High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples - PubMed

High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples

Cathie Garnis et al. Genomics. 2005 Jun.

Abstract

Recent advances in array comparative genomic hybridization (array CGH) technology are revolutionizing our understanding of tumor genomes. Marker-based arrays enable rapid survey at megabase intervals, while tiling path arrays examine the entire genome in unprecedented detail. Tumor biopsies are typically small and contain infiltrating stromal cells, requiring tedious microdissection. Tissue heterogeneity is a major barrier to high-throughput profiling of tumor genomes and is also an important consideration for the introduction of array CGH to clinical settings. We propose that increasing array resolution will enhance detection sensitivity in mixed tissues and as a result significantly reduce microdissection requirements. In this study, we first simulated normal cell contamination to determine the heterogeneity tolerance of array CGH and then validated this detection sensitivity model on cancer specimens using the newly developed submegabase resolution tiling-set (SMRT) array, which spans the human genome with 32,433 overlapping BAC clones.

Similar articles

• A tiling resolution DNA microarray with complete coverage of the human genome.

  Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL. Ishkanian AS, et al. Nat Genet. 2004 Mar;36(3):299-303. doi: 10.1038/ng1307. Epub 2004 Feb 15. Nat Genet. 2004. PMID: 14981516

• Array CGH technologies and their applications to cancer genomes.

  Davies JJ, Wilson IM, Lam WL. Davies JJ, et al. Chromosome Res. 2005;13(3):237-48. doi: 10.1007/s10577-005-2168-x. Chromosome Res. 2005. PMID: 15868418 Review.

• Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes.

  de Leeuw RJ, Davies JJ, Rosenwald A, Bebb G, Gascoyne RD, Dyer MJ, Staudt LM, Martinez-Climent JA, Lam WL. de Leeuw RJ, et al. Hum Mol Genet. 2004 Sep 1;13(17):1827-37. doi: 10.1093/hmg/ddh195. Epub 2004 Jun 30. Hum Mol Genet. 2004. PMID: 15229187

• Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer.

  Kloth JN, Oosting J, van Wezel T, Szuhai K, Knijnenburg J, Gorter A, Kenter GG, Fleuren GJ, Jordanova ES. Kloth JN, et al. BMC Genomics. 2007 Feb 20;8:53. doi: 10.1186/1471-2164-8-53. BMC Genomics. 2007. PMID: 17311676 Free PMC article.

• Array-based comparative genomic hybridization in clinical diagnosis.

  Bejjani BA, Theisen AP, Ballif BC, Shaffer LG. Bejjani BA, et al. Expert Rev Mol Diagn. 2005 May;5(3):421-9. doi: 10.1586/14737159.5.3.421. Expert Rev Mol Diagn. 2005. PMID: 15934818 Review.

Cited by

• MicroRNA-218 is deleted and downregulated in lung squamous cell carcinoma.

  Davidson MR, Larsen JE, Yang IA, Hayward NK, Clarke BE, Duhig EE, Passmore LH, Bowman RV, Fong KM. Davidson MR, et al. PLoS One. 2010 Sep 3;5(9):e12560. doi: 10.1371/journal.pone.0012560. PLoS One. 2010. PMID: 20838434 Free PMC article.

• Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports.

  Menten B, Maas N, Thienpont B, Buysse K, Vandesompele J, Melotte C, de Ravel T, Van Vooren S, Balikova I, Backx L, Janssens S, De Paepe A, De Moor B, Moreau Y, Marynen P, Fryns JP, Mortier G, Devriendt K, Speleman F, Vermeesch JR. Menten B, et al. J Med Genet. 2006 Aug;43(8):625-33. doi: 10.1136/jmg.2005.039453. Epub 2006 Feb 20. J Med Genet. 2006. PMID: 16490798 Free PMC article.

• A stepwise framework for the normalization of array CGH data.

  Khojasteh M, Lam WL, Ward RK, MacAulay C. Khojasteh M, et al. BMC Bioinformatics. 2005 Nov 18;6:274. doi: 10.1186/1471-2105-6-274. BMC Bioinformatics. 2005. PMID: 16297240 Free PMC article.

• The pitfalls of platform comparison: DNA copy number array technologies assessed.

  Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavaré S, Caldas C. Curtis C, et al. BMC Genomics. 2009 Dec 8;10:588. doi: 10.1186/1471-2164-10-588. BMC Genomics. 2009. PMID: 19995423 Free PMC article.

• Computational methods for the analysis of array comparative genomic hybridization.

  Chari R, Lockwood WW, Lam WL. Chari R, et al. Cancer Inform. 2007 Feb 10;2:48-58. Cancer Inform. 2007. PMID: 17992253 Free PMC article.

Publication types

MeSH terms

Substances