CASE STUDIES

Pharma Oncology

COMPANY & PROJECT

Pharmaceutical laboratory: identify nucleic acid-based oncology biomarkers (DNA and RNA) in liquid biopsies (plasma), with the aim of developing a non-invasive diagnostic tool and personalized therapy

REQUIREMENT

Implementation of a protocol for the sequencing and identification of tumor biomarkers

SERVICES PROVIDED

Protocol writing: sample preparation, choice of suitable NGS (high-speed) technologies (Illumina, Roche 454, Ion torrent: Proton / PGM, SOLiD
Quality control / data cleansing
In silico analysis of RNASeq and DNASeq data:
– Expression calculation
– Comparison of expression across samples
– Exploratory data analysis (principal component analysis, multiple correspondence analysis)

Identification of differentially expressed gene signatures based on fold change, adjusted p-value and AUC (Area Under ROC Curve) (Volcano Plot, list of differentially expressed genes and Venn diagram of signatures)
Gene visualization (Heatmap, scatter plot). Statistical sorting of multi-criteria data
Functional gene analysis
– Inclusion of data from public and private databases
– Exploration of metabolic data

Statistical sorting of multi-criteria data (RNA, mutations, CNV, etc.) (Elastic Net, Random Forest)
Report writing, assistance with publication and presentation of results

DELIVERABLES & BENEFITS

Study documentation (bibliography)
Genomic and transcriptomic databases (DNA, cDNA databases)
Functional analysis reports

Agronomics - Seeds

COMPANY & PROJECT

Agrifood company: Analysis of seed genomics data to identify the genes involved in the germination process in the face of water stress in the context of a plant selection project

REQUIREMENT

Carrying out the bioinformatics and biostatistics analysis stages of a genotyping project (identification of genetic and molecular signatures) for seeds.

SERVICES PROVIDED

Choice of sequencing strategy (illumina)
Analysis of NGS and microarray data (search for SSR microsatellites, SNP, insertion/deletion)
Analysis of NGS data
– Data mapping
– Identification of SSR microsatellites, SNP, insertion/ deletion

Quality control / data cleansing:
– Exploratory data analysis (PCA) enabling visual identification of a structure within the population (to then be factored into GWAS models)
– Data adjustment using a mixed model (with environmental effects as fixed and genotype effect as random)

Functional analysis of chromosomal events
Identification of differentially expressed gene signatures based on fold change, adjusted p-value.
Genome-wide association study (GWAS) enabling the analysis of genetic variations in several individuals in order to investigate the correlation between genotype and germination process
Analysis of linkage disequilibrium (LD) between markers
Visualization of p-values of genomic regions involved in character variation with a Manhattan plot
Writing of a report, assistance with publication and presentation of results

DELIVERABLES & BENEFITS

Study documentation
Genomic database
Reports presenting the genetic regions and/or candidate genes involved in the water stress process of the seeds in question

Cosmetics

COMPANY & PROJECT

Cosmetics company: development of innovative cosmetic products

REQUIREMENT

Analyze the impact of a cosmetic product on the skin using cutaneous microbiome data

SERVICES PROVIDED

Selection of the sequencing technology and analysis strategy: targeted 16S V3-V4 sequencing, Illumina
Implementation of analysis workflow
Data management: cross-referencing of metagenomic information with phenotype and environmental information
Identification of taxonomic profiles and microbial abundance of samples
– Alpha diversity (diversity, richness, variability indices)
– Beta diversity (distance calculations, PCoA)

Analysis at different levels of taxonomy: phylum, class, order, family, genus, (species)
Visualization interfaces (DataViz) and exploration of results

DELIVERABLES & BENEFITS

Study documentation
Description of analysis workflow
Interactive graphical visualizations
Report presenting product impact on cutaneous flora

Agrifood

COMPANY & PROJECT

Agrifood company: selection of bacterial strains

REQUIREMENT

Annotation of strain bank and identification of strains of interest

SERVICES PROVIDED

Hybrid assembly of NGS data
Structural and functional annotation of bacterial strains
Quality control
Comparative genomics
Characterization of operons of interest
Resistance and virulence research
Identification of metabolic pathways and prediction of enzymes of interest
Implementation of exploration interfaces

DELIVERABLES & BENEFITS

Study documentation
Analysis pipeline
Interactive graphical visualizations
Genomic database for the strain bank
Report

Epidemiology

COMPANY & PROJECT

Pharmaceutical laboratory: fighting infectious diseases

REQUIREMENT

Strain characterization and reconstruction of epidemiological history

SERVICES PROVIDED

Complete sequencing of bacterial strains
Mapping of data on the epidemiological reference genome
Identification of SNPs and chromosomal events
Characterization of variants (genes, functions)
Integration of specialized databases
Prediction of resistance and virulence
Phylogenetic classification

DELIVERABLES & BENEFITS

Study documentation
Interactive graphical visualizations
Classifications

Veterinary

COMPANY & PROJECT

Veterinary laboratory: joint analysis of multi-source data in association with productive livestock farms

REQUIREMENT

Creation of machine learning algorithms to detect genetic variations associated with phenotype data

SERVICES PROVIDED

Management of database infrastructure and calculation basis infrastructure
Creation of an algorithm/machine learning/deep learning
Building of an algorithm for imputation of missing data using various methods (machine learning, etc.)
Implementation of “benchmark” functionality for field teams with comparisons across individuals, products etc.
Creation of an application based on the algorithms developed and user training

DELIVERABLES & BENEFITS

Study documentation
Functional analysis reports

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