Computational protocol: A genomic approach to study down syndrome and cancer inverse comorbidity: untangling the chromosome 21

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Protocol publication

[…] We analyzed data from multiple platforms to generate both the disease-specific frequencies of amplification and deletion, as well as the frequency summaries for four tumor types described as low incidence tumors in DS by epidemiological studies based on previously published data (Table ). Raw Array CGH data files were downloaded from Gene Expression Omnibus, and normalization and conversion to log2 values of intensity were performed. Probe annotations from assemblies older than hg19 were remapped to hg19 using Lift Genome Annotation tool, software (http://genome.ucsc.edu/cgi-bin/hgLiftOver) which converts coordinates and genome annotation files between assemblies. To define amplification and deletion regions, we used the R-package CGHcall, which applies the Circular Binary Segmentation (CBS) algorithm (Hsu et al., ) it seeks out gain and loss segments by recursively dividing the genome until it identifies segments that have probe distributions different from their neighbors. This was followed by a CGHcall algorithm producing an objective and effective classification of the segmented data into copy number states. Once we had computed platform-specific data for amplification and deletion, we transformed them into multiplatform-comparable data. To do so, we defined 5000 anchor positions along chromosome 21, and performed an estimation of the amplification and deletion value for each of these anchors in every sample for every platform using custom R code (see Supplementary data). Once we had the amplification and deletion values for the anchors, we calculated the frequencies of amplification and deletion for the set of all diseases. […]

Pipeline specifications

Software tools CGHcall, DNA copy
Databases GEO
Application aCGH data analysis
Organisms Homo sapiens, Cucumber necrosis virus
Diseases Abnormalities, Drug-Induced, Leukemia, Melanoma, Movement Disorders, Neoplasms, Neoplasms, Germ Cell and Embryonal, Wilms Tumor