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Panuciak K, Nowicka E, Mastalerczyk A, Zawitkowska J, Niedźwiecki M, Lejman M. Overview on Aneuploidy in Childhood B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24108764. [PMID: 37240110 DOI: 10.3390/ijms24108764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Recent years have brought significant progress in the treatment of B-cell acute lymphoblastic leukemia (ALL). This was influenced by both the improved schemes of conventionally used therapy, as well as the development of new forms of treatment. As a consequence, 5-year survival rates have increased and now exceed 90% in pediatric patients. For this reason, it would seem that everything has already been explored in the context of ALL. However, delving into its pathogenesis at the molecular level shows that there are many variations that still need to be analyzed in more detail. One of them is aneuploidy, which is among the most common genetic changes in B-cell ALL. It includes both hyperdiploidy and hypodiploidy. Knowledge of the genetic background is important already at the time of diagnosis, because the first of these forms of aneuploidy is characterized by a good prognosis, in contrast to the second, which is in favor of an unfavorable course. In our work, we will focus on summarizing the current state of knowledge on aneuploidy, along with an indication of all the consequences that may be correlated with it in the context of the treatment of patients with B-cell ALL.
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Affiliation(s)
- Kinga Panuciak
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Emilia Nowicka
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Angelika Mastalerczyk
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland
| | - Maciej Niedźwiecki
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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Ma J, Ai X, Wang J, Xing L, Tian C, Yang H, Yu Y, Zhao H, Wang X, Zhao Z, Wang Y, Cao Z. Multiplex ligation-dependent probe amplification identifies copy number changes in normal and undetectable karyotype MDS patients. Ann Hematol 2021; 100:2207-2214. [PMID: 33990890 PMCID: PMC8357724 DOI: 10.1007/s00277-021-04550-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/01/2021] [Indexed: 10/31/2022]
Abstract
Chromosomal abnormalities play an important role in classification and prognostication of myelodysplastic syndrome (MDS) patients. However, more than 50% of low-risk MDS patients harbor a normal karyotype. Recently, multiplex ligation-dependent probe amplification (MLPA) has emerged as an effective and robust method for the detection of cytogenetic aberrations in MDS patients. To characterize the subset of MDS with normal karyotype or failed chromosome banding analysis, we analyzed 144 patient samples with normal karyotype or undetectable through regular chromosome banding analysis, which were subjected to parallel comparison via fluorescence in situ hybridization (FISH) and MLPA. MLPA identifies copy number changes in 16.7% of 144 MDS patients, and we observed a significant difference in overall survival (OS) (median OS: undefined vs 27 months, p=0.0071) in patients with normal karyotype proved by MLPA versus aberrant karyotype cohort as determined by MLPA. Interestingly, patients with undetectable karyotype via regular chromosome banding indicated inferior outcome. Collectively, MDS patients with normal or undetectable karyotype via chromosome banding analysis can be further clarified by MLPA, providing more prognostic information that benefit for individualized therapy.
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Affiliation(s)
- Jing Ma
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Xiaofei Ai
- Department of Pathology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 288 Nanjing Road, Heping District, Tianjin, 300020, China
| | - Jinhuan Wang
- Department of Oncology, The Second Hospital of Tianjin Medical University, No.23 Pingjiang Road, Hexi District, Tianjin, 300211, China
| | - Limin Xing
- Hematology Department of General Hospital, Tianjin Medical University, No.154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Chen Tian
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Hongliang Yang
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Yong Yu
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Haifeng Zhao
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Xiaofang Wang
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China
| | - Zhigang Zhao
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China.
| | - Yafei Wang
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China.
| | - Zeng Cao
- Department of Hematology and Blood and Marrow Transplantation, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, Tianjin, 300060, China.
