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Rosli AA, Azlan A, Rajasegaran Y, Mot YY, Heidenreich O, Yusoff NM, Moses EJ. Cytogenetics analysis as the central point of genetic testing in acute myeloid leukemia (AML): a laboratory perspective for clinical applications. Clin Exp Med 2023; 23:1137-1159. [PMID: 36229751 DOI: 10.1007/s10238-022-00913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/02/2022] [Indexed: 11/27/2022]
Abstract
Chromosomal abnormalities in acute myeloid leukemia (AML) have significantly contributed to scientific understanding of its molecular pathogenesis, which has aided in the development of therapeutic strategies and enhanced management of AML patients. The diagnosis, prognosis and treatment of AML have also rapidly transformed in recent years, improving initial response to treatment, remission rates, risk stratification and overall survival. Hundreds of rare chromosomal abnormalities in AML have been discovered thus far using chromosomal analysis and next-generation sequencing. As a result, the World Health Organization (WHO) has categorized AML into subgroups based on genetic, genomic and molecular characteristics, to complement the existing French-American classification which is solely based on morphology. In this review, we aim to highlight the most clinically relevant chromosomal aberrations in AML together with the technologies employed to detect these aberrations in laboratory settings.
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Affiliation(s)
- Aliaa Arina Rosli
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Adam Azlan
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Yaashini Rajasegaran
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Yee Yik Mot
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Olaf Heidenreich
- Prinses Máxima Centrum Voor Kinderoncologie, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Narazah Mohd Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Emmanuel Jairaj Moses
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia.
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Van Tricht C, Voet T, Lammertyn J, Spasic D. Imaging the unimaginable: leveraging signal generation of CRISPR-Cas for sensitive genome imaging. Trends Biotechnol 2022; 41:769-784. [PMID: 36369053 DOI: 10.1016/j.tibtech.2022.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
Abstract
Fluorescence in situ hybridization (FISH) is the gold standard for visualizing genomic DNA in fixed cells and tissues, but it is incompatible with live-cell imaging, and its combination with RNA imaging is challenging. Consequently, due to its capacity to bind double-stranded DNA (dsDNA) and design flexibility, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (CRISPR-Cas9) technology has sparked enormous interest over the past decade. In this review, we describe various nucleic acid (NA)- and protein-based (amplified) signal generation methods that achieve imaging of repetitive and single-copy sequences, and even single-nucleotide variants (SNVs), next to highly multiplexed as well as dynamic imaging in live cells. With future progress in the field, the CRISPR-(d)Cas9-based technology promises to break through as a next-generation cell-imaging technique.
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Hayashi Y, Ohnuma K, Furue MK. Pluripotent Stem Cell Heterogeneity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1123:71-94. [DOI: 10.1007/978-3-030-11096-3_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Chen CP, Ko TM, Chern SR, Wu PS, Chen SW, Lai ST, Yang CW, Pan CW, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of mosaicism for a small supernumerary marker chromosome derived from chromosome 16. Taiwan J Obstet Gynecol 2017; 56:545-549. [DOI: 10.1016/j.tjog.2017.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 10/19/2022] Open
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Andrews PW, Baker D, Benvinisty N, Miranda B, Bruce K, Brüstle O, Choi M, Choi YM, Crook JM, de Sousa PA, Dvorak P, Freund C, Firpo M, Furue MK, Gokhale P, Ha HY, Han E, Haupt S, Healy L, Hei DJ, Hovatta O, Hunt C, Hwang SM, Inamdar MS, Isasi RM, Jaconi M, Jekerle V, Kamthorn P, Kibbey MC, Knezevic I, Knowles BB, Koo SK, Laabi Y, Leopoldo L, Liu P, Lomax GP, Loring JF, Ludwig TE, Montgomery K, Mummery C, Nagy A, Nakamura Y, Nakatsuji N, Oh S, Oh SK, Otonkoski T, Pera M, Peschanski M, Pranke P, Rajala KM, Rao M, Ruttachuk R, Reubinoff B, Ricco L, Rooke H, Sipp D, Stacey GN, Suemori H, Takahashi TA, Takada K, Talib S, Tannenbaum S, Yuan BZ, Zeng F, Zhou Q. Points to consider in the development of seed stocks of pluripotent stem cells for clinical applications: International Stem Cell Banking Initiative (ISCBI). Regen Med 2015; 10:1-44. [PMID: 25675265 DOI: 10.2217/rme.14.93] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- P W Andrews
