DNA Copy Number Analysis of FFPE Samples

DNA copy number analysis was performed using an oligonucleotide a-CGH platform (SurePrint G3 Human CGH Microarray 8x60K; Agilent Technologies Inc., Santa Clara, CA, USA), using a previously established protocol for FFPE samples [43 (link), 44 (link)]. DNA was isolated using the standard phenol-chloroform method. Reference DNA was prepared from the peripheral blood of a pool of ten healthy donors [45 (link)]. Equal amounts of tumor and reference genomic DNA (1–2 μg) were digested, enzymatically labeled using the SureTag Complete DNA Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA), and hybridized to the arrays. The array data were analyzed with the Feature Extraction v.10.10 software and Agilent CytoGenomics v.3.0 software (Agilent Technologies Inc., Santa Clara, CA, USA) using the ADM-2 algorithm, threshold 6.0, and an aberration filter with a minimum of >3 probes [45 (link)]. Copy number gains and losses were defined as previously described [44 (link)].

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Gradowski Farias da Costa do Nascimento T., de Oliveira Thomazini M.E., de França Junior N., de Castro Poncio L., Fonseca A.S., de Figueiredo B.C., Weber S.H., Herai R.H., de Noronha L., Cavalli L.R., Feltes B.C, & Elifio-Esposito S. (2022). Systems biology network reveals the correlation between COX-2 expression and Ch 7q copy number alterations in Ch 11q-deleted pediatric neuroblastoma tumors. Genes & Cancer, 13, 60-71.

Publication 2022

SurePrint G3 Human CGH Microarray 8x60K SureTag Complete DNA Labeling Kit Agilent CytoGenomics v.3.0 software

Chloroform Genomic Human Microarray Oligonucleotide Peripheral blood donors Phenol Tumor

Corresponding Organization :

Other organizations : Pontifícia Universidade Católica do Paraná, Georgetown University Medical Center, Georgetown University, Universidade Federal do Rio Grande do Sul

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Variable analysis

independent variables

DNA copy number analysis

dependent variables

Copy number gains and losses

control variables

Peripheral blood of a pool of ten healthy donors
Equal amounts of tumor and reference genomic DNA (1–2 μg)

controls

Positive control: Reference DNA prepared from the peripheral blood of a pool of ten healthy donors
Negative control: Not explicitly mentioned

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