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Alkhayat N, Elborai Y, Al Sharif O, Al Shahrani M, Alsuhaibani O, Awad M, Elghezal H, Ben-Abdallah Bouhajar I, Alfaraj M, Al Mussaed E, Alabbas F, Elyamany G. Cytogenetic Profile and FLT3 Gene Mutations of Childhood Acute Lymphoblastic Leukemia. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2017; 11:1179554917721710. [PMID: 28811744 PMCID: PMC5528943 DOI: 10.1177/1179554917721710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/26/2017] [Indexed: 11/15/2022]
Abstract
Background: Childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent genetic aberrations. The identification of those abnormalities is clinically important because they are considered significant risk-stratifying markers. Aims: There are insufficient data of cytogenetic profiles in Saudi Arabian patients with childhood ALL leukemia. We have examined a cohort of 110 cases of ALL to determine the cytogenetic profiles and prevalence of FLT3 mutations and analysis of the more frequently observed abnormalities and its correlations to other biologic factors and patient outcomes and to compare our results with previously published results. Materials and methods: Patients—We reviewed all cases from 2007 to 2016 with an established diagnosis of childhood ALL. Of the 110 patients, 98 were B-lineage ALL and 12 T-cell ALL. All the patients were treated by UKALL 2003 protocol and risk stratified according previously published criteria. Cytogenetic analysis—Chromosome banding analysis and fluorescence in situ hybridization were used to detect genetic aberrations. Analysis of FLT3 mutations—Bone marrow or blood samples were screened for FLT3 mutations (internal tandem duplications, and point mutations, D835) using polymerase chain reaction methods. Result: Cytogenetic analysis showed chromosomal anomalies in 68 out of 102 cases with an overall incidence 66.7%. The most frequent chromosomal anomalies in ALL were hyperdiploidy, t(9;22), t(12;21), and MLL gene rearrangements. Our data are in accordance with those published previously and showed that FLT3 mutations are not common in patients with ALL (4.7%) and have no prognostic relevance in pediatric patients with ALL. On the contrary, t(9;22), MLL gene rearrangements and hypodiploidy were signs of a bad prognosis in childhood ALL with high rate of relapse and shorter overall survival compared with the standard-risk group (P = .031).The event-free survival was also found to be worse (P = .040). Conclusions: Our data are in accordance with those published previously, confirming the overall frequency of cytogenetic abnormalities and their prognostic relevance.
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Affiliation(s)
- Nawaf Alkhayat
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Yasser Elborai
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,National Cancer Institute, Cairo University, Giza, Egypt
| | - Omer Al Sharif
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mohammad Al Shahrani
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Omar Alsuhaibani
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mohammed Awad
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hatem Elghezal
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Inesse Ben-Abdallah Bouhajar
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mona Alfaraj
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Eman Al Mussaed
- College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fahad Alabbas
- Department of Pediatric Hematology/Oncology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ghaleb Elyamany
- Department of Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
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Zhang R, Lee JY, Wang X, Xu W, Hu X, Lu X, Niu Y, Tang R, Li S, Li Y. Identification of novel genomic aberrations in AML-M5 in a level of array CGH. PLoS One 2014; 9:e87637. [PMID: 24727659 PMCID: PMC3984075 DOI: 10.1371/journal.pone.0087637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/29/2013] [Indexed: 01/18/2023] Open
Abstract
To assess the possible existence of unbalanced chromosomal abnormalities and delineate the characterization of copy number alterations (CNAs) of acute myeloid leukemia-M5 (AML-M5), R-banding karyotype, oligonucelotide array CGH and FISH were performed in 24 patients with AML-M5. A total of 117 CNAs with size ranging from 0.004 to 146.263 Mb was recognized in 12 of 24 cases, involving all chromosomes other than chromosome 1, 4, X and Y. Cryptic CNAs with size less than 5 Mb accounted for 59.8% of all the CNAs. 12 recurrent chromosomal alterations were mapped. Seven out of them were described in the previous AML studies and five were new candidate AML-M5 associated CNAs, including gains of 3q26.2-qter and 13q31.3 as well as losses of 2q24.2, 8p12 and 14q32. Amplication of 3q26.2-qter was the sole large recurrent chromosomal anomaly and the pathogenic mechanism in AML-M5 was possibly different from the classical recurrent 3q21q26 abnormality in AML. As a tumor suppressor gene, FOXN3, was singled out from the small recurrent CNA of 14q32, however, it is proved that deletion of FOXN3 is a common marker of myeloid leukemia rather than a specific marker for AML-M5 subtype. Moreover, the concurrent amplication of MLL and deletion of CDKN2A were noted and it might be associated with AML-M5. The number of CNA did not show a significant association with clinico-biological parameters and CR number of the 22 patients received chemotherapy. This study provided the evidence that array CGH served as a complementary platform for routine cytogenetic analysis to identify those cryptic alterations in the patients with AML-M5. As a subtype of AML, AML-M5 carries both common recurrent CNAs and unique CNAs, which may harbor novel oncogenes or tumor suppressor genes. Clarifying the role of these genes will contribute to the understanding of leukemogenic network of AML-M5.
