|
| Status |
Public on Aug 31, 2018 |
| Title |
Breast cancer tissue [T40] copy number |
| Sample type |
genomic |
| |
|
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer tissue
cell type: Somatic cell fraction
population: Mexican hispanic
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from peripheral blood lymphocytes was extracted with the QIAamp DNA Blood Maxi Kit (Qiagen, Valencia, CA), according to manufacturer’s instructions
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was digested with NspI and StyI enzymes (New England Biolabs), ligated to the respective Affymetrix adapters using T4 DNA ligase (New England Biolabs) amplified (Clontech), purified using magnetic beads (Agencourt), labeled, fragmented, and hybridized to the arrays
|
| Scan protocol |
As per manufacturer (Affymetrix)
|
| Description |
Hybridized to SNP6 Affymetrix
|
| Data processing |
Background correction and extraction of raw fluorescence intensity were performed with the Affymetrix Genotyping Console. To generate the copy number profiles we used the “Copy Number Inference” pipeline implemented in genepattern: (http://genepattern.broadinstitute.org/gp/pages/index.jsf). In brief, probe-level signal intensities from Affymetrix SNP6 (cel files) were normalized to a uniform brightness and merged to obtain values for each probe set using SNP File Creator. These intensities measurements were converted into a copy number call by the Copy Number Inference model. After reducing the noise by subtracting out the variation that is also seen within the normal samples (peripheral blood), the CBS segmentation algorithm identifies regions in the genome that have a uniform underlying copy number, creating a segmentation file. Finally, we identified the significantly somatic alterations with GISTIC using the cnv segmentation results.
Matched normalized SCNA and SNPs
|
| |
|
| Submission date |
Sep 17, 2016 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Sandra Lorena Romero-Cordoba |
| E-mail(s) |
sromero_cordoba@hotmail.com
|
| Organization name |
National Instute of Genomic Medicine
|
| Department |
Cancer Genomics
|
| Street address |
Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.
|
| City |
Mexico |
| State/province |
Mexico |
| ZIP/Postal code |
14610 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE87048 |
Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [copy number] |
| GSE87049 |
Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women |
|
