Programs and algorithms for gene expression and sequencing (big) data analysis

Thanks to its over 18 years experience, Acobiom has acquired expertise on gene expression by bioinformatic analysis. Hence, the company has developed proprietary bioinformatic programs and databases for analyzing sequencing data.

Bioinformatic developments leading to new leads and diagnostic development

Based on more than 18 years of experience of working with computational experts and biological specialists, Acobiom’s bioinformatic platform has been dedicated to genomic data management and it is to play a leading role in the following developments:

  • analyzing the results generated by its new high throughput platforms, including:
    • Sequence analysis,
    • Analysis of gene expression,
    • Analysis of regulation,
    • Measuring biodiversity,
    • etc,
  • integrating all these data into a network of interacting routes which provides the biotechnology industry and clinicians with the accurate targets or right information for curing patients.

Due to the fact that diseases and physiological adaptations are not linked to a single genetic modification occurring in a specific manner, but to complex routes associated with genetic networks, which interact with each other, Acobiom has developed bioinformatic tools to help researchers and physicians to:

  • understand the complex interactions between the genetic networks,
  • gather considerable amounts of closely related medical and biological data,
  • provide a comprehensive overview of diseases through the data connection.

This comprehensive overview of disorders will enable to:

  • improve treatments,
  • reduce the cost of care through a more efficient treatment targeting strategy,
  • contribute to the development of new drugs or new treatments for serious diseases with significant unmet needs.

Therefore, Acobiom’s bioinformatic plateform represent a driving factor in computational sciences for managing the wealth of data that are to be generated in the medical revolution over the next decade.

 

Bioinformatics for gene expression analysis

Except for some particular cases which are now well-known, most recent medical improvements and studies have underlined that diseases and physiological adaptations are not linked to a single genetic modification occurring in a specific manner, but to complex routes associated with genetic networks, which interact with each other.

Understanding the complex interactions occurring between genetic networks is the key challenge to be met in the medical field over the next decade. In this aim, scientists worldwide have gathered an impressive amount of medical and biological data which need to be closely connected in order to provide a comprehensive overview of diseases. This comprehensive overview of medical disorders will enable to improve treatments within the field of Personalized Medicine and will help to design new drugs or treatments for serious diseases with significant unmet medical needs.

At the same time, high-performance computing applications have increasingly adopted new architecture–based servers. However, new sequencing technologies, producing DNA sequences, have also made huge progresses. Today, these new high throughput sequencing systems provide a considerable amount of data (BIG DATA) which have to be processed by a high-performance computer.

Acobiom provides private bioinformatic services platforms dedicated to genomic analyses and to the implementation of these data in pathways and clinical routes.

 

Bioinformatics for sequencing data analysis

Regarding the expansion of high throughput sequencing methods such as Roche-454 (GsFlx), Illumina (1G sequencer) or Applied (SOLID), new tools are now available and they offer efficient approaches for rapidly sequencing DNA. As a result, generating sequencing data becomes very easy, but analyzing these BIG DATA becomes a huge challenge.

Therefore, Acobiom has developped specific bioinformatic programs and databases for analyzing the results generated by the aforementioned high throughput systems, including sequence analysis, gene annotation, computational evolutionary biology, measuring biodiversity, analysis of regulation, analysis of protein expression, analysis of mutation in cancer, etc.

Within the quest for the $1,000 Human Genome, the bioinformatic platform of Acobiom will be a key tool for comparing each patient with known data regarding medical disorders.

Acobiom’s private bioinformatic platform is especially focused on genomic data management. This platform is based on 17 years of experience gained through the association of computational and biological experts.

 

Bioinformatic capabilities to treat omic BIG DATA

The ongoing development of molecular measurement technology provides a huge amount of data, the BIG DATA.

In two decade, scientists have gone from the sheet of paper for reading sequencing data to the receipt of a hard drive containing several Gigabits of Data, the Origin of Big Data; and to analyze these Big Data, scientists have to switch their traditional easy-to-use tool or database to multiprocessors, multicores and parallelism platforms and programs. But these changes allow observing cellular systems at an increasing number of levels and in increasing details, which impose increasing demands on statistical methods and bioinformatic tools for the analysis and the management of this huge amount of data generated by these technologies.

Beyond the early stages of the simple commercial availabilities, Acobiom proposes specific softwares, programs and algorithms to treat and analyze omic Big Data obtained from NGS or qPCR systems.

Facing to the increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data, Acobiom adjusts tools and parameters to the specifications of its partners and their specific biological requests. It may concern RNA profiling (RNAseq, microRNA, etc.), DNA (full genome, HLA typing, targeting resequencing, ATACseq, etc.), a De novo Assembly, a SNPs or InDels detection, an Alignment analysis..

 

MARS (Matrix of RNA-Seq) project

The aim of the MaRS research program is to collect and to allow the comparison of the NGS transcriptomic data produced by laboratories around the world. MaRS is focused on the RNA‐Seq method, which reflects the expression of the genes in a specific condition.

MaRS contains 27,000 Human RNA‐Seq profiles generated by Next Generation Sequencing.

All these data have been collected and computed with a single method to allow their compilation in one matrix: MaRS. It represents a huge amount of data (#BigData) and requires the use of High Performance Computing (HPC) on the cluster Occigen (CINES): 120 To of compressed data downloaded and 1.2 million hours/core consumed.

The MaRS (Matrix of RNA-Seq) project has been granted by the SHAPE EU Program organized by the PRACE Initiative.
SHAPE, the SME HPC Adoption Programme in Europe, is a pan-European, PRACE-based programme supporting HPC adoption by SMEs. This Programme aims to raise awareness and equip European SMEs with the expertise necessary to take advantage of the innovation possibilities opened up by High Performance Computing (HPC), thus increasing their competitiveness.

For more information: www.prace-ri.eu/hpc-access/shape-programme/

During the 12th meeting of the Grand Sud Ouest Canceropole (Nov. 23-25, 2016, La Grande Motte, France), the MaRS project has been presented to scientists through a presentation: GSO_2016_MaRS and a poster: GSO_MaRS_poster.

 

Examples of Bioinformatics and Biostatistics treatments associated with transcriptomics analyses