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Liu X, Zhang Z, Zhang X, Wang J, Jiang J, Li L, Wang H, Liu S, Hu T. Unbalanced X;Y translocations carrying SRY in prenatal settings: Clinical, molecular, and cytogenetic analysis of three cases. Prenat Diagn 2024; 44:580-585. [PMID: 38204192 DOI: 10.1002/pd.6520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND Generally, the translocation of SRY onto one of the X chromosomes leads to 46, XX testicular disorders of sex development, a relatively rare condition characterized by the presence of testicular tissue with a 46, XX karyotype. Three prenatal cases of unbalanced X; Y translocation carrying SRY were identified in this study. METHODS Structural variants were confirmed using single nucleotide polymorphism array and chromosomal karyotyping. X chromosome inactivation (XCI) was also analyzed. Detailed clinical features of the three cases were collected. RESULTS We identified two fetuses with maternal inherited unbalanced X; Y translocations carrying SRY and skewed XCI presenting with normal female external genitalia, and one fetus with de novo 46, XX (SRY+) and random XCI manifested male phenotypic external genitalia. CONCLUSION This study reports that cases with unbalanced X; Y translocations carrying SRY manifested a normal female external genitalia in a prenatal setting. We speculate that the skewed XCI mediates the silence of SRY. In addition, our study emphasizes that combining clinical findings with pedigree analysis is critical for estimating the prognosis of fetuses with sex chromosome abnormalities.
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Affiliation(s)
- Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xuan Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jieni Jiang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Lingping Li
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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Popov A, Henze G, Tsaur G, Budanov O, Roumiantseva J, Belevtsev M, Verzhbitskaya T, Movchan L, Lagoyko S, Zharikova L, Olshanskaya Y, Riger T, Valochnik A, Miakova N, Litvinov D, Khlebnikova O, Streneva O, Stolyarova E, Ponomareva N, Novichkova G, Aleinikova O, Fechina L, Karachunskiy A. Flow cytometric minimal residual disease measurement accounting for cytogenetics in children with non-high-risk acute lymphoblastic leukemia treated according to the ALL-MB 2008 protocol. Cancer Med 2024; 13:e7172. [PMID: 38651186 PMCID: PMC11036069 DOI: 10.1002/cam4.7172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/15/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Quantitative measurement of minimal residual disease (MRD) is the "gold standard" for estimating the response to therapy in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Nevertheless, the speed of the MRD response differs for different cytogenetic subgroups. Here we present results of MRD measurement in children with BCP-ALL, in terms of genetic subgroups with relation to clinically defined risk groups. METHODS A total of 485 children with non-high-risk BCP-ALL with available cytogenetic data and MRD studied at the end-of-induction (EOI) by multicolor flow cytometry (MFC) were included. All patients were treated with standard-risk (SR) of intermediate-risk (ImR) regimens of "ALL-MB 2008" reduced-intensity protocol. RESULTS AND DISCUSSION Among all study group patients, 203 were found to have low-risk cytogenetics (ETV6::RUNX1 or high hyperdiploidy), while remaining 282 children were classified in intermediate cytogenetic risk group. For the patients with favorable and intermediate risk cytogenetics, the most significant thresholds for MFC-MRD values were different: 0.03% and 0.04% respectively. Nevertheless, the most meaningful thresholds were different for clinically defined SR and ImR groups. For the SR group, irrespective to presence/absence of favorable genetic lesions, MFC-MRD threshold of 0.1% was the most clinically valuable, although for ImR group the most informative thresholds were different in patients from low-(0.03%) and intermediate (0.01%) cytogenetic risk groups. CONCLUSION Our data show that combining clinical risk factors with MFC-MRD measurement is the most useful tool for risk group stratification of children with BCP-ALL in the reduced-intensity protocols. However, this algorithm can be supplemented with cytogenetic data for part of the ImR group.