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Affiliation(s)
- Rui Zhang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Ji-Yun Lee
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, College of Medicine, Korea University, Seoul, South Korea
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Weihong Xu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Xiaoxia Hu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Yimeng Niu
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Rurong Tang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Yan Li
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- * E-mail:
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Savlı H, Uzülmez N, Ilkay Z, Yavuz D, Sünnetçi D, Hacıhanifioğlu A, Cine N. High Throughput FISH Analysis: A New, Sensitive Option For Evaluation of Hematological Malignancies. TURKISH JOURNAL OF HAEMATOLOGY : OFFICIAL JOURNAL OF TURKISH SOCIETY OF HAEMATOLOGY 2014; 30:122-8. [PMID: 24385774 PMCID: PMC3878481 DOI: 10.4274/tjh.2012.0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 11/22/2012] [Indexed: 01/18/2023]
Abstract
Objective: The aim of this study was to determine the efficiency of the high throughput FISH analysis (HTFA) method for detecting genetic alterations in hematological malignancies, which is a new bacterial artificial chromosome array-based approach. Materials and Methods: We performed a HTFA study of bone marrow aspiration and peripheral blood samples of 77 cases (n=19 myelodysplastic syndrome, n=17 acute lymphoblastic leukemia, n=9 chronic myeloid leukemia, n=32 acute myeloid leukemia) with hematological malignancies during the periods of initial diagnosis, treatment, and/or follow-up. Results: Both numerical and structural abnormalities were detected by HTFA. We observed aberrations in 88% of our acute lymphoblastic leukemia patients, 25% of acute myeloid leukemia patients, and 31% of myelodysplastic syndrome patients. In chronic myeloid leukemia cases, aberration was not detected by HTFA. Conclusion: Our results showed that HTFA, combined with other methods, will gradually take a place in the routine diagnosis of hematologic malignancies.
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Affiliation(s)
- Hakan Savlı
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
| | - Nilüfer Uzülmez
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
| | - Zeynep Ilkay
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
| | - Duygu Yavuz
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
| | - Deniz Sünnetçi
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
| | | | - Naci Cine
- Kocaeli University Faculty of Medicine, Department of Medical Genetics, Kocaeli, Turkey
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Lukackova R, Gerykova Bujalkova M, Majerova L, Mladosievicova B. Molecular genetic methods in the diagnosis of myelodysplastic syndromes. A review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2013; 158:339-45. [PMID: 24263214 DOI: 10.5507/bp.2013.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent a heterogeneous group of premalignant hematologic disorders characterized by ineffective hematopoiesis, peripheral blood cytopenias and increased risk of progression to acute leukemia. Cytogenetic analysis still plays a central role in the diagnosis of MDS, as clonal chromosomal abnormalities are observed in 30-50% of MDS patients. Despite their technical limitations, standard karyotyping and fluorescence in situ hybridization (FISH) are routinely used for identifying recurrent chromosomal rearrangements. However, using this approach means that submicroscopic and not targeted chromosomal aberrations, as well as somatic mutations and epigenetic changes remain largely undetected. METHODS AND RESULTS Introduction of methods for the analysis of copy-number variations (CNV), including array-based technologies and Multiplex ligation-dependent probe amplification (MLPA) has provided novel insights into the molecular pathogenesis of MDS and considerably extended possibilities for genetic laboratory testing. Several novel molecular markers have been discovered and used for diagnosis and prognostic evaluation of patients with MDS. At present, mutational analysis is not routinely performed, as the clinical significance of somatic mutations in MDS has only begun to emerge. However, recently introduced Next-generation sequencing (NGS) technologies could help to elucidate the relationship between chromosomal and molecular aberrations in MDS and lead to further improvement in its diagnosis. CONCLUSION This review focuses on the advantages, limitations, clinical applications and future perspectives of three molecular methods (array-based analysis, MLPA and NGS) currently used in genetic testing and/ or translational research of MDS. In conclusion, a brief summary for clinicians from the routine diagnostic point of view is given.
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Affiliation(s)
- Renata Lukackova
- Department of Clinical Genetics, Medirex a.s., Bratislava, Slovak Republic
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Thieme S, Groth P. Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data. ACTA ACUST UNITED AC 2013; 29:671-7. [PMID: 23341502 PMCID: PMC3597144 DOI: 10.1093/bioinformatics/btt028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches. RESULTS Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.
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Affiliation(s)
- Sebastian Thieme
- Department of Theoretical Biophysics, Humboldt-University of Berlin, 10115 Berlin, Germany and Therapeutic Research Group Oncology, Bayer Pharma AG, 13353 Berlin, Germany
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Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res 2012; 22:1833-44. [PMID: 22628462 PMCID: PMC3460179 DOI: 10.1101/gr.138511.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/03/2023]
Abstract
Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.
