Oligonucleotide Array-CGH for FFPE Samples

DNA copy number analysis was performed using an oligonucleotide array-CGH platform (SurePrint G3 Human CGH Microarray 8×60K; Agilent Technologies Inc., Santa Clara, CA), according to the protocol for FFPE samples that we have established in our lab [70 (link)]. DNA was isolated from consecutive FFPE sections of the cases profiled for miRNA. DNA isolated from peripheral blood from multiple normal individuals was used as control DNA. The array data was analyzed using the Feature Extraction (FE) v.10.10 and Agilent CGH Analytics v.7.0 software (Agilent Technologies Inc., Santa Clara, CA), using the ADM-2 algorithm, threshold 6.0 and an aberration filter with a minimum number > 3 probes. Gene amplifications and deletions were defined as minimum average absolute log2 ratio (intensity of the Cy5 dye (reference DNA)/intensity of the Cy3 dye (test DNA) value of > 0.25 and <−0.25, respectively, as per the CGH analytics analysis.

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Sugita B., Gill M., Mahajan A., Duttargi A., Kirolikar S., Almeida R., Regis K., Oluwasanmi O.L., Marchi F., Marian C., Makambi K., Kallakury B., Sheahan L., Cavalli I.J., Ribeiro E.M., Madhavan S., Boca S., Gusev Y, & Cavalli L.R. (2016). Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women. Oncotarget, 7(48), 79274-79291.

Publication 2016

SurePrint G3 Human CGH Microarray 8×60K

Blood Cy3 dye Deletions Gene amplifications Human Microarray Mirna Oligonucleotide array

Corresponding Organization :

Other organizations : Universidade Federal do Paraná, Georgetown University Medical Center, Georgetown University, AC Camargo Hospital, The Ohio State University, West University of Timişoara

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Variable analysis

independent variables

DNA copy number analysis platform (SurePrint G3 Human CGH Microarray 8×60K; Agilent Technologies Inc.)

dependent variables

DNA copy number (gene amplifications and deletions)

control variables

DNA isolated from peripheral blood from multiple normal individuals

controls

Positive control: DNA isolated from peripheral blood from multiple normal individuals
Negative control: Not explicitly mentioned

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