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Affiliation(s)
- Alexander Popov
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Guenter Henze
- Department of Pediatric Oncology HematologyCharité—Universitätsmedizin BerlinBerlinGermany
| | - Grigory Tsaur
- Regional Children's HospitalEkaterinburgRussian Federation
- Research Institute of Medical Cell TechnologiesEkaterinburgRussian Federation
- Ural State Medical UniversityEkaterinburgRussian Federation
| | - Oleg Budanov
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Julia Roumiantseva
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Mikhail Belevtsev
- Republican Scientific and Practical Center for Pediatric OncologyHematology and ImmunologyMinskBelarus
| | - Tatiana Verzhbitskaya
- Regional Children's HospitalEkaterinburgRussian Federation
- Research Institute of Medical Cell TechnologiesEkaterinburgRussian Federation
| | - Liudmila Movchan
- Republican Scientific and Practical Center for Pediatric OncologyHematology and ImmunologyMinskBelarus
| | - Svetlana Lagoyko
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Liudmila Zharikova
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia Olshanskaya
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Tatiana Riger
- Regional Children's HospitalEkaterinburgRussian Federation
| | - Alena Valochnik
- Republican Scientific and Practical Center for Pediatric OncologyHematology and ImmunologyMinskBelarus
| | - Natalia Miakova
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Dmitry Litvinov
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | | | - Olga Streneva
- Regional Children's HospitalEkaterinburgRussian Federation
- Research Institute of Medical Cell TechnologiesEkaterinburgRussian Federation
| | | | - Natalia Ponomareva
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Galina Novichkova
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Olga Aleinikova
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Larisa Fechina
- Regional Children's HospitalEkaterinburgRussian Federation
- Research Institute of Medical Cell TechnologiesEkaterinburgRussian Federation
| | - Alexander Karachunskiy
- National Research and Clinical Center for Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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Yurchenko A, Pšenička T, Mora P, Ortega JAM, Baca AS, Rovatsos M. Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos. Genes (Basel) 2024; 15:429. [PMID: 38674364 PMCID: PMC11049218 DOI: 10.3390/genes15040429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.
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Affiliation(s)
- Alona Yurchenko
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Tomáš Pšenička
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Juan Alberto Marchal Ortega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Antonio Sánchez Baca
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
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Gasperl A, Müller M. Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees. Methods Mol Biol 2024; 2787:95-103. [PMID: 38656484 DOI: 10.1007/978-1-0716-3778-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Our method describes how to collect forest tree root tips in the field, to store them for transfer to the lab, to pretreat root tips in order to arrest cells in metaphase, fix root tips to preserve specific morphological organizations, to stain fixed root tips by Feulgen's Reaction in order to increase contrast, and to prepare the root meristem for analyzing mitotic stages and chromosomal aberrations via light microscopy. We further describe how to classify chromosomal abnormalities and quantify them via aberration indices.
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Affiliation(s)
- Anna Gasperl
- Institute of Biology, Plant Sciences, University of Graz, NAWI Graz, Graz, Austria
| | - Maria Müller
- Institute of Biology, Plant Sciences, University of Graz, NAWI Graz, Graz, Austria.
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Coccaro N, Zagaria A, Anelli L, Tarantini F, Tota G, Conserva MR, Cumbo C, Parciante E, Redavid I, Ingravallo G, Minervini CF, Minervini A, Specchia G, Musto P, Albano F. Optical Genome Mapping as a Tool to Unveil New Molecular Findings in Hematological Patients with Complex Chromosomal Rearrangements. Genes (Basel) 2023; 14:2180. [PMID: 38137002 PMCID: PMC10742895 DOI: 10.3390/genes14122180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Standard cytogenetic techniques (chromosomal banding analysis-CBA, and fluorescence in situ hybridization-FISH) show limits in characterizing complex chromosomal rearrangements and structural variants arising from two or more chromosomal breaks. In this study, we applied optical genome mapping (OGM) to fully characterize two cases of complex chromosomal rearrangements at high resolution. In case 1, an acute myeloid leukemia (AML) patient showing chromothripsis, OGM analysis was fully concordant with classic cytogenetic techniques and helped to better refine chromosomal breakpoints. The OGM results of case 2, a patient with non-Hodgkin lymphoma, were only partially in agreement with previous cytogenetic analyses and helped to better define clonal heterogeneity, overcoming the bias related to clonal selection due to cell culture of cytogenetic techniques. In both cases, OGM analysis led to the identification of molecular markers, helping to define the pathogenesis, classification, and prognosis of the analyzed patients. Despite extensive efforts to study hematologic diseases, standard cytogenetic methods display unsurmountable limits, while OGM is a tool that has the power to overcome these limitations and provide a cytogenetic analysis at higher resolution. As OGM also shows limits in defining regions of a repetitive nature, combining OGM with CBA to obtain a complete cytogenetic characterization would be desirable.
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Affiliation(s)
- Nicoletta Coccaro
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Antonella Zagaria
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Luisa Anelli
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Francesco Tarantini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giuseppina Tota
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Maria Rosa Conserva
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Cosimo Cumbo
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Elisa Parciante
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Immacolata Redavid
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giuseppe Ingravallo
- Section of Molecular Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Crescenzio Francesco Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Angela Minervini
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Giorgina Specchia
- School of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
| | - Francesco Albano
- Hematology and Stem Cell Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy; (N.C.); (A.Z.); (L.A.); (F.T.); (G.T.); (M.R.C.); (C.C.); (E.P.); (I.R.); (C.F.M.); (A.M.); (P.M.)
