Omics Services

Precision Medicine - Biomarkers & Diagnostics

Services in Biomedical and Life Sciences Research

For 20 years, Acobiom provided a scientific expertise and a unique technical know-how in the fields of biomedical research, translational medicine and, more generally, life sciences. The objective is the development of new diagnostic tools and treatments through a collaborative and multidisciplinary approach, combining several technologies as genomics, transcriptomics, bioinformatics and biostatistics.

Customized services to meet the specific needs of each project

For 20 years, ACOBIOM has been analyzing, identifying and validating omic biomarkers (DNA, RNA, miRNA…) using a range of molecular biology technologies (sequencing, NGS, real-time PCR) combined with dedicated bioinformatics and biostatistics tools.

The company’s expertise in genomics and transcriptomics and its know-how in Omics data analysis allow it to provide a range of services to identify and/or validate biomarkers in the fields of translational medicine and life sciences research.

Hence, Acobiom provides several services as:
> Transcriptome analysis based on equencing (RNA-Seq)
> Whole genome sequencing, De novo genome sequencing, re-sequencing…
> Targeted sequencing of genomics regions of interest,
> Exome sequencing and analysis,
> Real-time PCR for analyzing gene expression
> Epigenomics analyses: methylome analysis, CHIP-Seq…
> Metagenomics analyses: Microbiome profiling…
> Genotyping / targeted genotyping…
> Microbiological analyses
> …

Why dealing with Acobiom?

Acobiom developed, validated and brought into clinical practice biomarkers and diagnostics based on its state-of-art experience and technologies.

Collaborating with Acobiom allows you to benefit from:
– A unique Biomarker Platform including multivariate Genotype/Phenotype resources,
– Over 20-years’ experience in customized analyses to identify and validate RNA/DNA biomarkers from different tissues and liquid biopsies,
– A scientific and process workflow approved/validated by clinical practice,
– Cutting-edge bioinformatics and data science tools,
– Methods and processes to analyze liquid biopsy, 
– Top down strategy for biomarker identification,
– No prior information required to identify new biomarkers,
– Large panel of health applications (cancer, infection, hematology, neurology, inflammation…),
– Patents on prognostic biomarkers/predictive biomolecular signatures,
– More than 60 scientific publications related to biomarkers, diagnostics and precision medicine.

Acobiom, a “Research Tax Credit” (CIR) organization approved by the French Ministry of Research

The services provided by Acobiom are eligible for the Research Tax Credit (CIR) of its clients, the Ministry of Higher Education, Research and Innovation has granted the company the “Research Tax Credit” approval until the end of 2019.

Customized services using a sequential approach

Acobiom provides Next Generation Sequencing services using the appropriate platform according to the project and to customer’s expectations.

From study design consuting, extraction of nucleic acids (RNA/DNA) to Bioinformatics treatment and Biostatistics analysis,  Acobiom provides a complete pipeline of services described in the following workflow:
> Experimental Design and analysis plan,
> Extraction and Sample preparation,
> NGS sequencing,
> Bioinformatics treatments and analysis,
> Biostatistics analysis,
> Report and monitoring.

Gene Expression or Transcriptome analysis by Sequencing

In transcriptomics domain, Acobiom provides analyses based on RNA sequencing approach (RNA-Seq, for instance) for the deep sequencing of RNA, supporting multiple applications including transcript identification, splice variant analysis and differential expression: coding or non coding RNA, miRNA, long RNA, RNA editing, alternative splicing, degradome…

This gene expression analysis allows to determine in different conditions which genes are differentially expressed by comparing their expression levels.

To perform this analysis, Acobiom realizes several technical steps:
> Experimental design,
> Optimization of sampling and storage preparation,
> RNA extraction and qualification,
> Library preparation,
> Sequencing,
> Data Quality check,
> Mapping on reference genome,
> Comparison of read counts,
> Annotation of sequences,
> Overview of expressed genes including statistics analysis, visualization and validation

RNA-Seq experiments

Acobiom provides personalized pipeline and algorithms for the gene expression analysis by RNA-Seq experiment according to the project and to customer’s expectations. A presentation of a RNA-Seq experiment is drawn below:

RNA Sequencing Presentation

PCR for biomarker analysis

Acobiom provides gene expression analysis services using customized Real-Time PCR (RT-qPCR) assays dedicated to targeted transcripts or a gene panel. The company possesses a huge expertise in PCR (qPCR, RT-PCR, qRT-PCR) for providing the most suitable and complete solution according to partner specifications.

From the PCR primer design to the hydrolysis probe, from data analysis to sample preparation, Acobiom’s team selects the appropriate PCR platform (Applied Biosystems, Roche Diagnostics, Fluidigm…) and chemistry (hydrolyse probessuch Taqman, Sybergreen, multiplex assays, HRM…) adapted to client/partner needs (RUO or In-Vitro Diagnostic/IVD device grade).

To make sense to Omics data, Acobiom delivers a report including raw data analysis, PCR specificity, PCR efficiency, assay repeatability/reproducibility, and specific information dedicated to the provided analyses (according to MIQE guidelines).

To complete its analysis services by PCR, Acobiom can select sets of RNA/DNA biomarkers for routine diagnostic kit through PCR (qPCR, RT-PCR, qRT-PCR) technology.

Microbiome profiling

Acobiom performs DNA extraction, PCR amplification and amplicon sequencing on the dedicated platform (Illumina, etc.).

