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Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016; 11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023] Open
Abstract
Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL) is still a challenge. Aims: To characterize the presence of additional DNA copy number alterations (CNAs) in children and adults with ALL by whole-genome oligonucleotide array (aCGH) analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults). The NimbleGen CGH 12x135K array (Roche) was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q). CNAs were associated with age, phenotype, genetic subtype and overall survival (OS). In the whole cohort of children, the losses on 14q32.33 (p = 0.019) and 15q13.2 (p = 0.04) were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001) and Xp21.1 (p = 0.029), and the loss of 17p (p = 0.014) were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.
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Affiliation(s)
- Maribel Forero-Castro
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- School of Biological Sciences (GEBIMOL), Pedagogical and Technological University of Colombia (UPTC), Tunja, Colombia
| | - Cristina Robledo
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Rocío Benito
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - María Abáigar
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
| | - Ana África Martín
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - Maryam Arefi
- Department of Hematology, Clinical University Hospital of Valladolid, Valladolid, Spain
| | - José Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, Murcia, Spain
| | | | - Juan N. Rodríguez
- Department of Hematology, Juan Ramón Jiménez Hospital, Huelva, Spain
| | | | - Susana Riesco
- Department of Pediatric Oncohematology, University Hospital of Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Department of Hematology, Jerez Hospital, Jerez de la Frontera, Cádiz, Spain
| | | | - Isabel Recio
- Department of Hematology, Nuestra Señora de Sonsoles Hospital, Avila, Spain
| | - Jordi Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jorge Labrador
- Department of Hematology, University Hospital of Burgos, Burgos, Spain
| | - José M. Alonso
- Department of Hematology, Rio Carrión Hospital, Palencia, Spain
| | - Carmen Olivier
- Department of Hematology, General Hospital of Segovia, Segovia, Spain
| | - Magdalena Sierra
- Department of Hematology, Virgen de la Concha Hospital, Zamora, Spain
| | - Marta Megido
- Department of Hematology, Bierzo Hospital, León/Ponferrada, Spain
| | | | - Juana Ciudad Pizarro
- Cytometry Service (NUCLEUS Research Support Platform), University of Salamanca (USAL), Salamanca, Spain
| | - Juan Luis García
- Institute of Health Science Studies of Castile and León (IESCYL), Salamanca, Spain
| | - José M. Ribera
- Department of Hematology, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Badalona, Spain
| | - Jesús M. Hernández-Rivas
- IBSAL, IBMCC, University of Salamanca, CSIC, Cancer Research Center, Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, Salamanca, Spain
- * E-mail:
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Genomic profiling in high hyperdiploid acute myeloid leukemia: a retrospective study of 19 cases. Cancer Genet 2012; 204:516-21. [PMID: 22018275 DOI: 10.1016/j.cancergen.2011.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 08/26/2011] [Accepted: 09/03/2011] [Indexed: 11/22/2022]
Abstract
Among patients with acute myeloid leukemia (AML), the rare group of complex aberrant karyotypes characterized by high hyperdiploidy (HH) is a subset with poor prognosis. Because of their rarity, few conventional cytogenetic studies have specifically addressed these patients. To identify DNA copy number aberrations at the submicroscopic level, we applied array-based comparative genomic hybridization (aCGH) to samples from 19 AML patients with complex karyotypes characterized by HH (≥49 chromosomes). We found a total of 155 imbalances (average: 8.2 per patient), and a high proportion of these imbalances involved whole chromosomes (n = 75). The chromosomes most commonly gained were chromosomes 8 (58%), 21 (42%), and 19 (32%). We identified 80 segmental genomic aberrations, and losses (n = 47) were more frequent than gains (n = 33). We identified common deleted regions at 5q, 15q, 18p, and 19p. The tumor suppressor gene L3MBTL4 and zinc finger proteins reside within 18p and 19p, respectively. The aCGH analysis added new information to the karyotypic interpretations in 16 of the 19 HH AML cases (84%), leading to a significantly higher detection rate of abnormalities.
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Enkemann SA. Standards affecting the consistency of gene expression arrays in clinical applications. Cancer Epidemiol Biomarkers Prev 2010; 19:1000-3. [PMID: 20332273 DOI: 10.1158/1055-9965.epi-10-0044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The use of microarray technology to measure gene expression has created optimism for the feasibility of using molecular assessments of tumors routinely in the clinical management of cancer. Gene expression arrays have been pioneers in the development of standards; both for research use and now for clinical application. Some of the existing standards have been driven by the early perception that microarray technology was inconsistent and perhaps unreliable. More recent experimentation has shown that reproducible data can be achieved and clinical standards are beginning to emerge. For the transcriptional assessment of tumors, this means a system that correctly samples a tumor, isolates RNA and processes this for microarray analysis, evaluates the data, and communicates findings in a consistent and timely fashion. The most important standard is to show that a clinically important assessment can be made with microarray data. The standards emerging from work on various parts of the entire process could guide the development of a workable system. However, the final standard for each component of the process depends on the accuracy required when the assay becomes part of the clinical routine: a routine that now includes the molecular evaluation of tumors.
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Affiliation(s)
- Steven A Enkemann
- Molecular Genomics Laboratory, H. Lee Moffitt Cancer Center and Research Institute, SRB2 12902 Magnolia Drive, Tampa, FL 33612, USA.
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