chromosome arms; and (ii) identifies regions that are significantly

focally amplified or deleted. For the focal analysis, the

significance levels (Q values) are calculated by comparing the

observed gains/losses at each locus to those obtained by randomly

permuting the events along the genome to reflect the null

hypothesis that they are all 'passengers' and could have occurred

anywhere. The locus-specific significance levels are then

corrected for multiple hypothesis testing. The arm-level

significance is calculated by comparing the frequency of

gains/losses of each arm to the expected rate given its size. The

method outputs genomic views of significantly amplified and

deleted regions, as well as a table of genes with gain or loss

scores. A more in depth discussion of the GISTIC algorithm and its

Regions of the genome that are prone to germ line variations in copy

number are excluded from the GISTIC analysis using a list of germ

line copy number variations (CNVs). A CNV is a DNA sequence that may

be found at different copy numbers in the germ line of two different

individuals. Such germ line variations can confound a GISTIC

analysis, which finds significant  somatic copy number variations in

cancer. A more in depth discussion is provided in

. GISTIC currently uses two CNV exclusion lists. One is based on the

literature describing copy number variation, and a second one comes

from an analysis of significant variations among the blood normals in

Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

The landscape of somatic copy-number alteration across human cancers

Integrated detection and population-genetic analysis of SNPs and copy number variation

The Sanger Institute: Cancer Gene Census