Methodology article

Array-CGH and multipoint FISH to decode complex chromosomal rearrangements

Eva Darai-Ramqvist¹ , Teresita Diaz de Ståhl² , Agneta Sandlund¹ , Kiran Mantripragada² , George Klein¹ , Jan Dumanski³ , Stefan Imreh¹ and Maria Kost-Alimova¹

¹  Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden

²  Department of Pathology, Rudbeck Laboratory, Uppsala University Hospital, S-75185, Uppsala, Sweden

³  Howell and Elizabeth Heflin Center for Human Genetics, University of Alabama at Birmingham (UAB), Medical School, Birmingham, AL 35294-0024, USA

author email corresponding author email

BMC Genomics 2006, 7:330doi:10.1186/1471-2164-7-330

Published:	29 December 2006

Abstract

Background

Recently, several high-resolution methods of chromosome analysis have been developed. It is important to compare these methods and to select reliable combinations of techniques to analyze complex chromosomal rearrangements in tumours. In this study we have compared array-CGH (comparative genomic hybridization) and multipoint FISH (mpFISH) for their ability to characterize complex rearrangements on human chromosome 3 (chr3) in tumour cell lines. We have used 179 BAC/PAC clones covering chr3 with an approximately 1 Mb resolution to analyze nine carcinoma lines. Chr3 was chosen for analysis, because of its frequent rearrangements in human solid tumours.

Results

The ploidy of the tumour cell lines ranged from near-diploid to near-pentaploid. Chr3 locus copy number was assessed by interphase and metaphase mpFISH. Totally 53 chr3 fragments were identified having copy numbers from 0 to 14. MpFISH results from the BAC/PAC clones and array-CGH gave mainly corresponding results. Each copy number change on the array profile could be related to a specific chromosome aberration detected by metaphase mpFISH. The analysis of the correlation between real copy number from mpFISH and the average normalized inter-locus fluorescence ratio (ANILFR) value detected by array-CGH demonstrated that copy number is a linear function of parameters that include the variable, ANILFR, and two constants, ploidy and background normalized fluorescence ratio.

Conclusion

In most cases, the changes in copy number seen on array-CGH profiles reflected cumulative chromosome rearrangements. Most of them stemmed from unbalanced translocations. Although our chr3 BAC/PAC array could identify single copy number changes even in pentaploid cells, mpFISH provided a more accurate analysis in the dissection of complex karyotypes at high ploidy levels.