Genome-wide DNA Profiling with Illumina Infinium HumanCode-24 BeadChip
Illumina Infinium HumanCode-24 BeadChip SNP arrays were used to analyze the DNA samples. 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 procedure31 (link). We used the circular binary segmentation algorithm32 (link) to segment genomic profiles and assign corresponding smoothed values of LRR and BAF. 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 segment33 (link).
Lomberk G., Blum Y., Nicolle R., Nair A., Gaonkar K.S., Marisa L., Mathison A., Sun Z., Yan H., Elarouci N., Armenoult L., Ayadi M., Ordog T., Lee J.H., Oliver G., Klee E., Moutardier V., Gayet O., Bian B., Duconseil P., Gilabert M., Bigonnet M., Garcia S., Turrini O., Delpero J.R., Giovannini M., Grandval P., Gasmi M., Secq V., De Reyniès A., Dusetti N., Iovanna J, & Urrutia R. (2018). Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nature Communications, 9, 1978.
Allele AssaysDyesGenome Genomic profiles Hybridization Normal cells
Corresponding Organization :
Other organizations :
Medical College of Wisconsin, La Ligue Contre le Cancer, Mayo Clinic, Inserm, Centre de Recherche en Cancérologie de Marseille, Centre National de la Recherche Scientifique, Aix-Marseille Université, Institut Paoli-Calmettes, Institut Pprime, Hôpital de la Timone, Hôpital Nord
Hybridization of DNA samples on Illumina Infinium HumanCode-24 BeadChip SNP arrays
dependent variables
Log R ratio (LRR) values
B allele frequency (BAF) values
Segmented genomic profiles with corresponding smoothed values of LRR and BAF
Ploidy of each sample
Level of contamination with normal cells
Allele-specific copy number of each segment
control variables
Manufacturer's recommendations for Illumina Infinium HumanCode-24 BeadChip SNP array hybridization
TQN normalization procedure to correct asymmetry in BAF signals
Circular binary segmentation algorithm to segment genomic profiles
Genome Alteration Print method to determine ploidy, contamination, and allele-specific copy number
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