmark. “Cancer is a highly complex disease, so the ability to obtain a complete and accurate genomic profile of malignant tumors and monitor changes in tumor burden is invaluable.”

Source: Roche, Basel



Finding A New Major Gene Expression Regulator in Fungi

MAY 8, 2017, Joint Genome Institute

In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as “early diverging lineages,” the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment.

Source: The U.S. Department of Energy Joint Genome Institute



DNA Methylation Status Predicts Mortality

20. March 2017, dkfz 
Methyl labels in the DNA regulate the activity of our genes and, thus, have a great influence on health and disease. Scientists from the German Cancer Research Center and from the Saarland cancer registry have now revealed that an altered methylation status at only ten specific sites in the genome can indicate that mortality is increased by up to seven times. Smoking has a particularly unfavorable impact on the methylation status.

In their present study, the researchers investigated the cases of 1,900 participants of two epidemiological studies called ESTHER and KORA*. They used DNA from blood cells as the basis of their investigation. All study subjects were older adults and had provided blood samples when they entered the study. This was up to 14 years ago and many of them had died since then.

Of the 58 CpGs, the scientists selected those ten with the strongest correlation with mortality. This epigenetic risk profile alone enabled them to predict the so-called all-cause mortality (cancer, cardiovascular diseases, and others). Study participants whose genome exhibited an "unfavorable" methylation status at five or more of these sites had a risk of death within the 14-year observation period that was seven times that of study participants whose methylation at these positions showed no abnormalities.

Source: dkfz German Cancer Research Center




21. March 2017, SIB 
Recent advances in the fight against type 2 diabetes (T2D) result from a pan-European collaborative project, called IMIDIA, in which the SIB Swiss Institute of Bioinformatics is closely involved since 2010. SIB was in charge of both coordinating the large amount of patients’ data (acting as Data Coordination Centre, DCC) as well as analysing the data to find biomarkers for early detection of the disease. The major findings of the research include the discovery of molecules, which could serve as biomarkers to detect the disease up to nine years before its diagnosis.

In a first study, coordinated by senior author Mark Ibberson of SIB’s Vital-IT group and published in Molecular Metabolism, the team identified a key gene associated with T2D. Using a network analysis that integrated transcriptomic and phenotypic data, the gene Elovl2 appeared to be related to insulin secretion in mice. The finding was confirmed in human pancreatic beta-cell lines, i.e. cells resembling those affected in T2D.

Source: SIB Swiss Institute of Bioinformatics



New Goat Genome Assembly Breaks Continuity Record, Expands Breeding Tools

Tuesday, March 21, 2017, PACBIO 
Efforts to produce a reference-grade goat genome assembly for improved breeding programs have paid off. A new Nature Genetics publication reports a high-quality, highly contiguous assembly that can be used to develop genotyping tools for quick, reliable analysis of traits such as milk and meat quality or adaptation to harsh environments. The program also offers a look at how different scaffolding approaches perform with SMRT Sequencing data.

The project was motivated by a clear need to develop methods for high-quality livestock genome assemblies to benefit breeding communities. Goat offers a particular boost to developing countries, where these animals are a primary source of textile fiber, milk, and meat.

They chose SMRT Sequencing because its long reads could characterize even the most difficult genomic regions. “Initial assembly of the PacBio data alone resulted in a contig NG50 ... of 3.8 Mb,” the team reports. PacBio contigs were then connected with optical mapping and Hi-C data to create extremely long scaffolds in the final 2.92 Gb assembly. “These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps,” they write. The assembly is 400 times more continuous than the previous short-read assembly.

Source: PACBIO 



Launch of the GridION X5 

Tue 14th March 2017, Oxford Nanopore Technologies announced the launch of the GridION X5, a new system that can drive up to five MinION Flow Cells and process all the data produced within a single benchtop device. GridION X5 can be used to offer nanopore sequencing as a service.

As the community of MinION users starts to reap the benefits of these releases, we are also preparing to release PromethION Flow Cells that are designed to yield up to six times the Gb of a MinION Flow Cell , so that the entire PromethION can yield Terabases of data. GridION fills a gap between MinION and PromethION.

The performance of MinION has improved 40-fold since its first introduction and data processing requirements at the newest high throughputs are now beginning to challenge the average PC. The GridION will adapt the MinION technology into a small benchtop production sequencer with the advantage of full on-board compute capable of generating 100GB of data over 48 hours.

This capacity is completely controlled by the user. All five flow cells can be dedicated to one project, or each flow cell can be used to sequence different samples. As with all nanopore sequencing there is no fixed run time.

Source: Oxford Nanopore Technologies