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Array-based genomic resequencing of human leukemia

Abstract

To identify oncogenes in leukemias, we performed large-scale resequencing of the leukemia genome using DNA sequence arrays that determine 9 Mbp of sequence corresponding to the exons or exon–intron boundaries of 5648 protein-coding genes. Hybridization of genomic DNA from CD34-positive blasts of acute myeloid leukemia (n=19) or myeloproliferative disorder (n=1) with the arrays identified 9148 nonsynonymous nucleotide changes. Subsequent analysis showed that most of these changes were also present in the genomic DNA of the paired controls, with 11 somatic changes identified only in the leukemic blasts. One of these latter changes results in a Met-to-Ile substitution at amino-acid position 511 of Janus kinase 3 (JAK3), and the JAK3(M511I) protein exhibited transforming potential both in vitro and in vivo. Further screening for JAK3 mutations showed novel and known transforming changes in a total of 9 out of 286 cases of leukemia. Our experiments also showed a somatic change responsible for an Arg-to-His substitution at amino-acid position 882 of DNA methyltransferase 3A, which resulted in a loss of DNA methylation activity of >50%. Our data have thus shown a unique profile of gene mutations in human leukemia.

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Acknowledgements

We thank D Cox, KA Frazer, DG Ballinger, J Montgomery, H Tao, C Chen, L Stuve, J Kwon, J Sheehan and Y Zhan for discussion on the wafer experiments, as well as JN Ihle, T Kitamura and SB Baylin for human JAK3 cDNA, the pMX plasmid and human DNMT3A cDNA, respectively. This study was supported in part by a grant for Third-Term Comprehensive Control Research for Cancer from the Ministry of Health, Labor, and Welfare of Japan, and by a grant for Scientific Research on Priority Areas ‘Applied Genomics’ from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

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Correspondence to H Mano.

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Yamashita, Y., Yuan, J., Suetake, I. et al. Array-based genomic resequencing of human leukemia. Oncogene 29, 3723–3731 (2010). https://doi.org/10.1038/onc.2010.117

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