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Analysis of chromosome copy number in leukemic cells by different microarray platforms

Leukemia volume 21, pages 1333–1337 (2007)Cite this article

Changes in the copy number of chromosomes, or copy number alterations (CNAs), are frequently apparent in the genome of cancer cells and may result in the amplification of oncogenes or deletion of tumor suppressor genes.1 Such CNAs range in size from an entire chromosome to several kilobase pairs, with many of the smaller changes being undetectable by conventional bacterial artificial chromosome-based comparative genomic hybridization (CGH), which has a resolution of several hundred kilobase pairs.2 This limitation has recently been overcome by the adaptation of high-density oligonucleotide microarrays that were originally developed for typing of single nucleotide polymorphisms (SNPs) to the evaluation of CNAs.3 Sophisticated software for such analysis, including dChip (http://biosun1.harvard.edu/complab/dchip) and CNAG (http://www.genome.umin.jp/CNAG.html), is now available online.

Although high-density SNP-typing arrays allow determination of CNAs at a resolution of <100 kbp, it is not a simple task to link such data to changes in the number of the corresponding genes. The HGU133 Plus 2.0 (HGU133P2) microarray manufactured by Affymetrix (USA) was designed to quantitate the abundance of >47 000 human transcripts and has been widely used for gene expression profiling. Most of the probe sequences on the array are targeted to exons corresponding to the 3′ untranslated region of each transcript. Although, as far as we are aware, there have been no reports on the use of this microarray for CNA assessment or CGH, we reasoned that HGU133P2 may be a useful platform for evaluation of CNAs because (1) cDNA sequences are one of the most updated and comprehensive information for human genome, and (2) copy number values could be calculated directly for each gene. Furthermore, it would be straightforward to compare the copy number and expression level of a given gene through separate hybridization of genomic DNA and mRNA to the array. For this purpose, we modified a protocol for labeling and hybridizing genomic DNA, provided by Affymetrix (Supplementary Information).

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Acknowledgements

We thank Dr Raji Pillai and her colleagues at Affymetrix for technical suggestions and for sharing data before publication. This work was supported in part by grants for Research on Human Genome and Tissue Engineering and for Third-Term Comprehensive Control Research for Cancer from the Ministry of Health, Labor, and Welfare of Japan, as well as by a Grant-in-Aid for Scientific Research on Priority Areas ‘Applied Genomics’ from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

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Authors and Affiliations

  1. Division of Functional Genomics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan,

    Y Yamashita, S-i Fujiwara, K Kurashina, H Watanabe, Y L Choi, M Soda, H Hatanaka, M Enomoto, S Takada & H Mano

  2. Bioapplication Group, Yokogawa Analytical Systems Inc., Tokyo, Japan,

    K Minoura & T Taya

  3. CREST, Japan Science and Technology Agency, Saitama, Japan,

    H Mano

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  1. Y Yamashita
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  2. K Minoura
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Correspondence to H Mano.

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Supplementary Information accompanies the paper on the Leukemia website (http://www.nature.com/leu)

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Yamashita, Y., Minoura, K., Taya, T. et al. Analysis of chromosome copy number in leukemic cells by different microarray platforms. Leukemia 21, 1333–1337 (2007). https://doi.org/10.1038/sj.leu.2404636

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