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Affiliation(s)
- Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Dana Battaglia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Bill H. Chang
- Division of Hematology and Oncology, Department of Pediatrics, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - James W. Shirley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Meenakshi Devidas
- COG and Department of Biostatistics, College of Medicine, University of Florida, Gainesville, Florida 32601, USA
| | - Brian J. Druker
- Division of Hematology and Medical Oncology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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Gunn SR, Robetorye RS, Mohammed MS. Comparative Genomic Hybridization Arrays in Clinical Pathology. Mol Diagn Ther 2012; 11:73-7. [PMID: 17397242 DOI: 10.1007/bf03256225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Array-based comparative genomic hybridization (array CGH) genome scanning is a powerful method for the global detection of gains and losses of genetic material in both congenital and neoplastic disorders. When used as a clinical diagnostic test, array CGH combines the whole genome perspective of traditional G-banded cytogenetics with the targeted identification of cryptic chromosomal abnormalities characteristic of fluorescence in situ hybridization (FISH). However, the presence of structural variants in the human genome can complicate analysis of patient samples, and array CGH does not provide morphologic information about chromosome structure, balanced translocations, or the actual chromosomal location of segmental duplications. Identification of such anomalies has significant diagnostic and prognostic implications for the patient. We therefore propose that array CGH should be used as a guide to the presence of genomic structural rearrangements in germline and tumor genomes that can then be further characterized by FISH or G-banding, depending on the clinical scenario. In this article, we share some of our experiences with diagnostic array CGH and discuss recent progress and challenges involved with the integration of array CGH into clinical laboratory medicine.
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Affiliation(s)
- Shelly R Gunn
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA.
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Wang JH. Mechanisms and impacts of chromosomal translocations in cancers. Front Med 2012; 6:263-74. [PMID: 22865120 DOI: 10.1007/s11684-012-0215-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/18/2012] [Indexed: 11/30/2022]
Abstract
Chromosomal aberrations have been associated with cancer development since their discovery more than a hundred years ago. Chromosomal translocations, a type of particular structural changes involving heterologous chromosomes, have made a critical impact on diagnosis, prognosis and treatment of cancers. For example, the discovery of translocation between chromosomes 9 and 22 and the subsequent success of targeting the fusion product BCR-ABL transformed the therapy for chronic myelogenous leukemia. In the past few decades, tremendous progress has been achieved towards elucidating the mechanism causing chromosomal translocations. This review focuses on the basic mechanisms underlying the generation of chromosomal translocations. In particular, the contribution of frequency of DNA double strand breaks and spatial proximity of translocating loci is discussed.
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Affiliation(s)
- Jing H Wang
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish Health, Denver, CO 80206, USA.
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Braoudaki M, Tzortzatou-Stathopoulou F. Clinical Cytogenetics in Pediatric Acute Leukemia: An Update. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2012; 12:230-7. [DOI: 10.1016/j.clml.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/25/2011] [Accepted: 04/13/2012] [Indexed: 12/28/2022]
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12
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Lin C, Yang L, Rosenfeld MG. Molecular logic underlying chromosomal translocations, random or non-random? Adv Cancer Res 2012; 113:241-79. [PMID: 22429857 DOI: 10.1016/b978-0-12-394280-7.00015-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chromosomal translocations serve as essential diagnostic markers and therapeutic targets for leukemia, lymphoma, and many types of solid tumors. Understanding the mechanisms of chromosomal translocation generation has remained a central biological question for decades. Rather than representing a random event, recent studies indicate that chromosomal translocation is a non-random event in a spatially regulated, site-specific, and signal-driven manner, reflecting actions involved in transcriptional activation, epigenetic regulation, three-dimensional nuclear architecture, and DNA damage-repair. In this review, we will focus on the progression toward understanding the molecular logic underlying chromosomal translocation events and implications of new strategies for preventing chromosomal translocations.
