Affymetrix SNP 6.0

Overview

A high-density microarray platform used for detecting DNA copy number variations and single nucleotide polymorphisms (SNPs).

Used by

  • Used for DNA copy number profiling in a cohort of 206 glioblastoma cases PMID:18772890.
  • Used for DNA copy number profiling in all 489 HGSOC samples in the TCGA ovarian carcinoma study; identified 113 significant focal copy number aberrations PMID:21720365
  • Used for copy number analysis on 42 HNSCC tumor/normal pairs in the JHU HNSCC study; identified recurrent gains at 11q (CCND1), 3q (PIK3CA), and 7p (EGFR) and deletions at 9p21.3 (CDKN2A) PMID:21798897
  • Used for copy-number profiling across 947 CCLE cancer cell lines as part of the pharmacogenomic characterization panel PMID:22460905
  • Affymetrix SNP 6.0 array used for copy-number profiling in BCCRC breast tumor WGS study PMID:22495314
  • Affymetrix SNP 6.0 used for genome-wide copy-number profiling of ~2,000 METABRIC breast tumors PMID:22522925
  • Affymetrix SNP 6.0 used for somatic copy-number analysis in the Broad prostate cancer WES study of 112 tumors PMID:22610119
  • Used for copy-number analysis in 100 breast cancer tumors (Sanger cohort, brca_sanger) alongside WES PMID:22722201
  • Used for copy-number analysis in 37 medulloblastoma tumors (PCGP cohort, mbl_pcgp) alongside WGS PMID:22722829
  • 257 of 276 TCGA colorectal carcinoma tumors profiled for somatic copy-number alterations using Affymetrix SNP 6.0 arrays PMID:22810696
  • Copy-number analysis of 121 melanoma samples (Broad) performed with Affymetrix SNP 6.0 arrays analyzed with GISTIC; identified focal amplifications and deletions PMID:22817889
  • Used in CLCGP SCLC study (29 tumors) for copy number profiling to complement WES/WGS somatic alteration discovery PMID:22941188
  • Used in TCGA LUSC study (178 tumors) for genome-wide copy number analysis informing GISTIC-derived focal amplification/deletion calls PMID:22960745
  • Affymetrix SNP 6.0 arrays used for somatic copy-number analysis across 510 breast tumors; identified ERBB2, MYC, CCND1 focal amplifications PMID:23000897
  • SNP 6.0 arrays used in ETP-ALL study to call copy-number alterations; identified deletions in ETV6, RB1, and other tumor suppressors PMID:23334668
  • SNP 6.0 array copy-number analysis of 160 CLL tumors; identified del(13q), del(11q), trisomy 12, and del(17p) as common chromosomal alterations PMID:23415222
  • Used Affymetrix SNP 6.0 arrays on 38 OSCC tumors for somatic copy-number profiling; ASCAT used for allele-specific CN and GISTIC v2 for recurrence calling PMID:23619168
  • Applied Affymetrix SNP 6.0 arrays for somatic DNA copy-number profiling of 57 prostate tumors; SCNA recurrence analyzed across an extended cohort of 199 tumors using GISTIC PMID:23622249
  • Profiled all 200 AML tumor/normal pairs by Affymetrix SNP 6.0 for somatic copy-number variant detection PMID:23634996
  • Used Affymetrix SNP 6.0 on 363 endometrial carcinoma samples for SCNA profiling; GISTIC identified recurrent focal amplifications including MYC, ERBB2, CCNE1, FGFR3, and SOX17 PMID:23636398
  • Used in 24-exome adenoid cystic carcinoma (ACC) study for SNP-array copy-number profiling, analyzed with ASCAT v2.1, revealing recurrent losses at 1p36, 6q, 9p, and 12q PMID:23778141
  • Used in TCGA CCRCC study for DNA copy-number profiling alongside whole-exome sequencing of 417 tumors, contributing to identification of chromosome 3p loss (91% of samples), 5q gain (67%), and 14q loss (45%) PMID:23792563
  • Used for copy-number/LOH profiling of MCL samples; CNA burden from SNP 6.0 arrays correlated with SOX11 status and clinical aggressiveness (SOX11+ MCL had mean 13±9 CNAs vs 2±2 in SOX11- MCL) PMID:24145436
  • SNP 6.0 copy-number arrays applied to 153 of 203 multiple myeloma patients; GISTIC analysis identified 7 recurrent homozygous deletion regions covering 32 genes including CDKN2C, TRAF3, BIRC2/BIRC3, CYLD, and PTPRD PMID:24434212
  • Illumina Omni 2.5M and 5M SNP arrays (analogous workflow to Affymetrix SNP6) applied to all 147 rhabdomyosarcoma tumor/normal pairs for copy-number alteration profiling; identified 11p15.5 LOH (50% of tumors), MYCN amplification (5%), CDK4/12q13-q14 amplification (9.7%), and CDKN2A homozygous deletion (3%) PMID:24436047
  • Affymetrix SNP 6.0 arrays used for somatic copy-number alteration profiling of 131 TCGA bladder carcinoma samples; identified CDKN2A focal deletion (47%), PPARG amplification (17%), E2F3/SOX4 amplification (20%), and NECTIN4 amplification (19%) as the most prevalent focal events PMID:24476821