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Jung K, Shin KS, Son BR, Park HS. The Discordance between G-Banding Karyotyping and Microarray in Structural Abnormality. Clin Lab 2023; 69. [PMID: 38084694 DOI: 10.7754/clin.lab.2023.230513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
BACKGROUND Cytomolecular genetic laboratory techniques have developed from conventional G-banding karyotyping to whole genome sequencing. Although resolution has greatly increased, various cytogenetic techniques have their advantages and limitations in detecting genomic variations. METHODS We compared the chromosomal abnormalities detected by G-banding karyotyping and SNP-based microarray testing in 62 patients from July 2020 to December 2022. We analyzed their difference according to chromosomal abnormalities, including numerical and structural and others. RESULTS Of the 62 patients, 28 patients showed chromosomal aberration detected in one or more of the two test methods. Aneuploidy was detected in both methods, while gain and loss less than 3 Mb were only detectable by the microarray. G-banding karyotyping is fundamental to detect structural chromosome rearrangement such as inversions, ring chromosomes, and translocations, but additional breakpoint or unknown origin materials informa-tion obtained from microarray. Loss of heterozygosity was only detectable in microarray, and mosaicism had limitations in both G-banding karyotyping and microarray. CONCLUSIONS Various disease cause genomic structural variants, it is very important to detect this. We showed discordance between G-banding karyotyping and SNP based microarray in clinical laboratory. It can be helpful to clinical physicians to decide which diagnostic tool to use.
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Zhang J, Wang Y, Lu Y, You W, Luo X, Ke C. Comparative Cytogenetic Analysis of Diploid and Triploid Pacific Abalone, Haliotis discus hannai. Cytogenet Genome Res 2023; 163:327-333. [PMID: 37956660 DOI: 10.1159/000535045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION The Pacific abalone, Haliotis discus hannai, is one of the most commercially important marine shellfish in China. Cell engineering breeding is an important tool in abalone genetic breeding, and the triploids obtained through this method have high commercial value. However, current research mainly focuses on establishing induction methods and evaluating the growth traits of triploids, while there is a lack of basic research on triploid cytogenetics. METHOD In this study, Cytogenetic analysis of triploid Haliotis discus hannai larvae (produced by chemical treatment) and diploid larvae was performed. RESULT The results showed that triploid H. discus hannai had a chromosome number of 3n = 54, consisting of 30 metacentric (m) and 24 submetacentric (sm) chromosomes, while the diploids had a chromosome number of 2n = 36, consisting of 20 metacentric (m) and 16 submetacentric (sm) chromosomes. Notably, both triploids and diploids displayed variation in the number of NORs and/or their diameter. The average number of NORs in triploid was significantly higher than that in diploids (p < 0.05), but the average diameter of NORs of triploid was no significant different from that of diploid (p > 0.05). Additionally, 5S rDNA localization to 3 submetacentric chromosomes was observed in triploids, compared to 2 submetacentric chromosomes in diploids. The number of 18S rDNA sites displayed positional conservancy and quantitative variability in both diploids and triploids. Specifically, 18S rDNA was found at the end of the chromosome in both groups, with triploids exhibiting a significantly higher number of loci than diploids (p < 0.01). CONCLUSION This study provides valuable insights into the cytogenetic characteristics of triploid H. discus hannai, which could facilitate further research on the stability of the chromosome set in this species.
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Affiliation(s)
- Jianpeng Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China,
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China,
| | - Yi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Ying Lu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, China
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Rengifo LY, Smits S, Boeckx N, Michaux L, Vandenberghe P, Dewaele B. Shallow whole-genome sequencing of bone marrow aspirates in myelodysplastic neoplasms: A retrospective comparison with cytogenetics. Genes Chromosomes Cancer 2023; 62:663-671. [PMID: 37293982 DOI: 10.1002/gcc.23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Copy number alterations (CNA) are powerful prognostic markers in myelodysplastic neoplasms (MDS) and are routinely analyzed by conventional cytogenetic analysis (CCA) on bone marrow (BM). Although CCA is still the gold standard, it requires extensive hands-on time and highly trained staff for the analysis, making it a laborious technique. To reduce turn-around-time per case, shallow whole genome sequencing (sWGS) technologies offer new perspectives for the diagnostic work-up of this disorder. We compared sWGS with CCA for the detection of CNAs in 33 retrospective BM samples of patients with MDS. Using sWGS, CNAs were detected in all cases and additionally allowed the analysis of three cases for which CCA failed. The prognostic stratification (IPSS-R score) of 27 out of 30 patients was the same with both techniques. In the remaining cases, discrepancies were caused by the presence of balanced translocations escaping sWGS detection in two cases, a subclonal aberration reported with CCA that could not be confirmed by FISH or sWGS, and the presence of an isodicentric chromosome idic(17)(p11) missed by CCA. Since sWGS can almost entirely be automated, our findings indicate that sWGS is valuable in a routine setting validating it as a cost-efficient tool.