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Affiliation(s)
- Chunru Lin
- Howard Hughes Medical Institute, University of California, San Diego, School of Medicine, La Jolla, California, USA
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Dawson AJ, Yanofsky R, Vallente R, Bal S, Schroedter I, Liang L, Mai S. Array comparative genomic hybridization and cytogenetic analysis in pediatric acute leukemias. ACTA ACUST UNITED AC 2011; 18:e210-7. [PMID: 21980252 DOI: 10.3747/co.v18i5.770] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Most patients with acute lymphocytic leukemia (all) are reported to have acquired chromosomal abnormalities in their leukemic bone marrow cells. Many established chromosome rearrangements have been described, and their associations with specific clinical, biologic, and prognostic features are well defined. However, approximately 30% of pediatric and 50% of adult patients with all do not have cytogenetic abnormalities of clinical significance. Despite significant improvements in outcome for pediatric all, therapy fails in approximately 25% of patients, and these failures often occur unpredictably in patients with a favorable prognosis and "good" cytogenetics at diagnosis.It is well known that karyotype analysis in hematologic malignancies, although genome-wide, is limited because of altered cell kinetics (mitotic rate), a propensity of leukemic blasts to undergo apoptosis in culture, overgrowth by normal cells, and chromosomes of poor quality in the abnormal clone. Array comparative genomic hybridization (acgh-"microarray") has a greatly increased genomic resolution over classical cytogenetics. Cytogenetic microarray, which uses genomic dna, is a powerful tool in the analysis of unbalanced chromosome rearrangements, such as copy number gains and losses, and it is the method of choice when the mitotic index is low and the quality of metaphases is suboptimal. The copy number profile obtained by microarray is often called a "molecular karyotype."In the present study, microarray was applied to 9 retrospective cases of pediatric all either with initial high-risk features or with at least 1 relapse. The conventional karyotype was compared to the "molecular karyotype" to assess abnormalities as interpreted by classical cytogenetics. Not only were previously undetected chromosome losses and gains identified by microarray, but several karyotypes interpreted by classical cytogenetics were shown to be discordant with the microarray results. The complementary use of microarray and conventional cytogenetics would allow for more sensitive, comprehensive, and accurate analysis of the underlying genetic profile, with concomitant improvement in prognosis and treatment, not only for pediatric all, but for neoplastic disorders in general.
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Affiliation(s)
- A J Dawson
- Cytogenetics Laboratory, Diagnostic Services Manitoba, Winnipeg, MB
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14
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Donahue AC, Abdool AK, Gaur R, Wohlgemuth JG, Yeh CH. Multiplex ligation-dependent probe amplification for detection of chromosomal abnormalities in myelodysplastic syndrome and acute myeloid leukemia. Leuk Res 2011; 35:1477-83. [PMID: 21764131 DOI: 10.1016/j.leukres.2011.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 06/10/2011] [Accepted: 06/15/2011] [Indexed: 11/16/2022]
Abstract
Current strategies for detecting chromosome abnormalities in MDS/AML include FISH or traditional cytogenetics. MLPA detects abnormalities in multiple loci simultaneously, with higher resolution and throughput. Peripheral blood from 50 healthy subjects was used to establish probe-specific reference ranges, increasing MLPA sensitivity and specificity. MLPA was then performed on 110 FISH-tested blood or bone marrow samples from suspected leukemia patients. Our novel MLPA analysis system combined maximum stringency with sensitive detection of low-frequency abnormalities. Accuracy/specificity of MLPA were excellent compared to FISH. Our MLPA analysis/interpretation method provides a clinically robust, high-throughput, high-resolution option for detection of abnormalities associated with MDS/AML.
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Affiliation(s)
- Amber C Donahue
- Department of Hematopathology, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
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15
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Feasibility of mcroRNAs as biomarkers for Barrett's Esophagus progression: a pilot cross-sectional, phase 2 biomarker study. Am J Gastroenterol 2011; 106:1055-63. [PMID: 21407181 DOI: 10.1038/ajg.2011.37] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Risk stratification of Barrett's esophagus (BE) using biomarkers remains an important goal. We evaluated feasibility and clinical accuracy of novel microRNA (miRNA) biomarkers for prediction of BE dysplasia. METHODS Paired fresh-frozen and hematoxylin/eosin specimens from a prospective tissue repository where only biopsies with the lesion of interest (i.e., intestinal metaplasia (IM) or high-grade dysplasia (HGD)/esophageal adenocarcinoma (EAC)) occupying >50% of biopsy area were included. Tissue miRNA expression was determined by microarrays and validated by quantitative reverse transcription-PCR (qRT-PCR). Three groups were compared-group A, IM tissues from BE patients without dysplasia; group B, IM tissues from group C patients; and group C, dysplastic tissues from BE patients with HGD/EAC. RESULTS Overall, 22 BE patients, 11 with and without dysplasia (mean age 64 ± 8.2 and 63 ± 11.6 years, respectively, all Caucasian males) were evaluated. Nine miRNAs were identified by high-throughout analysis (miR-15b, -21, -192, -205, 486-5p, -584, -1246, let-7a, and -7d) and qRT-PCR confirmed expression of miR-15b, -21, 486-5p, and let-7a. Two of 4 miRNAs (miR-145 and -203, but not -196a and -375) previously described in BE patients also exhibited differential expression. Sensitivity and specificity of miRNAs for HGD/EAC were miR-15b: 87 and 80%, miR-21: 93 and 70%, miR-203: 87 and 90%, miR-486-5p: 82 and 55%, and miR-let-7a: 88 and 70%. MiRNA-15b, -21, and -203 exhibited field effects (i.e., groups A and B tissues while histologically similar yet exhibited different miRNA expression). CONCLUSIONS This pilot study demonstrates feasibility of miRNAs to discriminate BE patients with and without dysplasia with reasonable clinical accuracy. However, the specific miRNAs need to be evaluated further in future prospective trials.
