GISTIC

Overview

Genomic Identification of Significant Targets in Cancer (GISTIC) is a bioinformatic tool used to identify regions of the genome that are significantly amplified or deleted across a set of samples.

Used by

  • Used to analyze DNA copy number data from 206 glioblastoma samples to identify significantly altered regions and core pathways PMID:18772890.
  • Used alongside RAE to identify statistically significant somatic copy-number alterations in 207 high-grade soft tissue sarcoma samples across seven subtypes, including ~90% frequency of 12q amplification in DDLS PMID:20601955.
  • Applied to Affymetrix SNP6 copy number data from 489 HGSOC samples to identify 113 significant focal DNA copy number aberrations in the TCGA ovarian carcinoma study PMID:21720365
  • GISTIC applied to identify significant somatic copy-number alterations in prostate adenocarcinoma from the Broad WES cohort PMID:22610119
  • GISTIC applied to Affymetrix SNP 6.0 copy-number data from 257 TCGA colorectal carcinoma tumors to identify significant focal amplifications and deletions PMID:22810696
  • GISTIC applied to Affymetrix SNP 6.0 copy-number data from 121 melanoma samples (Broad) to identify significant focal amplifications and deletions including CDKN2A loss, BRAF amplification PMID:22817889
  • Applied to JHU SCLC cohort (36 tumors) to identify recurrent focal amplifications including SOX2 and MYCL and deletions of RB1 PMID:22941189
  • Applied to TCGA LUSC cohort (178 tumors) to identify focal amplifications (SOX2, FGFR1) and deletions (CDKN2A) from SNP6 array data PMID:22960745
  • GISTIC analysis of SNP 6.0 copy-number data from 160 CLL tumors identified del(13q14), del(11q22-23), and del(17p13) as recurrent focal deletions PMID:23415222
  • GISTIC v2.0.12 applied to Affymetrix SNP 6.0 copy-number profiles of 38 OSCC tumors; identified recurrent focal amplifications (CCND1, EGFR) and deletions (CDKN2A, FHIT) PMID:23619168
  • GISTIC v2 applied to an extended cohort of 199 prostate adenocarcinomas to call recurrent SCNAs; CHD1 deletion associated with elevated recurrent SCNA burden (p=1.5×10⁻⁸) and Gleason grade tracked SCNA count (p=0.0059) PMID:23622249
  • GISTIC applied to Affymetrix SNP 6.0 data from 363 endometrial carcinomas; identified recurrent focal amplifications of MYC, ERBB2, CCNE1, FGFR3, and SOX17 defining the copy-number-high serous-like subgroup PMID:23636398
  • Applied as GISTIC2.0 in 60-sample ACC study to identify significant recurrent copy-number alterations: high-level losses at 6q24, 12q13, and 14q; 14q loss associated with solid histology (Fisher p=2.0×10⁻⁴), 6q24 loss enriched for advanced stage (p=4.0×10⁻²) PMID:23685749
  • Used on 492 GBM samples for SCNA peak calling; identified recurrent amplifications on chr7 (EGFR/MET/CDK6), chr12 (CDK4/MDM2), chr4 (PDGFRA) and defined QKI as sole target of 6q26 minimal deletion PMID:24120142
  • Reimplemented GISTIC-style analysis on WGS-derived CNA data from 99 BLCA tumors; identified 84 focal amplification regions and 80 focal deletion regions including DHFR amplification (14%) and CDKN2A/B deletion (50%) PMID:24121792
  • GISTIC applied to Affymetrix SNP 6.0 copy-number data from 153 multiple myeloma patients; identified 7 significant homozygous deletion peaks covering NF-kB regulators (TRAF3, BIRC2/BIRC3, CYLD), CDKN2C, PTPRD, and an 8p23.1 locus PMID:24434212
  • GISTIC 2.0 applied to Affymetrix SNP 6.0 data from 131 TCGA bladder carcinoma samples; identified most common focal deletion at 9p21.3 (CDKN2A, 47% of samples) and multiple focal amplifications including PPARG (17%), EGFR (11%), MDM2 (9%), and ERBB2 (7%) PMID:24476821
  • GISTIC used for copy-number peak calling in 65 TET cases; identified focal BCL2 amplification correlated with increased BCL2 mRNA expression PMID:24974848
  • GISTIC applied to gastric adenocarcinoma copy-number data (stad_tcga_pub) identified focal amplifications of JAK2/CD274/PDCD1LG2 at 9p24.1 (enriched in EBV-positive tumors, 15%) and recurrent oncogene amplifications (ERBB2, CCNE1, KRAS, MYC, EGFR, VEGFA) in the CIN subtype PMID:25079317
  • GISTIC applied to lung adenocarcinoma copy-number data (luad_tcga_pub) identified significant focal amplifications (NKX2-1, TERT, MDM2, KRAS, EGFR, MET, CCNE1, CCND1, CCND3, TERC, MECOM, 8q24/MYC) and the most significant deletion peak at CDKN2A; focal MET and ERBB2 amplifications were enriched in oncogene-negative tumors PMID:25079552
