Science Inventory

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

Citation:

HESTER, S. D., L. Reid, N. Nowak, W. D. Jones, J. S. Parker, K. Knudtson, W. O. WARD, J. Tiesman, AND N. D. DENSLOW. Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms. Journal of Biomolecular Techniques. The Association of Biomolecular Resource Facilities, Santa Fe, NM, 20(2):135-151, (2009).

Impact/Purpose:

This manuscript is the product of the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project. This research project investigated the ability of five comparative genomic hybridization platforms to detect copy number changes in a well-described cell line, HL-60. We analyzed HL-60 DNA with the following platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed using Circular Binary Segmentation (CBS) analysis of log ratio scores from four independently assessed hybridizations of each platform. Data obtained from these platforms were assessed for reproducibility and the ability to detect formerly reported CNVs in HL-60. In HL-60, all of the tested platforms detected genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2~q31, 9p21.3~p22, 10p12~p15, 14q22~q31, 17p12~p13.3, and monosomy X. In the HL-60 genome at least two of the five platforms detected five novel losses and five novel gains. This report provides guidance in the selection of platforms based on this wide-ranging evaluation of available CGH platforms.

Description:

In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed using Circular Binary Segmentation (CBS) analysis of log ratio scores from four independently assessed hybridizations of each platform. Data obtained from these platforms were assessed for reproducibility and the ability to detect formerly reported CNVs in HL-60. In HL-60, all of the tested platforms detected genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2~31, 9p21.3~p22, 10~12~p15, 14q22~31 17p12 ~p13.3. 126;p13.3, and monosomy X. In the HL-60 genome at least two of the five platforms detected five novel losses and five novel gains. This report provides guidance in the selection of platforms based on this wide-ranging evaluation of available CGH platforms.

Record Details:

Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Product Published Date: 04/01/2009
Record Last Revised: 12/07/2009
OMB Category: Other
Record ID: 200221

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY

ENVIRONMENTAL CARCINOGENESIS DIVISION

CELLULAR TOXICOLOGY BRANCH