{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Guillaume Assié"],"study_type":["genotyping by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-42171"],"description":["AIMAH is an ACTH-independent bilateral enlargement of the adrenal cortex occuring during adulthood. The enlargment is related to the growth of multiple benign nodules. This condition is associated with various degrees of cortisol hypersecretion. The occurence of several nodules in both adrenals, and the existence of familial forms, suggest the existence of a germline genetic predisposition. To find the gene(s), the aim of the project was to look for recurrent chromosomal alterations in the AIMAH nodules. Extensive mapping of somatic gains, losses and copy-neutral loss of heterozygosity (LOH) was performed with Affymetrix SNP6 arrays. A copy neutral LOH of 16p, occuring in 7 of 26 patients, was one of the only recurrent alterations, pointing towards a candidate gene in this region. Of note this condition differs from the congenital adrenal hyperplasias, related to genetic alterations of steroidogenesis (the latter is an ACTH dependent adrenal hyperplasia). Affymetrix SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved tumor samples or peripheral blood samples. Copy number and LOH analysis of Affymetrix SNP6 arrays was performed for AIMAH nodules from 26 patients, including 18 with paired leucocyte and nodules (1 to 4 nodules per patient), and 8 with a single nodule (no paired leucocyte available)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - As per manufacturer (Affymetrix)","Nucleic Acid Extraction - AIMAH nodules DNA was extracted with Qiagen QIAamp MinElute. Leucocyte DNA was extracted with the Roche DNA isolation kit for mammalian blood. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.","Scaning - The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.","Labeling - As per manufacturer (Affymetrix)"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Bruno Ragazzon","Jérôme Bertherat","Windy Luscap","Rossella Libé","Guillaume Assié"],"data_protocol":["Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H2L_CNState =  H2L_Genotype =  H2L_signalA =  H2L_signalB =  H2L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H44L_CNState =  H44L_Genotype =  H44L_signalA =  H44L_signalB =  H44L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H6T2_CNState =  H6T2_Genotype =  H6T2_signalA =  H6T2_signalB =  H6T2_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H6T1_CNState =  H6T1_Genotype =  H6T1_signalA =  H6T1_signalB =  H6T1_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H2T4_CNState =  H2T4_Genotype =  H2T4_signalA =  H2T4_signalB =  H2T4_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H8T_CNState =  H8T_Genotype =  H8T_signalA =  H8T_signalB =  H8T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H3L_CNState =  H3L_Genotype =  H3L_signalA =  H3L_signalB =  H3L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H44T1_CNState =  H44T1_Genotype =  H44T1_signalA =  H44T1_signalB =  H44T1_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H7T_CNState =  H7T_Genotype =  H7T_signalA =  H7T_signalB =  H7T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H4L_CNState =  H4L_Genotype =  H4L_signalA =  H4L_signalB =  H4L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H11T_CNState =  H11T_Genotype =  H11T_signalA =  H11T_signalB =  H11T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H23T_CNState =  H23T_Genotype =  H23T_signalA =  H23T_signalB =  H23T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H25T_CNState =  H25T_Genotype =  H25T_signalA =  H25T_signalB =  H25T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H27T_CNState =  H27T_Genotype =  H27T_signalA =  H27T_signalB =  H27T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H9L_CNState =  H9L_Genotype =  H9L_signalA =  H9L_signalB =  H9L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H17L_CNState =  H17L_Genotype =  H17L_signalA =  H17L_signalB =  H17L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H1T_CNState =  H1T_Genotype =  H1T_signalA =  H1T_signalB =  H1T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H44T2_CNState =  H44T2_Genotype =  H44T2_signalA =  H44T2_signalB =  H44T2_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H15L_CNState =  H15L_Genotype =  H15L_signalA =  H15L_signalB =  H15L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H13L_CNState =  H13L_Genotype =  H13L_signalA =  H13L_signalB =  H13L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H11L_CNState =  H11L_Genotype =  H11L_signalA =  H11L_signalB =  H11L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H1L_CNState =  H1L_Genotype =  H1L_signalA =  H1L_signalB =  H1L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H6L_CNState =  H6L_Genotype =  H6L_signalA =  H6L_signalB =  H6L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H44T3_CNState =  H44T3_Genotype =  H44T3_signalA =  H44T3_signalB =  H44T3_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H9T_CNState =  H9T_Genotype =  H9T_signalA =  H9T_signalB =  H9T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H7L_CNState =  H7L_Genotype =  H7L_signalA =  H7L_signalB =  H7L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H4T_CNState =  H4T_Genotype =  H4T_signalA =  H4T_signalB =  H4T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H17T2_CNState =  H17T2_Genotype =  H17T2_signalA =  H17T2_signalB =  H17T2_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H16T_CNState =  H16T_Genotype =  H16T_signalA =  H16T_signalB =  H16T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H8L_CNState =  