Computational protocol: Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci

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Protocol publication

[…] All arrays from this study were imaged using a single Molecular Devices GenePix 4000B microarray scanner, processed with Agilent Feature Extraction 9.5 and analyzed with Nexus (Biosdiscovery) software version 4.1. Preliminary analysis was conducted using Rank Segmentation (an extension of the circular binary segmentation algorithm [] as implemented in Nexus 4.1. Final results presented in this manuscript are based on the Nexus Rank segmentation algorithm with the gain/loss LogR threshold set to 0.25, maximum inter-probe distance at 25 kb, and the (default) minimum of five probes required per called CNV event. […]

Pipeline specifications

Software tools Agilent Feature Extraction, DNA copy
Application aCGH data analysis
Organisms Homo sapiens, Cucumber necrosis virus
Chemicals gamma-Aminobutyric Acid, Nucleotides