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Bacher U, Kohlmann A, Haferlach T. Gene expression profiling for diagnosis and therapy in acute leukaemia and other haematologic malignancies. Cancer Treat Rev 2010; 36:637-46. [DOI: 10.1016/j.ctrv.2010.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/09/2010] [Accepted: 05/10/2010] [Indexed: 01/05/2023]
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Martín-Ezquerra G, Salgado R, Toll A, Gilaberte M, Baró T, Alameda Quitllet F, Yébenes M, Solé F, Garcia-Muret M, Espinet B, Pujol R. Multiple genetic copy number alterations in oral squamous cell carcinoma: study of MYC
, TP53
, CCDN1, EGFR
and ERBB2
status in primary and metastatic tumours. Br J Dermatol 2010; 163:1028-35. [DOI: 10.1111/j.1365-2133.2010.09947.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Array comparative genomic hybridization analysis of adult acute leukemia patients. ACTA ACUST UNITED AC 2010; 197:122-9. [PMID: 20193845 DOI: 10.1016/j.cancergencyto.2009.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 12/27/2022]
Abstract
We have performed a retrospective array-based comparative hybridization (array-CGH) study on 41 acute leukemia samples [n=17 acute lymphoblastic leukemia (ALL) patients only at diagnosis, n=3 ALL patients both at diagnosis and relapse; n=20 acute myeloid leukemia (AML) patients only at diagnosis and n=1 AML patient both at diagnosis and relapse] using an Agilent 44K array. In addition to previously detected cytogenetic aberrations, we observed cryptic aberrations in 95% of ALL and 90.5% of AML cases. ALL-specific recurrent abnormalities were RB1 (n=3), PAX5 (n=4), and CDKN2B (n=3) deletions; AML-specific recurrent abnormalities were HOXA9 and HOXA10 (n=2) deletions and NOTCH1 duplication (n=2). Recurrent duplication of the ELK1 oncogene was observed in both ALL (n=2) and AML (n=3) cases. Our results demonstrate that oligo-array CGH (oaCGH) is an effective method for defining copy number alterations and identification of novel recurring unbalanced abnormalities. At least for now, however, the use of oaCGH for routine diagnosis still has some restrictions.
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Usvasalo A, Räty R, Harila-Saari A, Koistinen P, Savolainen ER, Vettenranta K, Knuutila S, Elonen E, Saarinen-Pihkala UM. Acute lymphoblastic leukemias with normal karyotypes are not without genomic aberrations. ACTA ACUST UNITED AC 2009; 192:10-7. [PMID: 19480931 DOI: 10.1016/j.cancergencyto.2009.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 02/17/2009] [Accepted: 02/24/2009] [Indexed: 12/15/2022]
Abstract
Current cytogenetic techniques have enabled more accurate definition of genetic aberrations in the lymphoblasts of patients with acute lymphoblastic leukemia (ALL), at least in most cases. Detecting the cryptic aberrations undetected by conventional cytogenetic methods is important for disease classification, evaluation of prognosis, and minimal residual disease follow-up. We have studied DNA copy number alterations of 27 adolescent ALL patients with normal (n=26) or failed (n=1) karyotype at diagnosis using microarray comparative genomic hybridization (CGH). Aberrations were detected in 85% of cases, deletions being more frequent (39 in 19 patients) than gains (14 in 10 patients). Deletions of 9p21.3 were the most common aberration, and 41% of deletions were cryptic and <5 Mb in size. We conclude that ALL without any form of genetic alteration probably does not exist. Microarray CGH is a powerful tool to reveal otherwise cryptic aberrations in adolescent ALL.
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Affiliation(s)
- Anu Usvasalo
- Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland.
