Journal: Communications Biology

Article Title: Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype

doi: 10.1038/s42003-020-01175-x

Figure Lengend Snippet: Alteration frequency of NAALADL2 and TBL1XR1 called via the GISTIC2 method in three non-overlapping primary, organ-confined, radical prostatectomy cohorts from the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA).

Article Snippet: GISTIC2 (version 6.15.28) analysis was performed in the publicly available GenePattern platform ( http://genepattern.broadinstitute.org/ ) using the settings described by the broad institute .

Techniques: Amplification

Journal: Scientific Reports

Article Title: Cancer systems biology of TCGA SKCM: Efficient detection of genomic drivers in melanoma

doi: 10.1038/srep07857

Figure Lengend Snippet: Somatic copy number alteration analysis identifies genomic regions that are significantly gained or lost across a set of tumors. GISTIC 2.0.21 found 21 significant arm-level results, 23 significant focal amplifications, and 29 significant focal deletions in segmented SNP array data of 292 SKCM metastatic tumor samples. Among those results, amplification of BRAF, as well as reduction of NRAS and PTEN is found. The genomic position is indicated by chromosome number in the middle panel; chromosome bands and altered genes are labeled at the sides. Normalized amplifications and deletions are labeled on top and shown in red and blue, respectively.

Article Snippet: We executed GISTIC 2.0.21 on Illumina HiSeq data recorded with a low coverage whole-genome sequencing protocol, MD Anderson Cancer Center, TX, as well as on Agilent SNP 6.0 gene expression microarrays G4502A_07_01, UNC Chapel Hill, NC.

Techniques: Amplification, Labeling