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Affiliation(s)
| | - Sanne Smits
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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9
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De Bie J, Quessada J, Tueur G, Lefebvre C, Luquet I, Toujani S, Cuccuini W, Lafage-Pochitaloff M, Michaux L. Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103431. [PMID: 38016418 DOI: 10.1016/j.retram.2023.103431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.
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Affiliation(s)
- Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Saloua Toujani
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes 35033, France
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium.
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10
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Tueur G, Quessada J, De Bie J, Cuccuini W, Toujani S, Lefebvre C, Luquet I, Michaux L, Lafage-Pochitaloff M. Cytogenetics in the management of B-cell acute lymphoblastic leukemia: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103434. [PMID: 38064905 DOI: 10.1016/j.retram.2023.103434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023]
Abstract
Cytogenetic analysis is mandatory at initial assessment of B-cell acute lymphoblastic leukemia (B-ALL) due to its diagnostic and prognostic value. Results from chromosome banding analysis and complementary FISH are taken into account in therapeutic protocols and further completed by other techniques (RT-PCR, SNP-array, MLPA, NGS, OGM). Indeed, new genomic entities have been identified by NGS, mostly RNA sequencing, such as Ph-like ALL that can benefit from targeted therapy. Here, we have attempted to establish cytogenetic guidelines by reviewing the most recent published data including the novel 5th World Health Organization and International Consensus Classifications. We also focused on newly described cytogenomic entities and indicate alternative diagnostic tools such as NGS technology, as its importance is vastly increasing in the diagnostic setting.
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Affiliation(s)
- Giulia Tueur
- Laboratoire d'hématologie, Hôpital Avicenne, AP-HP, Bobigny 93000, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France; CRCM, Inserm UMR1068, CNRS UMR7258, Aix Marseille Université U105, Institut Paoli Calmettes, Marseille 13009, France
| | - Jolien De Bie
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Wendy Cuccuini
- Laboratoire d'Hématologie, Unité de Cytogénétique, Hôpital Saint-Louis, AP-HP, Paris 75010, France
| | - Saloua Toujani
- Service de cytogénétique et biologie cellulaire, CHU de Rennes, Rennes 35033, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble 38000, France
| | - Isabelle Luquet
- Laboratoire d'Hématologie, CHU Toulouse (IUCT-O), Toulouse 31000, France
| | - Lucienne Michaux
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium; Katholieke Universiteit Leuven, Leuven 3000, Belgium
| | - Marina Lafage-Pochitaloff
- Laboratoire de Cytogénétique Hématologique, Département d'Hématologie, CHU Timone, APHM, Aix Marseille Université, Marseille 13005, France.
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11
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Gaillard JB, Chapiro E, Daudignon A, Nadal N, Penther D, Chauzeix J, Nguyen-Khac F, Veronese L, Lefebvre C. Cytogenetics in the management of mature T-cell and NK-cell neoplasms: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103428. [PMID: 38016421 DOI: 10.1016/j.retram.2023.103428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023]
Abstract
Mature T-cell and natural killer (NK)-cell neoplasms (MTNKNs) are a highly heterogeneous group of lymphomas that represent 10-15 % of lymphoid neoplasms and have usually an aggressive behavior. Diagnosis can be challenging due to their overlapping clinical, histological and immunophenotypic features. Genetic data are not a routine component of the diagnostic algorithm for most MTNKNs. Indeed, unlike B-cell lymphomas, the genomic landscape of MTNKNs is not fully understood. Only few characteristic rearrangements can be easily identified with conventional cytogenetic methods and are an integral part of the diagnostic criteria, for instance the t(14;14)/inv(14) or t(X;14) abnormality harbored by 95 % of patients with T-cell prolymphocytic leukemia, or the ALK gene translocation observed in some forms of anaplastic large cell lymphoma. However, advances in molecular and cytogenetic techniques have brought new insights into MTNKN pathogenesis. Several recurrent genetic alterations have been identified, such as chromosomal losses involving tumor suppressor genes (SETD2, CDKN2A, TP53) and gains involving oncogenes (MYC), activating mutations in signaling pathways (JAK-STAT, RAS), and epigenetic dysregulation, that have improved our understanding of these pathologies. This work provides an overview of the cytogenetics knowledge in MTNKNs in the context of the new World Health Organization classification and the International Consensus Classification of hematolymphoid tumors. It describes key genetic alterations and their clinical implications. It also proposes recommendations on cytogenetic methods for MTNKN diagnosis.
