Illumina SNP arrays were used to analyse the DNA samples from 161 tumour samples (74 Illumina HumanCNV610-Quad v1.0, 52 HumanCNV370, 34 HumanOmniExpress-12v1 and 1 HumanCore-12v1). Integragen SA (Evry, France) carried out hybridization, according to the manufacturer’s recommendations. The BeadStudio software (Illumina) was used to normalize raw fluorescent signals and to obtain log R ratio (LRR) and B allele frequency (BAF) values. Asymmetry in BAF signals due to bias between the two dyes used in Illumina assays was corrected using the tQN normalization procedure.39 (link) We used the circular binary segmentation algorithm40 to segment genomic profiles and assign corresponding smoothed values of log R ratio and B allele frequency. The Genome Alteration Print method was used to determine the ploidy of each sample, the level of contamination with normal cells and the allele-specific copy number of each segment41 (link).
Kamoun A., Idbaih A., Dehais C., Elarouci N., Carpentier C., Letouzé E., Colin C., Mokhtari K., Jouvet A., Uro-Coste E., Martin-Duverneuil N., Sanson M., Delattre J.Y., Figarella-Branger D., de Reyniès A, & Ducray F. (2016). Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas. Nature Communications, 7, 11263.
Allele AssaysDyesGenome Genomic profiles Hybridization Normal cells Tumour dna
Corresponding Organization : Hospices Civils de Lyon
Other organizations :
La Ligue Contre le Cancer, Institut du Cerveau, Pitié-Salpêtrière Hospital, Sorbonne Université, Assistance Publique – Hôpitaux de Paris, Institut de Neurobiologie de la Méditerranée, Hôpital Rangueil, Inserm, Centre National de la Recherche Scientifique, Bicêtre Hospital, Peuplements végétaux et bioagresseurs en milieu tropical, Centre Hospitalier Universitaire Dijon Bourgogne, Centre Hospitalier Universitaire de Montpellier, Centre Hospitalier Régional et Universitaire de Nancy, Centre hospitalier régional d'Orléans, Centre Hospitalier René-Dubos, Hôpital Avicenne, Clinique des Cèdres, Hôpital Beaujon, Centre Hospitalier Universitaire de Rennes, Hôpital de la Timone, Assistance Publique Hôpitaux de Marseille, Institut Claudius Regaud, Hôpital Nord, Hôpital d'Instruction des Armées Sainte-Anne, Institut Gustave Roussy, Centre Hospitalier Universitaire de Reims, Université de Reims Champagne-Ardenne, Hôpital Pellegrin, Centre Hospitalier Universitaire de Bordeaux, Centre Hospitalier Universitaire de Nice, Hôpital Foch, Hopitaux Civils de Colmar, Centre Georges François Leclerc, Centre Hospitalier Universitaire de Besançon, Hôpital Dupuytren, Centre Hospitalier Universitaire de Limoges, Université de Caen Normandie, Centre Hospitalier Universitaire de Caen, Hôpital Lariboisière, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Charles-Nicolle, Centre Hospitalier Universitaire de Poitiers, Hôpitaux Universitaires Henri-Mondor, Centre Hospitalier Universitaire de Nantes, Centre Hospitalier Universitaire de Lille, Centre Hospitalier Universitaire d'Angers, HIA du Val-de-Grâce à Paris, Centre Eugène Marquis
Illumina SNP arrays used to analyse DNA samples from 161 tumour samples
Hybridization carried out by Integragen SA (Evry, France) according to the manufacturer's recommendations
BeadStudio software (Illumina) used to normalize raw fluorescent signals and obtain log R ratio (LRR) and B allele frequency (BAF) values
TQN normalization procedure used to correct asymmetry in BAF signals
Circular binary segmentation algorithm used to segment genomic profiles and assign corresponding smoothed values of log R ratio and B allele frequency
Genome Alteration Print method used to determine the ploidy of each sample, the level of contamination with normal cells and the allele-specific copy number of each segment
dependent variables
Log R ratio (LRR) values
B allele frequency (BAF) values
Ploidy of each sample
Level of contamination with normal cells
Allele-specific copy number of each segment
control variables
Manufacturer's recommendations for hybridization
Annotations
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