Bioinformatics data processing and various biostatistical analyses make it possible to characterize bacterial species and monitor the correlations between the evolution of the different genera identified in the samples studied: Venn diagram, similarity analysis, similarity analysis, use of frequency distribution matrices of sequencing results…

Omics Services dedicated to Cosmetics

Acobiom uses its genomics and pharmacogenomics expertise to evaluate the effects of natural and synthetic compounds on skin and skin changes.

The company is involved in several studies to identify or analyze (skin) biomarkers that will make it possible to further comprehend and/or to validate pharmacogenomics effects of cosmetics products, allowing to generate assets and data about toxicity and efficacy.

Moreover, thanks to a dedicated transcriptomic database including more than 1,100 RNA-Seq human skin profiles, Acobiom can assist its clients and partners on finding or validating biomarkers or targets in order to develop new formulation, new compounds and products.

Bioinformatic and biostatistic treatments

Dedicated analyzes and customized treatments in bioinformatics

Facing to the growing demand about new bioinformatics tools and statistical methods for the analysis and management of massive amounts of sequencing data, Acobiom developed methods and tools dedicated to these genomic and transcriptomic analyses.

The technical team selected a set of software and algorithms adapted to each specific processing.

Based on its technical expertise and its library of computer programs, the company adapts its tools and parameters to meet the specifications of each request or project.

Acobiom’s team offers customized pipelines and algorithms for:
> the study of the transcriptome, including the expression of genes (encoding or not encoding) or splicing variants,
> the study of the genome, including the analysis of the genome and metagenome, the exome, the methyloma or the degeneration.

For each of the analyses and each of the stages constituting these analyses, Acobiom selects and adapts the tools and parameters to answer as precisely as possible the biological question studied.

Bioinformatic treatments of transcriptome analysis by RNA-Seq approach

For the bioinformatic analysis of the transcriptome by RNA-Seq, Acobiom follows a workflow including the following steps:
a/ Gene expression profiling for different biological conditions (mapping on an annotated reference genome, counting, normalization, sequence annotation),
b/ Overview and comparisons of expressed genes (differential analyses, visualization and statistical validation) .

Services provided include:
i) Quality control and sequence cleaning,
ii) Sequence mapping on the reference genome,
iii) Differential analysis of gene expression (genes differentially expressed or co-expressed).

Deliverables include:
i) Raw sequences (FASTQ),
ii) Mapping results (BAM),
iii) Tables of results of counting mapped sequences,
iv) Comparison tables of read counts with annotations and statistical analyses.

Bioinformatic treatments for exome analysis

The exome study corresponds to the analysis of the genetic variations of the coding part of the genome (exons) for a defined condition.

For the bioinformatic analysis of exomes, Acobiom follows a workflow including the following steps:
a) Exons analysis by NGS sequencing for the detection of splicing variant,
b) Precise detection of InDel and SNP, and SNP mutations.

Services provided include:
i) Quality control and sequence cleaning,
ii) Sequence mapping on the reference genome,
iii) Analysis of variants in relation to a reference or other condition.

Deliverables include:
i) Raw sequences (FASTQ),
ii) Mapping results (BAM),
iii) Variant tables (VCF), annotations,
iv) Statistical analysis to identify variants of interest.

Bioinformatic treatments of the metagenome and microbiome

The bioinformatics analysis of the microbiome includes the following steps:
a) Study of the microbial composition of a sample under a given condition,
b) Cleaning and clustering of representative sequences into OTUs (Operational Taxonomic Units), counting of populations,
c) Taxonomic analysis of samples (species detection),
d) Population and diversity analysis (Alpha-, Beta-diversity).

Services provided include:
i) Quality control and sequence cleaning,
ii) OTUs clustering tables and counts,
iii) Visualization files (species distribution, histograms…).

Bioinformatics treatments of the De Novo assembly of genomes and transcriptome

The bioinformatics analysis of the De Novo genome and transcriptome assembly includes the following steps:
a) De Novo Assembly: Genome or transcriptome assembly without using a reference,
b) Cleaning and assembly of sequences from high throughput sequencing,
c) Contig creation (continuous and ordered genomic sequences generated by the assembly),
d) Consensus sequence creation,
e) Sequence annotations,
f) Optimal strategy, specifically adapted to the type of sequencing and the organism studied.

Services provided include:
i) Quality control and sequence cleaning,
ii) Sequence files (FASTA/FASTQ),
iii) Annotation files,
(iv) Statistical overview and proposal of tools for visualizing results.

Study Design

Acobiom supports its partners in the design/experience plan of their studies by proposing designs optimized to their needs:
i) Classic and adaptive design,
ii) Calculation of power and individuals,
iii) Drafting of the Statistical Analysis Plan (SAP),
iv) Writing the statistical parts of the protocol,
v) CRF review,
vi) Randomization of individuals…

Statistical analysis & Reporting

The statistical analyses proposed by the company include the following steps:
i) Inferential analysis, descriptive analysis, multivariate analysis, machine learning, supervised/unsupervised clustering, time series, geostatistics…
ii) Production of tables, lists and graphs dedicated to communication and regulated information,
iii) Writing the statistical parts of the clinical study, producing statistics,
iv) Statistical reporting in compliance with regulatory authorities,
v) ISE and ISS (Integrated Summaries of Efficacy and Safety) writing for health authorities.

Services provided include:
i) Differential Expression cross-analysis,
ii) Dimension reduction,
iii) Classifier building,
iv) Modelling,
v) Features extraction and Parameter optimization…

Deliverables include:
i) Complete graphic synthesis, ready to use for any kind of presentation,
ii) Analytical synthesis for health authorities compliance,
iii) Predictive/Diagnostic tool for helping decision,
iv) Writing for scientific/marketing valorization,
v) List of validated biomarkers…