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High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line

Naoki Adati1, Ming-Chih Huang13, Takahiro Suzuki2, Harukazu Suzuki2 and Toshio Kojima1*

Author Affiliations

1 Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

2 RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

3 Current address : Department of Biological Sciences and Technology, National University of Tainan, 33, Sec. 2, Shu-Lin St., Tainan 700-05, Taiwan, Republic of China

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BMC Research Notes 2009, 2:153  doi:10.1186/1756-0500-2-153

Published: 27 July 2009

Abstract

Background

THP-1 is a human monocytic leukemia cell line derived from a patient with acute monocytic leukemia. The cell line differentiates into macrophage-like cells by stimulation with phorbol myristate acetate (PMA). Although it has been used frequently as a model for macrophage differentiation in research including the FANTOM4/Genome Network Project, there are few reports on its genomic constitution. Therefore, we attempted to reveal the genomic aberrations in these cells with the microarray-based comparative genomic hybridization (aCGH) technique.

Findings

We report large aberrations, including deletions 6p, 12p, 17p, and trisomy 8, and revealed breakpoints in the MLL and MLLT3 genes. Moreover, we found novel genomic aberrations such as a hemizygous narrow deletion partially containing the TP73 gene and homozygous deletions, including the CDKN2A, CDKN2B and PTEN genes.

Conclusion

In this study, we identified 119 aberrant regions in autosomal chromosomes, and at least 16 of these aberrations were less than 100 kb, most of which were undetectable in the previous works. We also revealed a total of 4.6 Mb of homozygous deleted regions. Our results will provide a base to precisely understand studies involving the THP-1 cell line, especially the huge amount of data generated from the FANTOM4/Genome Network Project.