Copy Number Variation Analysis

Raw CEL signal intensity files (Generated using the Affymetrix Genome-Wide Human SNP 6.0 Array) were processed with Affymetrix power tools and BIRDSUITE (Version 1.5.5)^{28 ,75 (link)}. Segmented copy-number calls were log2 transformed and further processed with GISTIC 2.0^{24 (link)} using an amplification and deletion threshold of 0.1. Samples with NSD1 copy number calls meeting the GISTIC 2.0 (Version 2.0.0) threshold and designated at least −1 or +1 were considered to have NSD1 deletions and amplifications, respectively.

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Brennan K., Shin J.H., Tay J.K., Prunello M., Gentles A.J., Sunwoo J.B, & Gevaert O. (2017). NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma. Scientific Reports, 7, 17064.

Publication 2017

Genome-Wide Human SNP 6.0 Array power tools

Deletion Deletions Genome human Nsd1

Corresponding Organization :

Other organizations : Stanford University, National University of Rosario

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Variable analysis

independent variables

NSD1 copy number calls meeting the GISTIC 2.0 (Version 2.0.0) threshold and designated at least -1 or +1

dependent variables

Segmented copy-number calls (log2 transformed)

control variables

Affymetrix power tools and BIRDSUITE (Version 1.5.5) used to process raw CEL signal intensity files
GISTIC 2.0 (Version 2.0.0) used to further process the log2 transformed segmented copy-number calls with an amplification and deletion threshold of 0.1

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