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Open Access Research article

Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays

Paul J Gardina1, Ken C Lo2, Walter Lee1, John K Cowell3* and Yaron Turpaz14

Author Affiliations

1 Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA

2 Roche NimbleGen Inc., 500 South Rosa Road, Madison WI 53719, USA

3 MCG Cancer Center, Medical College of Georgia Medical School, CN 4112, 1120 15th Street, Augusta Georgia 30912, USA

4 Lilly Singapore Centre for Drug Discovery, 8A Biomedical Grove, #02-05 Immunos, 138648, Singapore

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BMC Genomics 2008, 9:489  doi:10.1186/1471-2164-9-489

Published: 17 October 2008

Abstract

Background

Genomic hybridization platforms, including BAC-CGH and genotyping arrays, have been used to estimate chromosome copy number (CN) in tumor samples by detecting the relative strength of genomic signal. The methods rely on the assumption that the predominant chromosomal background of the samples is diploid, an assumption that is frequently incorrect for tumor samples. In addition to generally greater resolution, an advantage of genotyping arrays over CGH arrays is the ability to detect signals from individual alleles, allowing estimation of loss-of-heterozygosity (LOH) and allelic ratios to enhance the interpretation of copy number alterations. Copy number events associated with LOH potentially have the same genetic consequences as deletions.

Results

We have utilized allelic ratios to detect patterns that are indicative of higher ploidy levels. An integrated analysis using allelic ratios, total signal and LOH indicates that many or most of the chromosomes from 24 glioblastoma tumors are in fact aneuploid. Some putative whole-chromosome losses actually represent trisomy, and many apparent sub-chromosomal losses are in fact relative losses against a triploid or tetraploid background.

Conclusion

These results suggest a re-interpretation of previous findings based only on total signal ratios. One interesting observation is that many single or multiple-copy deletions occur at common putative tumor suppressor sites subsequent to chromosomal duplication; these losses do not necessarily result in LOH, but nonetheless occur in conspicuous patterns. The 500 K Mapping array was also capable of detecting many sub-mega base losses and gains that were overlooked by CGH-BAC arrays, and was superior to CGH-BAC arrays in resolving regions of complex CN variation.