Comprehensive Genomic Profiling Protocol

Affymetrix SNP6 array data from the CCLE were processed together, quantile-normalized, and median-polished with Affymetrix power tools (25 (link)). The birdseed algorithm was used for genotyping. PennCNV was employed to generate log R ratio and B-allele frequencies (26 (link)). ASCAT was used to generate allele-specific copy number information, which was then used to compute LST, N_tAI, HRD-LOH scores in the R statistical environment (v3.0.2) following methods outlined in the initial publications (17 (link)–19 (link)).

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Lok B.H., Gardner E.E., Schneeberger V.E., Ni A., Desmeules P., Rekhtman N., de Stanchina E., Teicher B.A., Riaz N., Powell S.N., Poirier J.T, & Rudin C.M. (2016). PARP Inhibitor Activity Correlates with SLFN11 Expression and Demonstrates Synergy with Temozolomide in Small Cell Lung Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 23(2), 523-535.

Publication 2016

SNP6 array power tools

Allele

Corresponding Organization : Cornell University

Other organizations : Johns Hopkins University, National Cancer Institute

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Variable analysis

independent variables

Affymetrix SNP6 array data from the CCLE
Quantile normalization
Median polishing with Affymetrix power tools
Birdseed algorithm for genotyping
PennCNV to generate log R ratio and B-allele frequencies
ASCAT to generate allele-specific copy number information

dependent variables

LST score
N_tAI score
HRD-LOH score

control variables

R statistical environment (v3.0.2)

controls

No positive or negative controls were explicitly mentioned.

Annotations

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