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21
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Bacher U, Kohlmann A, Haferlach T. Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:184-93. [PMID: 19474126 DOI: 10.1093/bfgp/elp011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Considering the heterogeneity of leukaemias and the widening spectrum of therapeutic strategies, novel diagnostic methods are urgently needed for haematological malignancies. For a decade, gene expression profiling (GEP) has been applied in leukaemia research. Thus, various studies demonstrated worldwide that the majority of genetically defined leukaemia subtypes are accurately predictable by GEP, for example, with respect to reciprocal rearrangements in acute myeloid leukaemia (AML). Moreover, novel prognostically relevant gene classifiers were developed as, for example, in normal karyotype AML. Considering the lymphatic malignancies, GEP studies defined novel clinically relevant subtypes in diffuse large B cell lymphoma (DLBCL), and improved the discrimination of Burkitt lymphoma and DLBCL cases, overcoming considerable overlaps of these entities that exist from morphological and genetic perspectives. Treatment-specific sensitivity assays are being developed for targeted drugs such as farnesyl transferase inhibitors in AML or imatinib in BCR-ABL1 positive acute lymphoblastic leukaemia (ALL). Irrespectively of these proceedings, an introduction of the microarray technology in haematological practice requires diagnostic algorithms and strategies for interaction with currently established diagnostic techniques. Large multicentre studies such as the MILE Study (Microarray Innovations in LEukemia) aim at translating this methodology into clinical routine workflows and to catalyze this process.
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Affiliation(s)
- Ulrike Bacher
- MLL Munich Leukemia Laboratory, D-81377 Munich, Germany
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22
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Bacher U, Kohlmann A, Haferlach T. Current status of gene expression profiling in the diagnosis and management of acute leukaemia. Br J Haematol 2009; 145:555-68. [PMID: 19344393 DOI: 10.1111/j.1365-2141.2009.07656.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gene expression profiling (GEP) enables the simultaneous investigation of the expression of tens of thousands of genes and was successfully introduced in leukaemia research a decade ago. Aiming to better understand the diversity of genetic aberrations in acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL), pioneer studies investigated and confirmed the predictability of many cytogenetic and molecular subclasses in AML and ALL. In addition, GEP can define new prognostic subclasses within distinct leukaemia subgroups, as illustrated in AML with normal karyotype. Another approach is the development of treatment-specific sensitivity assays, which might contribute to targeted therapy studies. Finally, GEP might enable the detection of new molecular targets for therapy in patients with acute leukaemia. Meanwhile, large multicentre studies, e.g. the Microarray Innovations in LEukaemia (MILE) study, prepare for a standardised introduction of GEP in leukaemia diagnostic algorithms, aiming to translate this novel methodology into clinical routine for the benefit of patients with the complex disorders of AML and ALL.
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Affiliation(s)
- Ulrike Bacher
- Department of Stem Cell Transplantation, University Cancer Center Hamburg, Hamburg
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23
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Blandin AT, Mühlematter D, Bougeon S, Gogniat C, Porter S, Beyer V, Parlier V, Beckmann JS, van Melle G, Jotterand M. Automated four-color interphase fluorescence in situ hybridization approach for the simultaneous detection of specific aneuploidies of diagnostic and prognostic significance in high hyperdiploid acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2008; 186:69-77. [PMID: 18940469 DOI: 10.1016/j.cancergencyto.2008.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/12/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
In high hyperdiploid acute lymphoblastic leukemia (ALL), the concurrence of specific trisomies confers a more favorable outcome than hyperdiploidy alone. Interphase fluorescence in situ hybridization (FISH) complements conventional cytogenetics (CC) through its sensitivity and ability to detect chromosome aberrations in nondividing cells. To overcome the limits of manual I-FISH, we developed an automated four-color I-FISH approach and assessed its ability to detect concurrent aneuploidies in ALL. I-FISH was performed using centromeric probes for chromosomes 4, 6, 10, and 17. Parameters established for nucleus selection and signal detection were evaluated. Cutoff values were determined. Combinations of aneuploidies were considered relevant when each aneuploidy was individually significant. Results obtained in 10 patient samples were compared with those obtained with CC. Various combinations of aneuploidies were identified. All clones detected by CC were observed also by I-FISH, and I-FISH revealed numerous additional abnormal clones in all patients, ranging from < or =1% to 31.6% of cells analyzed. We conclude that four-color automated I-FISH permits the identification of concurrent aneuploidies of potential prognostic significance. Large numbers of cells can be analyzed rapidly. The large number of nuclei scored revealed a high level of chromosome variability both at diagnosis and relapse, the prognostic significance of which is of considerable clinical interest and merits further evaluation.
