High Quality Analyses & Collaborative Approach
AltraBio leverages its renowned expertise in bioinformatics, biostatistics, and biology to offer services in the analysis and interpretation of various omics data types, including genomics, epigenomics, transcriptomics, proteomics, and more.
Our team works closely with clients and partners on each project to ensure their goals are met. This collaborative approach guarantees that our analyses align with your research objectives.
Expertise in Biostatistics and Bioinformatics
Before conducting differential analyses, we implement various methods to assess data quality and consistency with the experimental design. We address outliers and effects unrelated to the design, ensuring the relevance of the analysis.
Experimental designs often involve multiple factors such as donor, cell type, treatment, dose, and time points. To address the biological questions of the study, AltraBio identifies the most appropriate statistical model, considering paired designs, batch effect corrections, estimation of hidden factors, and outlier weighting.
AltraBio excels in integrating various data types, including multi-omics, cytometry, and medical data. We employ both supervised and unsupervised machine learning for applications such as biomarker identification, classification, and predictive models for diagnostics or treatment response. Our clients benefit from our proficiency in state-of-the-art machine learning algorithms.
Expertise in Biology
We identify biological processes and pathways through complementary methods of functional category enrichment. These automated results are reviewed to assess their relevance within the biological context of the study.
Beyond providing lists of molecules and pathways, AltraBio extracts meaningful insights. During the interpretation phase, we consider the initial biological questions and evaluate the results while integrating available scientific literature and databases. Our goal is to understand the biological mechanisms and formulate new hypotheses for validation.
Reporting
All work conducted is summarized in a comprehensive report, provided to our clients and explained during a video conference. This exchange clarifies the chosen methodological approaches and their results, ensuring a thorough understanding of the data.
The results of statistical analyses are accessible through the WikiBioPath web interface. This platform provides clients with visualization and analysis tools to continue exploring their data. Users can easily visualize volcano plots, generate heat maps, perform PCA, and conduct enrichment analyses on gene selections.
Our Publications
2012
Idbaih, Ahmed; Ducray, François; Dehais, Caroline; Courdy, Célia; Carpentier, Catherine; de Bernard, Simon; Uro-Coste, Emmanuelle; Mokhtari, Karima; Jouvet, Anne; Honnorat, Jérôme; Chinot, Olivier; Ramirez, Carole; Beauchesne, Patrick; Benouaich-Amiel, Alexandra; Godard, Joël; Eimer, Sandrine; Parker, Fabrice; Lechapt-Zalcman, Emmanuelle; Colin, Philippe; Loussouarn, Delphine; Faillot, Thierry; Dam-Hieu, Phong; Elouadhani-Hamdi, Selma; Bauchet, Luc; Langlois, Olivier; Guerinel, Caroline Le; Fontaine, Denys; Vauleon, Elodie; Menei, Philippe; Fotso, Marie Janette Motsuo; Desenclos, Christine; Verrelle, Pierre; Ghiringhelli, François; Noel, Georges; Labrousse, François; Carpentier, Antoine; Dhermain, Frédéric; Delattre, Jean-Yves; Figarella-Branger, Dominique
SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas Journal Article
In: PLoS One, vol. 7, no. 10, pp. e45950, 2012, ISSN: 1932-6203.
@article{pmid23071531,
title = {SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas},
author = {Ahmed Idbaih and François Ducray and Caroline Dehais and Célia Courdy and Catherine Carpentier and Simon de Bernard and Emmanuelle Uro-Coste and Karima Mokhtari and Anne Jouvet and Jérôme Honnorat and Olivier Chinot and Carole Ramirez and Patrick Beauchesne and Alexandra Benouaich-Amiel and Joël Godard and Sandrine Eimer and Fabrice Parker and Emmanuelle Lechapt-Zalcman and Philippe Colin and Delphine Loussouarn and Thierry Faillot and Phong Dam-Hieu and Selma Elouadhani-Hamdi and Luc Bauchet and Olivier Langlois and Caroline Le Guerinel and Denys Fontaine and Elodie Vauleon and Philippe Menei and Marie Janette Motsuo Fotso and Christine Desenclos and Pierre Verrelle and François Ghiringhelli and Georges Noel and François Labrousse and Antoine Carpentier and Frédéric Dhermain and Jean-Yves Delattre and Dominique Figarella-Branger},
doi = {10.1371/journal.pone.0045950},
issn = {1932-6203},
year = {2012},
date = {2012-01-01},
urldate = {2012-01-01},
journal = {PLoS One},
volume = {7},
number = {10},
pages = {e45950},
abstract = {Anaplastic oligodendrogliomas (AOD) are rare glial tumors in adults with relative homogeneous clinical, radiological and histological features at the time of diagnosis but dramatically various clinical courses. Studies have identified several molecular abnormalities with clinical or biological relevance to AOD (e.g. t(1;19)(q10;p10), IDH1, IDH2, CIC and FUBP1 mutations).To better characterize the clinical and biological behavior of this tumor type, the creation of a national multicentric network, named "Prise en charge des OLigodendrogliomes Anaplasiques (POLA)," has been supported by the Institut National du Cancer (InCA). Newly diagnosed and centrally validated AOD patients and their related biological material (tumor and blood samples) were prospectively included in the POLA clinical database and tissue bank, respectively.At the molecular level, we have conducted a high-resolution single nucleotide polymorphism array analysis, which included 83 patients. Despite a careful central pathological review, AOD have been found to exhibit heterogeneous genomic features. A total of 82% of the tumors exhibited a 1p/19q-co-deletion, while 18% harbor a distinct chromosome pattern. Novel focal abnormalities, including homozygously deleted, amplified and disrupted regions, have been identified. Recurring copy neutral losses of heterozygosity (CNLOH) inducing the modulation of gene expression have also been discovered. CNLOH in the CDKN2A locus was associated with protein silencing in 1/3 of the cases. In addition, FUBP1 homozygous deletion was detected in one case suggesting a putative tumor suppressor role of FUBP1 in AOD.Our study showed that the genomic and pathological analyses of AOD are synergistic in detecting relevant clinical and biological subgroups of AOD.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}