  • Applied to Affymetrix SNP6 copy-number data from 66 ChRCC tumors; found no focal amplifications or deletions, only recurrent whole-chromosome losses. PMID:25155756
  • GISTIC2 applied to TCGA PTC SNP6 data; identified focal SCNAs in 27.2% of 495 tumors, including focal PTEN deletions; enriched in driver-mutation-negative cases (Fisher’s exact P=4.4×10⁻⁴) PMID:25417114
  • Applied (version 2.0 with arm-level peel correction; minimum segment size raised from 4 to 6) to identify recurrent copy-number alterations in 29 metastatic cSCC; identified 25 amplified and 11 deleted gene peaks including TP63 (24%), MYC (34%), and CDKN2A/CDKN2B as top deletion PMID:25589618
  • Applied to SNP6.0 array data from 279 HNSC tumors; identified 39 recurrent deletion and 23 amplification peaks (q<0.1); key alterations include 9p21.3 (CDKN2A) deletion absent in HPV(+), and 3q26/28 amplification of SOX2/TP63/PIK3CA spanning both HPV groups PMID:25631445
  • GISTIC 2.0 (join_segment_size=4, conf=0.95) used to identify significant focal copy-number peaks in 109 PDA exomes, including MYC amplification at 8q24.13 uniquely associated with poor survival. PMID:25855536
  • GISTIC used to identify significantly amplified and deleted genomic regions in adrenocortical carcinoma PMID:26095796
  • Used in the TCGA breast cancer ILC/IDC study (n=817) for somatic copy-number calling from Affymetrix SNP6 data, identifying focal amplifications (MYC, CCNE1) enriched in IDC and deletions enriched in ILC PMID:26451490
  • Applied as GISTIC 2.0 to identify focal somatic copy-number alterations in 333 primary prostate adenocarcinomas; detected 20 amplifications and 35 deletions (q < 0.25), including homozygous PTEN deletion in 15% — among the highest rates in any TCGA tumor type PMID:26544944.
  • GISTIC analysis of Illumina HumanOmni2.5-8 SNP-array data from periampullary tumors identified focal 9p23.1 CDKN2A deletion and a chromosome-9 deletion removing the promoter/5′ end of KDM4C as statistically significant in AMPAC PMID:26804919
  • GISTIC2 applied to copy-number data from 1,084 diffuse gliomas in the TCGA pan-glioma study to map focal amplifications and deletions across the cohort PMID:26824661
  • GISTIC 2.0 applied to CBS-segmented array-CGH data from 149 tumors of 60 men with metastatic CRPC; identified focal and arm-level CNA drivers including 8q gain (MYC), 8p loss, AR amplification, RB1 and PTEN deletions. PMID:26928463
  • GISTIC2.0 applied to Affymetrix SNP 6.0 copy-number data from 1,144 NSCLC pairs to identify recurrent SCNAs; novel focal amplifications (MIR21, MIR205, MAPK1) and deletions (SMARCA4, B2M, TRAF3) discovered PMID:27158780
  • GISTIC2 applied to METABRIC copy-number data to identify recurrent CNAs underpinning the 10 Integrative Clusters in 2,433 primary breast tumours PMID:27161491
  • GISTIC2 applied to metastatic breast cancer WES data to identify recurrent copy number alterations including ESR1 focal amplification and PTEN deletion; thresholds set at amp >0.3 and del <−0.3 log2 ratio PMID:28027327.
  • GISTIC 2.0 used to identify recurrent somatic copy-number alterations in 164 oesophageal carcinomas including CCND1 amplification in 57% of ESCC and CCNE1 amplification in EAC PMID:28052061.
  • GISTIC 2.0 applied to Affymetrix SNP6 data from 412 BLCA tumors identifying 34 amplified and 32 deleted focal SCNA regions at q<0.1 PMID:28988769
  • GISTIC applied to TCGA Broad Firehose melanoma data (downloaded Jan 28 2016) for recurrent SCNA identification used as reference in the CA209-038 nivolumab pharmacodynamic study PMID:29033130
  • GISTIC applied to Affymetrix SNP6 data from 206 TCGA sarcomas to identify recurrent SCNA peaks; DDLPS showed 100% MDM2 amplification, 92% CDK4 amplification, and 96% FRS2 amplification at 12q13~15 PMID:29100075
  • GISTIC 2.0 applied to 1,013 prostate WES samples to call copy-number alterations, alongside FACETS for allele-specific copy number PMID:29610475
  • GISTIC2.0 used to derive recurrent SCNA scores across 10,522 TCGA pan-cancer samples for integration with arm-level aneuploidy analysis PMID:29622463

Notes

  • Helped identify frequent alterations in EGFR (45%), CDKN2A/B (>50%), and other key drivers in GBM PMID:18772890.
  • Identified CDK4 and MDM2 as focal 12q amplification targets in DDLS; results informed functional shRNA validation and pharmacologic CDK4/CDK6 inhibition with palbociclib PMID:20601955.

Sources

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