U. Fischer, M. Dugas, J. Hu, and A. Borkhardt contributed equally to this work.
Article first published online: 18 MAR 2013
Copyright © 2013 Wiley Periodicals, Inc.
Genes, Chromosomes and Cancer
Volume 52, Issue 6, pages 564–579, June 2013
How to Cite
Chen, C., Bartenhagen, C., Gombert, M., Okpanyi, V., Binder, V., Röttgers, S., Bradtke, J., Teigler-Schlegel, A., Harbott, J., Ginzel, S., Thiele, R., Fischer, U., Dugas, M., Hu, J. and Borkhardt, A. (2013), Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosom. Cancer, 52: 564–579. doi: 10.1002/gcc.22054
Dedicated to Fritz Lampert, pioneer of cytogenetic evaluation in childhood leukemia and former head of the Department of Pediatric Oncology at the Children's University Hospital Giessen (Germany) on the occasion of his 80th birthday.
German “Kinderkrebsstiftung,” Bonn, Germany Parents Initiative Gieβen.
- Issue published online: 17 APR 2013
- Article first published online: 18 MAR 2013
- Manuscript Accepted: 29 JAN 2013
- Manuscript Received: 20 NOV 2012
Near haploidy (23–29 chromosomes) is a numerical cytogenetic aberration in childhood acute lymphoblastic leukemia (ALL) associated with particularly poor outcome. In contrast, high hyperdiploidy (51–67 chromosomes) has a favorable prognosis. Correct classification and appropriate risk stratification of near haploidy is frequently hampered by the presence of apparently high hyperdiploid clones that arise by endoreduplication of the original near haploid clone. We evaluated next-generation-sequencing (NGS) to distinguish between “high hyperdiploid” leukemic clones of near haploid and true high hyperdiploid origin. Five high hyperdiploid ALL cases and the “high hyperdiploid” cell line MHH-CALL-2, derived from a near haploid clone, were tested for uniparental isodisomy. NGS showed that all disomic chromosomes of MHH-CALL-2, but none of the patients, were of uniparental origin, thus reliably discriminating these subtypes. Whole-exome- and whole-genome-sequencing of MHH-CALL-2 revealed homozygous non-synonymous coding mutations predicted to be deleterious for the protein function of 63 genes, among them known cancer-associated genes, such as FANCA, NF1, TCF7L2, CARD11, EP400, histone demethylases, and transferases (KDM6B, KDM1A, PRDM11). Only eight of these were also, but heterozygously, mutated in the high hyperdiploid patients. Structural variations in MHH-CALL-2 include a homozygous deletion (MTAP/CDKN2A/CDKN2B/ANRIL), a homozygous inversion (NCKAP5), and an unbalanced translocation (FAM189A1). Together, the sequence variations provide MHH-CALL-2 with capabilities typically acquired during cancer development, e.g., loss of cell cycle control, enhanced proliferation, lack of DNA repair, cell death evasion, and disturbance of epigenetic gene regulation. Poorer prognosis of near haploid ALL most likely results from full penetrance of a large array of detrimental homozygous mutations. © 2013 Wiley Periodicals, Inc.