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Different characteristics identified by single nucleotide polymorphism array analysis in leukemia suggest the need for different application strategies depending on disease category

Authors

  • Jungwon Huh,

    1. Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, Korea
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    • J.H. and C.W.J. contributed to the work equally and served as first authors equally.

  • Chul Won Jung,

    1. Division of Hematology and Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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    • J.H. and C.W.J. contributed to the work equally and served as first authors equally.

  • Hyeoung-Joon Kim,

    Corresponding author
    1. Department of Hematology and Oncology, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun, Korea
    • Department of Hematology and Oncology, Chonnam National University, Hwasun Hospital, Chonnam National University, 160 Ilsimri, Hwasun-eup, Hwasun, Korea 519-763
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  • Yeo-Kyeoung Kim,

    1. Department of Hematology and Oncology, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun, Korea
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  • Joon Ho Moon,

    1. Department of Hematology and Oncology, Kyungpook National University Hospital, Kyungpook National University, Daegu, Korea
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  • Sang Kyun Sohn,

    Corresponding author
    1. Department of Hematology and Oncology, Kyungpook National University Hospital, Kyungpook National University, Daegu, Korea
    • Department of Hematology and Oncology, Kyungpook National University Hospital, Kyungpook National University, 50 Samduk Dong, Jung-gu, Daegu, Korea
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  • Hee-Je Kim,

    1. Department of Hematology, Catholic Blood and Marrow Transplantation Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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  • Woo Sung Min,

    1. Department of Hematology, Catholic Blood and Marrow Transplantation Center, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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  • Dong Hwan (Dennis) Kim

    1. Department of Medical Oncology and Hematology, Princess Margaret Hospital, University of Toronto, Toronto, Canada
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Abstract

The purpose of this study was to evaluate the detection rate of chromosomal rearrangements in leukemia using single nucleotide polymorphism array (SNP-A) in combination with metaphase cytogenetics (MC), with the aim of proposing a practical approach for clinical karyotyping applications of SNP-A. The Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA) was applied in 469 patients with a variety of hematologic malignancies. Combined use of SNP-A with MC improved the detection rate in comparison with MC alone: acute myeloid leukemia (AML) with normal karyotype (NK), 32% versus 0%; core binding factor (CBF)-AML 40% versus 29%; myelodysplastic syndrome (MDS), 54% versus 39%; chronic myeloid leukemia (CML), 24% versus 3%; and acute lymphoblastic leukemia (ALL), 88% versus 63%. Different patterns of abnormalities (especially the type, size, and location) were noted in the leukemia subtypes. Copy neutral loss of heterozygosity lesions was detected in 23% of AML-NK, 3% of CBF-AML, 25% of MDS, 2% of CML, and 20% of ALL. SNP-A also provided information on cryptic deletions and a variety of aneuploidies in ALL, while the benefit was minimal in CML. In conclusion, different patterns of abnormal lesions were presented according to the disease category, thus requiring a different approach of adopting SNP-A-based karyotyping among different leukemia subtypes. © 2012 Wiley Periodicals, Inc.

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