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Affiliation(s)
- Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France.
| | - Elise Chapiro
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS_1138, Drug Resistance in Hematological Malignancies Team, F-75006 Paris, France; Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Service d'Hématologie Biologique, F-75013 Paris, France
| | - Agnès Daudignon
- Institut de Génétique Médicale - Hôpital Jeanne de Flandre - CHRU de Lille, France
| | - Nathalie Nadal
- Service de génétique chromosomique et moléculaire, CHU Dijon, Dijon, France
| | - Dominique Penther
- Laboratoire de Génétique Oncologique, Centre Henri Becquerel, Rouen, France
| | - Jasmine Chauzeix
- Service d'Hématologie biologique CHU de Limoges - CRIBL, UMR CNRS 7276/INSERM 1262, Limoges, France
| | - Florence Nguyen-Khac
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS_1138, Drug Resistance in Hematological Malignancies Team, F-75006 Paris, France; Sorbonne Université, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Service d'Hématologie Biologique, F-75013 Paris, France
| | - Lauren Veronese
- Service de Cytogénétique Médicale, CHU Estaing, 1 place Lucie et Raymond Aubrac, 63003 Clermont-Ferrand; EA7453 CHELTER, Université Clermont Auvergne, France
| | - Christine Lefebvre
- Unité de Génétique des Hémopathies, Service d'Hématologie Biologique, CHU Grenoble Alpes, Grenoble, France
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12
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Livingston GK, Ryan TL, Escalona MB, Foster AE, Balajee AS. Retrospective Evaluation of Cytogenetic Effects Induced by Internal Radioiodine Exposure: A 27-Year Follow-Up Study. Cytogenet Genome Res 2023; 163:154-162. [PMID: 37573786 DOI: 10.1159/000533396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
Radioiodine (131I) is widely used in the treatment of hyperthyroidism and as an effective ablative therapy for differentiated thyroid cancer. Radioiodine (131I) constitutes 90% of the currently used therapies in the field of nuclear medicine. Here, we report the cytogenetic findings of a long-term follow-up study of 27 years on a male patient who received two rounds of radioiodine treatment within a span of 26 months between 1992 and 1994 for his papillary thyroid cancer. A comprehensive cytogenetic follow-up study utilizing cytokinesis blocked micronucleus assay, dicentric chromosome assay, genome wide translocations and inversions was initiated on this patient since the first administration of radioiodine in 1992. Frequencies of micronuclei (0.006/cell) and dicentric chromosomes (0.008/cell) detected in the current study were grossly similar to that reported earlier in 2019. The mFISH analysis detected chromosome aberrations in 8.6% of the cells in the form of both unbalanced and balanced translocations. Additionally, a clonal translocation involving chromosomes 14p; 15q was observed in 2 of the 500 cells analyzed. Out of the 500 cells examined, one cell showed a complex translocation (involving chromosomes 9, 10, and 16) besides 5 other chromosome rearrangements. Collectively, our study indicates that the past radioiodine exposure results in long-lasting chromosome damage and that the persistence of translocations can be useful for both retrospective biodosimetry and for monitoring chromosome instability in the lymphocytes of radioiodine exposed individuals.
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Affiliation(s)
- Gordon K Livingston
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Terri L Ryan
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Maria B Escalona
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Alvis E Foster
- Indiana University Health, Ball Memorial Hospital, Muncie, Indiana, USA
| | - Adayabalam S Balajee
- Cytogenetic Biodosimetry Laboratory, Radiation Emergency Assistance Center/Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
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13
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Sahajpal NS, Mondal AK, Fee T, Hilton B, Layman L, Hastie AR, Chaubey A, DuPont BR, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing. J Mol Diagn 2023; 25:234-246. [PMID: 36758723 DOI: 10.1016/j.jmoldx.2023.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.
