• Project Design: Understanding goals, picking the most appropriate NGS technology...
• Sequencing
• Assembly
• Data analysis: Including Annotation with BG7 method

Reports and Deliverables

What do you get at the end?

• Reports including quality control results
• A complete catalog of protein coding and RNA genes
• A rich functional annotation of protein coding genes including ontologies like GO or KEGG

Annotation files in standard formarts: gff, genbank, xml...

Klebsiella pneumoniae is a bacterium frequently found in the mouth and gut of healthy humans. In most instances, it does not lead to disease but it can mutate opportunistically and cause diverse types of infections. The bacterium also has a significant capacity to acquire antibiotic resistance. Three closely related isolates of a pathogenic strain of K. pneumonia with increasing degrees of antibiotic resistance were obtained in the Microbiology department at Hospital Universitario La Paz and sequenced at LifeSequencing in Valencia, Spain using the long read GS FLX+ System, developed by 454 Life Sciences, a Roche Company

The sequencing data was assembled using the GS De Novo Assembler software and functional annotation was performed to identify the relevant genes codified in the three genomes with BG7, the optimized system developed by Era 7 Bioinformatics, providing rich functional annotation of 454 Sequencing data.
The researchers found that the three bacteria strains showed an increasing resistance pattern to a wide range of the antibiotics most commonly used at the hospital. Comparison of the genomes will give insights regarding how antibiotic resistance evolves within K. pneumonia and will aid in efforts to reduce the increasing prevalence of antibiotic resistance worldwide. In addition, the comparison of these genomes with other previously studied bacteria will help to understand how a microorganism that is part of our normal microbiome can become a dangerous pathogen.
“Fast and affordable sequencing of pathogenic bacteria is a huge qualitative and quantitative advance that is radically changing the way researchers and clinicians view the infectious disease process,” said Dr. Jesús Mingorance lead researcher at the Hospital Universitario La Paz. The GS FLX+ and GS Junior Systems from Roche are aiding in these pathogen detection and bacterial comparative genomics efforts worldwide.

About Roche
Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world’s largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in diabetes management. Roche’s personalized healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2011, Roche had over 80,000 employees worldwide and invested over 8 billion Swiss francs in R&D. The Group posted sales of 42.5 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan. For more information: www.roche.com.

About IdiPAZ
The IdiPAZ Institute for Health Research was created as a place for biomedical research, as a result of the relationship that has been forged over the years between La Paz University Hospital (HULP) and the Autonomous University of Madrid (UAM). This strategic alliance has enabled multidisciplinary teams belonging to the above institutions to be set up in order to take on joint research projects, making the most of the human and material research resources at their disposal and promoting fundraising for research. For more information: www.idipaz.es.

About Era7 Bioinformatics
Era7 bioinformatics is the leading Spanish Next Generation Sequencing bioinformatics company with a business model based on Research, Open Source and the use of Amazon Cloud Computing. Its focus on bacterial genomics has led to the development of BG7, an innovative pipeline for bacterial genome annotation designed for Next Generation Sequencing data. For more information: www.era7bioinformatics.com.

About LifeSequencing
LifeSequencing is based in Valencia, Spain. It is the leading Spanish company in Next Generation Sequencing data generation and interpretation. Lifesequencing is specialized in developing Taylor made massive sequencing solutions for answering any question that researchers and private companies may arise. For further information: www.lifesequencing.com.

Era7 Bioinformatics Inc will be focused on bacterial genomics, metagenomics and cloud computing. Besides tailored projects, this new subsidiary will market:

• Complete BG7: A complete service from sequencing experiment design to final bioinformatics analysis for bacterial genomes

• MG7 Metagenomics: A fast and reliable service for metagenomics analysis using cloud computing

And other NGS related services like

• Exome or

• Transcriptome analysis