  • SNP-array copy-number calls from 704 HCC patients used to characterise focal amplifications (MYC 12%, CCND1 7%, FGF19 6%, VEGFA 5%, TERT 5%) and homozygous deletions (CDKN2A 5%, RB1 5%) PMID:24798001
  • Used for array-based somatic copy-number profiling in the TCGA gastric adenocarcinoma study (stad_tcga_pub, N=295) to classify CIN vs GS subtypes and detect focal amplifications/deletions including RTK loci and 9p24.1 PMID:25079317
  • Used for copy-number profiling of 230 lung adenocarcinomas (luad_tcga_pub); GISTIC identified significant focal amplifications (NKX2-1, TERT, MDM2, KRAS, EGFR, MET, CCNE1) and the most significant deletion peak at CDKN2A PMID:25079552
  • Used to profile somatic copy-number alterations in 66 ChRCC tumors in the TCGA ChRCC study; no focal events detected by GISTIC, only recurrent whole-chromosome losses. PMID:25155756
  • SNP6.0 copy-number arrays used in MPNST discovery cohort (15 tumors) to detect EED/SUZ12 deletions and copy-neutral LOH alongside WES PMID:25240281
  • Illumina HumanOmni2.5-8 SNP arrays used for copy-number profiling in 167 nccRCC tumors; identified frequent chr7 amplification (MET locus, ~70% of pRCC) and chr1/2/6/8/10/13/17/21 losses in chRCC PMID:25401301
  • Used for somatic copy number alteration calling in the TCGA PTC study; GISTIC2 identified focal SCNAs in 27.2% of 495 tumors, enriched in mutation-negative PTC cases (Fisher’s exact P=4.4×10⁻⁴) PMID:25417114
  • Used for CNA/LOH profiling across all 30 breast cancer PDX lines; CNA clonal dynamics from SNP6 arrays were concordant with SNV-based PyClone cluster dynamics, confirming clonal selection at engraftment PMID:25470049
  • Used for copy-number analysis in TCGA HNSC (n=279); identified mean 141 CNAs per tumor, 39 recurrent deletion and 23 amplification regions (q<0.1), including 3q26/28 gains (SOX2/TP63/PIK3CA) and 11q13/22 co-amplifications in HPV(−) tumors PMID:25631445
  • Affymetrix SNP 6.0 array used for DNA copy-number profiling on 333 cutaneous melanoma samples; copy-number purity/ploidy estimated via ABSOLUTE. PMID:26091043
  • Affymetrix SNP 6.0 array used for copy-number profiling in breast cancer genomic study PMID:26168399
  • Used for copy-number profiling in the TCGA breast cancer ILC/IDC analysis (n=817), generating somatic copy-number calls for comparison of genomic alterations between invasive lobular and ductal carcinoma subtypes PMID:26451490
  • Applied for copy-number alteration profiling in 333 primary prostate adenocarcinomas in the TCGA molecular taxonomy study; focal SCNAs identified with GISTIC 2.0 PMID:26544944.
  • Used for DNA copy-number profiling in the TCGA pan-glioma study (n=1,084 samples); copy-number data from SNP6 arrays combined with exome and RNA-seq data for integrated pathway alteration analysis PMID:26824661
  • Affymetrix SNP 6.0 array used for copy-number profiling of 1,144 NSCLC (660 ADC + 484 SqCC) tumor/normal pairs; GISTIC2.0 applied to identify recurrent SCNAs PMID:27158780
  • Affymetrix SNP 6.0 copy-number profiling applied to all 1,913 B-ALL cases to detect focal ERG deletions (55.6% of DUX4/ERG subtype) and other copy-number alterations. PMID:27776115
  • Affymetrix SNP 6.0 arrays used for copy-number profiling of 164 oesophageal carcinomas and 359 gastric adenocarcinomas in the TCGA esophageal/stomach study, identifying CCND1 (57% ESCC) and CCNE1 (EAC-enriched) amplifications PMID:28052061.
  • Affymetrix SNP6 arrays used for somatic copy-number analysis in 173 PCPG tumors; 95% of NF1-mutated tumors carried 17q11.2 focal deletions detected by this platform PMID:28162975.
  • HumanOmniExpress SNP arrays (Affymetrix-style SNP copy-number profiling) applied to 175 CCA cases for somatic copy-number alteration calling in the ICGC cholangiocarcinoma cohort PMID:28667006
  • Used for copy-number analysis in 412 BLCA tumors with GISTIC 2.0 and ABSOLUTE; identified 34 amplified and 32 deleted focal regions, with CDKN2A (9p21.3) deletion in 22% of tumors PMID:28988769
  • Used for somatic copy-number analysis in 206 TCGA sarcomas; DDLPS showed the highest SCNA frequency of any TCGA tumor type, driven by recurrent 12q13~15 amplification PMID:29100075
  • Affymetrix SNP 6.0 arrays used for copy-number profiling of 10,522 TCGA pan-cancer samples; processed with ABSOLUTE to derive arm-level aneuploidy scores PMID:29622463

Notes

  • Data from this platform was used in conjunction with GISTIC to identify significantly altered genomic regions in GBM PMID:18772890.

Sources

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This page was processed by crosslinker on 2026-05-14. - PMID:22495314

This page was processed by crosslinker on 2026-05-14. - PMID:22522925

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