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Affiliation(s)
- Nikhil S Sahajpal
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Timothy Fee
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Benjamin Hilton
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Lawrence Layman
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | | | - Barbara R DuPont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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14
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Sv S, Augustine D, Haragannavar VC, Khudhayr EA, Matari MH, Elagi WA, Gujjar N, Patil S. Cytogenetics in Oral Cancer: A Comprehensive Update. J Contemp Dent Pract 2022; 23:123-131. [PMID: 35656669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
AIM To evaluate the application of cytogenetic techniques in determining the diagnosis, prognosis, and therapeutics in oral cancer. BACKGROUND Genetic aberrations that play an important role in oral oncogenesis demand substantial research for in-depth characterization of the tumor. Cytogenetic techniques have the potential to detect these aberrations. This review highlights about various cytogenetic approaches in cancer and how these findings support its application in the field of oral oncology. METHODS Google scholar search was done for articles on cancer cytogenetics, and in particular, PubMed database was queried for articles published from 2015 to 2020 using keywords cytogenetics, chromosomal aberrations, conventional cytogenetics, karyotyping, banding techniques, molecular cytogenetics, fluorescent in situ hybridization, spectral karyotyping, comparative genomic hybridization, multiplex ligation probe analysis, and next-generation sequencing (NGS) in oral cancer. Abstracts were reviewed, and relevant full text was accessed to extract the cytogenetic findings in oral cancer. RESULTS Data regarding various cytogenetic approaches from conventional to molecular techniques have been published in oral cancer. They convey a highly complex cytogenetic finding from gross chromosomal aberrations to specific gene mutations in oral cancer. CONCLUSION Crucial information in the development and progression of oral cancer is achieved through cytogenetic findings in particular with the molecular cytogenetic techniques. Novel technologies like NGS have emerged in recent years that hold promise in the detection of these alterations more efficiently. CLINICAL SIGNIFICANCE An appraisal of cytogenetic analysis in oral cancer helps to determine the diagnosis and the most important prognosticators. It assists in building targeted therapies for patient benefit.
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Affiliation(s)
- Sowmya Sv
- Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Dominic Augustine
- Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Vanishri C Haragannavar
- Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | | | | | - Wahba A Elagi
- General Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Neethi Gujjar
- Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia, Phone: +966507633755, e-mail:
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15
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Mezzasalma M, Guarino FM, Odierna G. Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data? Genes (Basel) 2021; 12:1341. [PMID: 34573323 PMCID: PMC8468487 DOI: 10.3390/genes12091341] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/19/2023] Open
Abstract
Lizards represent unique model organisms in the study of sex determination and sex chromosome evolution. Among tetrapods, they are characterized by an unparalleled diversity of sex determination systems, including temperature-dependent sex determination (TSD) and genetic sex determination (GSD) under either male or female heterogamety. Sex chromosome systems are also extremely variable in lizards. They include simple (XY and ZW) and multiple (X1X2Y and Z1Z2W) sex chromosome systems and encompass all the different hypothesized stages of diversification of heterogametic chromosomes, from homomorphic to heteromorphic and completely heterochromatic sex chromosomes. The co-occurrence of TSD, GSD and different sex chromosome systems also characterizes different lizard taxa, which represent ideal models to study the emergence and the evolutionary drivers of sex reversal and sex chromosome turnover. In this review, we present a synthesis of general genome and karyotype features of non-snakes squamates and discuss the main theories and evidences on the evolution and diversification of their different sex determination and sex chromosome systems. We here provide a systematic assessment of the available data on lizard sex chromosome systems and an overview of the main cytogenetic and molecular methods used for their identification, using a qualitative and quantitative approach.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairaõ, Portugal
| | - Fabio M. Guarino
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, I-80126 Naples, Italy; (F.M.G.); (G.O.)
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16
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Kostmann A, Augstenová B, Frynta D, Kratochvíl L, Rovatsos M. Cytogenetically Elusive Sex Chromosomes in Scincoidean Lizards. Int J Mol Sci 2021; 22:ijms22168670. [PMID: 34445371 PMCID: PMC8395508 DOI: 10.3390/ijms22168670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 01/11/2023] Open
Abstract
The lizards of the species-rich clade Scincoidea including cordylids, gerrhosaurids, skinks, and xantusiids, show an almost cosmopolitan geographical distribution and a remarkable ecological and morphological divergence. However, previous studies revealed limited variability in cytogenetic traits. The sex determination mode was revealed only in a handful of gerrhosaurid, skink, and xantusiid species, which demonstrated either ZZ/ZW or XX/XY sex chromosomes. In this study, we explored the karyotypes of six species of skinks, two species of cordylids, and one gerrhosaurid. We applied conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization with probes specific for telomeric motifs and rDNA loci, and comparative genomic hybridization. The diploid chromosome numbers are rather conserved among these species, but the chromosome morphology, the presence of interstitial telomeric sequences, and the topology of rDNA loci vary significantly. Notably, XX/XY sex chromosomes were identified only in Tiliqua scincoides, where, in contrast to the X chromosome, the Y chromosome lacks accumulations of rDNA loci. We confirm that within the lizards of the scincoidean clade, sex chromosomes remained in a generally poor stage of differentiation.
