Intess™ - InteRNA Genomics Software and Services

While the generation of MPS data can be outsourced to a number of sequencing service providers, data processing and interpretation requires highly skilled bioinformaticians and a dedicated computational infrastructure - a challenge for many organizations. The software and services that are developed by InteRNA Genomics are build on many years of experience analyzing DNA sequencing data as well as pioneering work in the generationa and analysis of small RNA data generated by massively parallel sequencing (See publications).

The Intess™ solutions deliver complete, up-to-date and ready-to-interpret analyses of raw sequencing data, allowing the researcher to focus on the biological problem at hand. The informatics solutions are modular and easily customized, enabling development of data analysis pipelines that take into account specifics of every individual project.

The Intess™ solutions are platform-independent and have been validated with experimental data obtained on Roche/454 (GS-20 and GS-FLX), Illumina (Genome Analyzer) and Applied Biosystems (SOLiD) platforms. InteRNA Genomics provides solutions for all U-HTP application areas, including:

Small RNA analysis (miR-Intess™)
Gene expression profiling (Gene-Intess™)
ChIP sequencing (ChIP-Intess™)
Genome variation (Genome-Intess™)

InteRNA Genomics also provides a complete U-HTP sequencing service, which includes consultancy for the experimental design, preparation and sequencing of customer samples on various sequencing platforms and data analysis. The state of the art facilities and enormous know how and experience guarantee high quality results. InteRNA Genomics provides its customized services to academic institutions as well as commercial organizations.


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Massively parallel sequencing gains ground

It took more than a decade and hundreds of millions of dollars to determine the sequence of the first human genome. The second genome was finished within three months and cost less than $1 million, thanks to the development of novel sequencing technology. Several companies are currently perfecting their versions of massively parallel sequencing (MPS) in a race towards the ultimate goal of determining a complete human genome for $1000 - this would start an era of personalized genomics and medicine. While a one-thousand-dollar genome is still a distant prospective, the current U-HTP sequencing technologies are quickly gaining momentum in basic genomics and biomedical research. Most microarray-based experiments, such as gene expression profiling and ChIP-on-chip, can be adapted to these new sequencing platforms, resulting in a significant increase in quantity and quality of the generated data. Small RNA discovery and expression profiling and genome (re)sequencing for single nucleotide polymorphism (SNP) detection are also increasingly performed by MPS.

miR-Intess™ small RNA analysis pipeline

The miR-Intess™ analysis platform utilizes proprietary miRNA discovery and small RNA classification tools, as well as miRNA target-prediction tools, based on the latest insights and standards in the field. Versatile summaries, both graphically and tabular, are provided to obtain insight in the small RNA component of any sample that was analyzed on any of the next-generation sequencing platforms. The figure belows shows a graphical representation of the modular structure of the miR-Intess pipeline. Visit the Demo page for examples of analysis output. Please contact us for customized solutions or to obtain a quote for analysis of your project.

Publications based on informatics pipelines from InteRNA Genomics

Berezikov, E. and Cuppen E. (2008). MicroRNA discovery and expression profiling using next-generation sequencing. In: Genome Sequencing, Editor Janitz, Wiley, Wienheim, Germany, in press.

Berezikov, E., Chung, W.J., Willis, J., Cuppen, E., and Lai, E.C. (2007). Mammalian mirtron genes. Mol. Cell 28:328-336

Berezikov, E., van Tetering, G., Verheul, M., van de Belt, J., van Laake, L., Vos, J., Verloop, R., van de Wetering, M., Guryev, V., Takada, S., van Zonneveld, A. J., Mano, H., Plasterk, R. and Cuppen, E. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 16, 1289-1298.

Berezikov, E., Thuemmler, F., van Laake, L., Kondova, I., Bontrop, R., Cuppen, E. and Plasterk, R. H. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38, 1375-1377.

Kloosterman, W. P., Steiner, F. A., Berezikov, E., de Bruijn, E., van de Belt, J., Verheul, M., Cuppen, E. and Plasterk, R. H. A. (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res. 34, 2558-2569.

Takada, S., Berezikov, E., Yamashita, Y., Lagos-Quintana, M., Kloosterman, W. P., Enomoto, M., Hatanaka, H., Fujiwara, S., Watanabe, H., Soda, M., Choi, Y. L., Plasterk, R. H. A., Cuppen, E. and Mano, H. (2006) Mouse microRNA profiles determined with a new and sensitive cloning method. Nucleic Acids Res. 34, e115.

Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H. and Cuppen, E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21-24.