H8L_Genotype =  H8L_signalA =  H8L_signalB =  H8L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H15T_CNState =  H15T_Genotype =  H15T_signalA =  H15T_signalB =  H15T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H3T_CNState =  H3T_Genotype =  H3T_signalA =  H3T_signalB =  H3T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H22T_CNState =  H22T_Genotype =  H22T_signalA =  H22T_signalB =  H22T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H13T_CNState =  H13T_Genotype =  H13T_signalA =  H13T_signalB =  H13T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H12T_CNState =  H12T_Genotype =  H12T_signalA =  H12T_signalB =  H12T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H21T_CNState =  H21T_Genotype =  H21T_signalA =  H21T_signalB =  H21T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H20T_CNState =  H20T_Genotype =  H20T_signalA =  H20T_signalB =  H20T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H14T_CNState =  H14T_Genotype =  H14T_signalA =  H14T_signalB =  H14T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H12L_CNState =  H12L_Genotype =  H12L_signalA =  H12L_signalB =  H12L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H26T_CNState =  H26T_Genotype =  H26T_signalA =  H26T_signalB =  H26T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H6T3_CNState =  H6T3_Genotype =  H6T3_signalA =  H6T3_signalB =  H6T3_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H24T_CNState =  H24T_Genotype =  H24T_signalA =  H24T_signalB =  H24T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H10T_CNState =  H10T_Genotype =  H10T_signalA =  H10T_signalB =  H10T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H2T3_CNState =  H2T3_Genotype =  H2T3_signalA =  H2T3_signalB =  H2T3_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H16L_CNState =  H16L_Genotype =  H16L_signalA =  H16L_signalB =  H16L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H14L_CNState =  H14L_Genotype =  H14L_signalA =  H14L_signalB =  H14L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H17T1_CNState =  H17T1_Genotype =  H17T1_signalA =  H17T1_signalB =  H17T1_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H10L_CNState =  H10L_Genotype =  H10L_signalA =  H10L_signalB =  H10L_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H5T_CNState =  H5T_Genotype =  H5T_signalA =  H5T_signalB =  H5T_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H2T2_CNState =  H2T2_Genotype =  H2T2_signalA =  H2T2_signalB =  H2T2_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H6T4_CNState =  H6T4_Genotype =  H6T4_signalA =  H6T4_signalB =  H6T4_BAF =","Data Transformation - The array image was acquired using Affymetrix GeneChip® Command Console Scan Controle 3.2.3.1515. Affymetrix Genotyping Console 4.0 (default parameters) was used to extract from CEL files, for each marker (SNPs and copy number markers), the DNA copy number (Log2Ratio) and the copy number state, and for each SNP, the signal intensities of alleles A and B and genotype calls. With this information, chromsomomal segments gained, lost or with copy-neutral LOH were detected automatically using SOMATICs (Assié et al, 2007) adapted for Affymetrix (Assié et al, 2013) in R. SOMATICs also specifies the comptarment (somatic or germline) for each alteration observed in the tumor, whether the paired leucocyte is available or not. primary data description: Pos_GRCh36: physical position provided in the built 36 of the Genome Reference Consortium Human genome; Log2Ratio: normalized DNA copy number in Log2 scale; Genotype: AA AB BB NoCall; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B; BAF (B-allele frequency): normalized quantification of the allelic ratio, ranging from 0 for AA,  to 0.5 for AB SNPs without LOH, and to 1 for BB genotypes (generated by SOMATICs) ID_REF =  VALUE = normalized DNA copy number in Log2 scale H27L_CNState =  H27L_Genotype =  H27L_signalA =  H27L_signalB =  H27L_BAF ="],"additional_accession":[]},"is_claimable":false,"name":"Affymetrix SNP6 array data for ACTH-Independent Macronodular Adrenal Hyperplasia (AIMAH) samples","description":"AIMAH is an ACTH-independent bilateral enlargement of the adrenal cortex occuring during adulthood. The enlargment is related to the growth of multiple benign nodules. This condition is associated with various degrees of cortisol hypersecretion. The occurence of several nodules in both adrenals, and the existence of familial forms, suggest the existence of a germline genetic predisposition. To find the gene(s), the aim of the project was to look for recurrent chromosomal alterations in the AIMAH nodules. Extensive mapping of somatic gains, losses and copy-neutral loss of heterozygosity (LOH) was performed with Affymetrix SNP6 arrays. A copy neutral LOH of 16p, occuring in 7 of 26 patients, was one of the only recurrent alterations, pointing towards a candidate gene in this region. Of note this condition differs from the congenital adrenal hyperplasias, related to genetic alterations of steroidogenesis (the latter is an ACTH dependent adrenal hyperplasia). Affymetrix SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved tumor samples or peripheral blood samples. Copy number and LOH analysis of Affymetrix SNP6 arrays was performed for AIMAH nodules from 26 patients, including 18 with paired leucocyte and nodules (1 to 4 nodules per patient), and 8 with a single nodule (no paired leucocyte available)","dates":{"release":"2013-11-28T00:00:00Z","modification":"2023-08-25T11:15:51.305Z","creation":"2022-01-31T19:38:43.631Z"},"accession":"E-GEOD-42171","cross_references":{"GEO":["GSE42171"],"EFO":["EFO_0002767"]}}