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Affiliation(s)
- Alexander Kostmann
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (A.K.); (B.A.); (L.K.)
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (A.K.); (B.A.); (L.K.)
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (A.K.); (B.A.); (L.K.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (A.K.); (B.A.); (L.K.)
- Correspondence:
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17
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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18
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Mantere T, Neveling K, Pebrel-Richard C, Benoist M, van der Zande G, Kater-Baats E, Baatout I, van Beek R, Yammine T, Oorsprong M, Hsoumi F, Olde-Weghuis D, Majdali W, Vermeulen S, Pauper M, Lebbar A, Stevens-Kroef M, Sanlaville D, Dupont JM, Smeets D, Hoischen A, Schluth-Bolard C, El Khattabi L. Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet 2021; 108:1409-1422. [PMID: 34237280 PMCID: PMC8387289 DOI: 10.1016/j.ajhg.2021.05.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Céline Pebrel-Richard
- Department of Chromosomal and Molecular Genetics, University Hospital of Clermont-Ferrand, 63003 Clermont-Ferrand, France
| | - Marion Benoist
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Imane Baatout
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Tony Yammine
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Unit of Medical Genetics, Saint-Joseph University, 1107 2180 Beyrouth, Lebanon
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Faten Hsoumi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Daniel Olde-Weghuis
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Wed Majdali
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Aziza Lebbar
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Damien Sanlaville
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Jean Michel Dupont
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
| | - Caroline Schluth-Bolard
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Laïla El Khattabi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France.
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19
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Neveling K, Mantere T, Vermeulen S, Oorsprong M, van Beek R, Kater-Baats E, Pauper M, van der Zande G, Smeets D, Weghuis DO, Stevens-Kroef MJPL, Hoischen A. Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping. Am J Hum Genet 2021; 108:1423-1435. [PMID: 34237281 DOI: 10.1016/j.ajhg.2021.06.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Somatic structural variants (SVs) are important drivers of cancer development and progression. In a diagnostic set-up, especially for hematological malignancies, the comprehensive analysis of all SVs in a given sample still requires a combination of cytogenetic techniques, including karyotyping, FISH, and CNV microarrays. We hypothesize that the combination of these classical approaches could be replaced by optical genome mapping (OGM). Samples from 52 individuals with a clinical diagnosis of a hematological malignancy, divided into simple (<5 aberrations, n = 36) and complex (≥5 aberrations, n = 16) cases, were processed for OGM, reaching on average: 283-fold genome coverage. OGM called a total of 918 high-confidence SVs per sample, of which, on average, 13 were rare and >100 kb. In addition, on average, 73 CNVs were called per sample, of which six were >5 Mb. For the 36 simple cases, all clinically reported aberrations were detected, including deletions, insertions, inversions, aneuploidies, and translocations. For the 16 complex cases, results were largely concordant between standard-of-care and OGM, but OGM often revealed higher complexity than previously recognized. Detailed technical comparison with standard-of-care tests showed high analytical validity of OGM, resulting in a sensitivity of 100% and a positive predictive value of >80%. Importantly, OGM resulted in a more complete assessment than any previous single test and most likely reported the most accurate underlying genomic architecture (e.g., for complex translocations, chromoanagenesis, and marker chromosomes). In conclusion, the excellent concordance of OGM with diagnostic standard assays demonstrates its potential to replace classical cytogenetic tests as well as to rapidly map novel leukemia drivers.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Daniel Olde Weghuis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6532 GA Nijmegen, the Netherlands.