- Department of Biomedical Science, The University of Sheffield, Sheffield, UK
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Rai PS, Pai GC, Alvares JF, Bellampalli R, Gopinath PM, Satyamoorthy K. Intraindividual somatic variations in MTHFR gene polymorphisms in relation to colon cancer. Pharmacogenomics 2014; 15:349-59. [PMID: 24533714 DOI: 10.2217/pgs.14.4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AIM MTHFR mediates the one carbon metabolism pathway. Two common genetic variants, C677T and A1298C, of MTHFR are associated with number of human diseases, including cancer, as well as being involved in the modulation of therapy outcome to antifolate drugs. To understand the distribution pattern of SNPs among different tissues of an individual, we examined MTHFR polymorphisms in normal and colon cancer tissues and compared the genotype frequencies in peripheral blood samples. MATERIALS & METHODS DNA was isolated from tumor tissue and matched normal tissues from 155 colon cancer patients. These samples as well as DNA from blood samples of the control group (n = 294) were analyzed for MTHFR polymorphisms by PCR-RFLP and confirmed by a direct DNA sequencing method. RESULTS Our data suggest that the allele and genotype frequencies of C677T and A1298C were significantly different between tumor tissues and both types of normal tissues. We have established that MTHFR variants that exist in tumor and matched normal tissues of colon cancer patients differ suggesting somatic variation in MTHFR polymorphisms among different tissues of an individual. The MTHFR A1298C polymorphism was associated with risk of colon cancer. CONCLUSION Different MTHFR variants may exist in different tissues to maintain physiological functions and may have implications for disease susceptibility and pharmacogenomics based therapies. Original submitted 21 January 2013; Revision submitted 3 January 2014.
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Affiliation(s)
- Padmalatha S Rai
- Division of Biotechnology, School of Life Sciences, Planetarium Complex, Manipal University, Manipal-576104, India
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Chen CP, Chen M, Su YN, Huang JP, Chern SR, Wu PS, Su JW, Chang SP, Chen YT, Lee CC, Chen LF, Pan CW, Wang W. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review. Gene 2013; 529:169-75. [PMID: 23933412 DOI: 10.1016/j.gene.2013.07.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/01/2013] [Accepted: 07/10/2013] [Indexed: 11/28/2022]
Abstract
We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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O'Brien B, Zeng H, Polyzos AA, Lemke KH, Weier JF, Wang M, Zitzelsberger HF, Weier HUG. Bioinformatics tools allow targeted selection of chromosome enumeration probes and aneuploidy detection. J Histochem Cytochem 2012. [PMID: 23204113 PMCID: PMC3636690 DOI: 10.1369/0022155412470955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Accurate determination of cellular chromosome complements is a highly relevant issue beyond prenatal/pre-implantation genetic analyses or stem cell research, because aneusomy may be an important mechanism by which organisms control the rate of fetal cellular proliferation and the fate of regenerating tissues. Typically, small amounts of individual cells or nuclei are assayed by in situ hybridization using chromosome-specific DNA probes. Careful probe selection is fundamental to successful hybridization experiments. Numerous DNA probes for chromosome enumeration studies are commercially available, but their use in multiplexed hybridization assays is hampered due to differing probe-specific hybridization conditions or a lack of a sufficiently large number of different reporter molecules. Progress in the International Human Genome Project has equipped the scientific community with a wealth of unique resources, among them recombinant DNA libraries, physical maps, and data-mining tools. Here, we demonstrate how bioinformatics tools can become an integral part of simple, yet powerful approaches to devise diagnostic strategies for detection of aneuploidy in interphase cells. Our strategy involving initial in silico optimization steps offers remarkable savings in time and costs during probe generation, while at the same time significantly increasing the assay’s specificity, sensitivity, and reproducibility.
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Affiliation(s)
- Benjamin O'Brien
- William Harvey Research Institute, Queen Mary University London, UK.
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