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Affiliation(s)
- Anna Talamo Blandin
- Cancer Cytogenetics Unit, Medical Genetics Service, University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
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Kamath A, Tara H, Xiang B, Bajaj R, He W, Li P. Double-minute MYC amplification and deletion of MTAP, CDKN2A, CDKN2B, and ELAVL2 in an acute myeloid leukemia characterized by oligonucleotide-array comparative genomic hybridization. ACTA ACUST UNITED AC 2008; 183:117-20. [PMID: 18503831 DOI: 10.1016/j.cancergencyto.2008.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 02/20/2008] [Indexed: 10/22/2022]
Abstract
Chromosomal analysis and fluorescence in situ hybridization (FISH) have been routinely used in detecting recurrent chromosomal abnormalities in patients with various hematological malignancies. However, the genomic imbalances underlying many recurrent abnormalities could not be delineated due to the low resolution of chromosome analysis. We have performed oligonucleotide-array comparative genomic hybridization (oaCGH) in an AML case with a 15p/17p translocation, a suspected 9p21 deletion, monosomies of chromosomes X and 9, and 2 to 60 double minutes. The oaCGH findings confirmed the chromosomal observations and further characterized a 21.338-Mb 17p deletion, a 3.916-Mb deletion at 9p21.3 containing the MTAP, CDKN2A, CDKN2B, and ELAVL2 genes, and a 3.981-Mb 8q24 double minute containing the TRIB1, FAM84B, MYC, and PVT1 genes, with an average of 30 double minutes in each cell. FISH using MYC probes and bacterial artificial chromosome clone probes confirmed the genomic findings and revealed a progressional pattern for the 9p21.3 deletion. These results demonstrate the potential of oaCGH as a powerful diagnostic tool for characterizing genomic imbalances for patients with hematological malignancies.
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Affiliation(s)
- Anitha Kamath
- Molecular Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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25
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Gunn SR, Mohammed MS, Mellink CHM, Abruzzo LV, Robetorye RS. The HemeScan test for genomic prognostic marker assessment in chronic lymphocytic leukemia. ACTA ACUST UNITED AC 2008; 2:731-40. [DOI: 10.1517/17530059.2.6.731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Calasanz MJ, Cigudosa JC. Molecular cytogenetics in translational oncology: when chromosomes meet genomics. Clin Transl Oncol 2008; 10:20-9. [DOI: 10.1007/s12094-008-0149-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Nassiri M, Gugic D, Olczyk J, Ramos S, Vincek V. Preservation of skin DNA for oligonucleotide array CGH studies: a feasibility study. Arch Dermatol Res 2007; 299:353-7. [PMID: 17665208 PMCID: PMC1950585 DOI: 10.1007/s00403-007-0773-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 06/27/2007] [Accepted: 07/10/2007] [Indexed: 10/25/2022]
Abstract
Array-based comparative genomic hybridization (a-CGH) is a promising tool for clinical genomic studies. However, pre-analytical sample preparation methods have not been fully evaluated for this purpose. Parallel sections of normal male human skin biopsy samples were collected and immediately immersed in saline, formalin and a molecular fixative for 8, 12 and 24 h. Genomic DNA was isolated from the samples and subjected to amplification and labeling. Labeled samples were then co-hybridized with normal reference female DNA to Agilent oligonucleotide-based a-CGH 44k slides. Pre-analytic parameters such as DNA yield, quality of genomic DNA and labeling efficacy were evaluated. Also microarray analytical variables, including the feature signal intensity, data distribution dynamic range, signal to noise ratio and background intensity levels were assessed for data quality. DNA yield and quality of genomic DNA--as evaluated by spectrophotometry and gel electrophoresis--were similar for fresh and molecular fixative-exposed samples. In addition, labeling efficacy of dye incorporation was not drastically different. There was no difference between fresh and molecular fixative material comparing scan parameters and stem plot analysis of a-CGH result. Formalin-fixed samples, on the other hand, showed various errors such as oversaturation, non-uniformity in replicates, and decreased signal to noise ratio. Overall, the a-CGH result of formalin samples was not interpretable. DNA extracted from formalin-fixed tissue samples is not suitable for oligonucleotide-based a-CGH studies. On the other hand, the molecular fixative preserves tissue DNA similar to its fresh state with no discernable analytical differences.
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Affiliation(s)
- Mehdi Nassiri
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
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Abstract
Chromosome aberrations, in particular translocations and their corresponding gene fusions, have an important role in the initial steps of tumorigenesis; at present, 358 gene fusions involving 337 different genes have been identified. An increasing number of gene fusions are being recognized as important diagnostic and prognostic parameters in malignant haematological disorders and childhood sarcomas. The biological and clinical impact of gene fusions in the more common solid tumour types has been less appreciated. However, an analysis of available data shows that gene fusions occur in all malignancies, and that they account for 20% of human cancer morbidity. With the advent of new and powerful investigative tools that enable the detection of cytogenetically cryptic rearrangements, this proportion is likely to increase substantially.
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Affiliation(s)
- Felix Mitelman
- Lund University, Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden.
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