Agilent 1M Human Oligonucleotide aCGH

Overview

Array comparative genomic hybridization (aCGH) using the Agilent 1M human oligonucleotide microarray platform. Tumor DNA is co-hybridized with reference normal DNA; resulting log2 ratios are segmented (e.g., by circular binary segmentation) and subjected to copy-number calling algorithms such as RAE. At ~1 million probes, the platform provides high-resolution somatic copy-number alteration (SCNA) detection across the genome.

Used by

  • Applied to 97 high-grade urothelial carcinomas of the bladder (BLCA) cohybridized with reference normal DNA; segmented by circular binary segmentation and analyzed with the RAE algorithm at FDR <1%; identified two distinct CNA-burden subsets and recurrent focal amplifications including ERBB2 (17q12) and CCND1 (11q13.2–13.3) PMID:23897969
  • 44K Agilent array-CGH performed on 59 ESCC samples as part of a 184-sample SCNV analysis identifying 14 recurrent focal copy-number events including CCND1 amplification and CDKN2A deletion PMID:24686850
  • Array CGH (Agilent) performed on 65 TET cases; data deposited in GEO (GSE55852); identified frequent arm-level gains (1q 55%) and losses (6q 29%, 6p 26%, 3p 22%, 13q 18%), with focal BCL2 amplification in aggressive histotypes PMID:24974848
  • Profiling of 104 prostatectomy cases (prad_mskcc_2014 contemporary cohort) by Agilent 1M-feature array-CGH on snap-frozen samples with >70% tumor content; used to compute CNA burden as a fraction of the autosomal genome, which was independently associated with BCR (HR 1.05, P=0.008) PMID:25024180
  • Agilent SurePrint G3 1M array-CGH used to profile copy-number alterations in seven prostate cancer organoid lines; identified PTEN homozygous deletions, CHD1 loss, AR amplification, and RB1/CDKN2A alterations (note: missed a complete RB1 deletion detected by RNA-seq). PMID:25201530
  • Agilent Human Genome 244A + Sureprint G3 array-CGH applied to 18 PCNSL cases; CNA calling via Nexus RANK segmentation filtered with TCAG and 10 in-house HapMap controls; identified median 21 copy-number abnormalities/patient. PMID:25991819
  • Agilent 1M array-CGH used for copy-number alteration profiling in colorectal cancer PMID:26343386
  • Agilent SurePrint G3 1x1M array-CGH used to profile 37 fresh-frozen advanced thyroid tumors; identified arm-level CNAs including 8p, 17p, 20q alterations enriched in ATCs, and 22q loss enriched in RAS-mutant PDTCs. PMID:26878173
  • Agilent 2x400K SurePrint G3 CGH array used on 149 tumors from 60 men with metastatic CRPC at rapid autopsy; CBS segmentation and GISTIC 2.0 analysis identified 8q gain (MYC), 8p loss, AR amplification, and RB1/PTEN loss across metastatic sites. PMID:26928463

Notes

  • Co-hybridization with reference normal DNA controls for dye bias; circular binary segmentation is the standard downstream segmentation approach.
  • High-CNA-burden bladder tumors identified by this platform had structural-aberration loads second only to serous ovarian cancer across 14 tumor types (n=5,135).
  • Superseded in large-scale studies by SNP 6.0 arrays and WGS-based CNA inference, but remains in use for clinical and research validation.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:24686850

This page was processed by crosslinker on 2026-05-14. - PMID:24974848

This page was processed by crosslinker on 2026-05-14. - PMID:25024180

This page was processed by crosslinker on 2026-05-14. - PMID:25201530

This page was processed by crosslinker on 2026-05-14. - PMID:25991819

This page was processed by crosslinker on 2026-05-14. - PMID:26343386

This page was processed by entity-page-writer on 2026-05-15. - PMID:26878173

This page was processed by entity-page-writer on 2026-05-15. - PMID:26928463

This page was processed by entity-page-writer on 2026-05-15.