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20
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Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
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Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
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21
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Tian XL, Lu X, Cai TJ, Lyu YM, Tian M, Liu QJ. Cytogenetic monitoring of peripheral blood lymphocytes from medical radiation professionals occupationally exposed to low-dose ionizing radiation. Mutat Res 2021; 867:503370. [PMID: 34266630 DOI: 10.1016/j.mrgentox.2021.503370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/11/2023]
Abstract
In order to assess the health risk of low-dose radiation to radiation professionals, monitoring is performed through chromosomal aberration analysis and micronuclei (MN) analysis. MN formation has drawbacks for monitoring in the low-dose range. Nucleoplasmic bridge (NPB) analysis, with a lower background level, has good dose-response relationships at both high and relatively low dose ranges. Dicentric and ring chromosomes were analyzed in 199 medical radiation professionals, and NPB/MN yields were analyzed in 205 radiation professionals. The effects of sex, age of donor, types of work, and length of service on these cytogenetic endpoints were also analyzed. The yields of the three cytogenetic endpoints were significantly higher in radiation professionals versus controls. Frequencies of dicentric plus ring chromosomes were affected by length of service. NPB frequencies were influenced by type of work and length of service. MN yields were affected not only by types of work and length of service but also by donor sex and age. In conclusion, dicentric plus ring chromosomes, NPB, and MN can be induced by low-dose radiation in radiation professionals. NPB is a potential biomarker to assess the health risk of occupational low-dose radiation exposure.
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Affiliation(s)
- Xue-Lei Tian
- China CDC Key Laboratory of Radiation Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing, 100088, PR China
| | - Xue Lu
- China CDC Key Laboratory of Radiation Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing, 100088, PR China
| | - Tian-Jing Cai
- China CDC Key Laboratory of Radiation Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing, 100088, PR China
| | - Yu-Min Lyu
- Laboratory of Toxicology, Henan Institute of Occupational Medicine, Zheng Zhou, 450052, PR China
| | - Mei Tian
- China CDC Key Laboratory of Radiation Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing, 100088, PR China
| | - Qing-Jie Liu
- China CDC Key Laboratory of Radiation Protection and Nuclear Emergency, National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing, 100088, PR China.
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22
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Ai X, Li B, Xu Z, Liu J, Qin T, Li Q, Xiao Z. Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization for detecting chromosome abnormalities in myelodysplastic syndromes: A retrospective study. Medicine (Baltimore) 2021; 100:e25768. [PMID: 33950965 PMCID: PMC8104212 DOI: 10.1097/md.0000000000025768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/10/2021] [Indexed: 01/04/2023] Open
Abstract
This study aimed to compare interphase fluorescence in situ hybridization (iFISH) and multiplex ligation dependent probe amplification (MLPA) for identifying genetic changes in myelodysplastic syndromes (MDS).The frequencies of cytogenetic changes in MDS patients treated at the Institute of Hematology and Blood Disease Hospital (China) in 2009 to 2018 were assessed by iFISH based on bone marrow samples. Then, the effectiveness of MLPA in detecting these anomalies was evaluated.Specimens from 287 MDS patients were assessed. A total of 36.9% (103/279) of MDS cases had chromosomal abnormalities detected by iFISH; meanwhile, 44.1% (123/279) harbored ≥1 copy-number variation (CNV) based on MLPA: +8 (n=46), -5 (n = 39), -7 (n = 27), del 20 (n = 32) and del 17 (n = 17). Overall, 0 to 4 aberrations/case were detected by MLPA, suggesting the heterogeneous and complex nature of MDS cytogenetics. There were 29 cases detected by MLPA, which were undetected by FISH or showed low signals. Sixteen of these cases had their risk classification changed due to MLPA detection, including 9 reassigned to the high-risk IPSS-R group. These findings demonstrated that MLPA is highly efficient in assessing cytogenetic anomalies, with data remarkably corroborating FISH findings (overall consistency of 97.1%). The sensitivities of MLPA in detecting +8, -5, -7, del 20 and del 17 were 92.3%, 97.1%, 100%, 100%, and 90%, respectively, with specificities of 95.8%, 97.6%, 97.7%, 97.6%, and 97%, respectively.MLPA represents a reliable approach, with greater efficiency, accuracy, and speed than iFISH in identifying cytogenetic aberrations in MDS.
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Affiliation(s)
| | - Bing Li
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zefeng Xu
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jinqin Liu
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Tiejun Qin
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | | | - Zhijian Xiao
- Department of Pathology
- MDS and MPN Centre, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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23
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Nakata K, Nagashima H, Inaba N, Yamashita H, Shinozaki Y, Kanekatsu M, Marubashi W, Yamada T. Analysis of the possible cytogenetic mechanism for overcoming hybrid lethality in an interspecific cross between Nicotiana suaveolens and Nicotiana tabacum. Sci Rep 2021; 11:7812. [PMID: 33837225 PMCID: PMC8035154 DOI: 10.1038/s41598-021-87242-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022] Open
Abstract
Hybrid lethality is a type of reproductive isolation in which hybrids die before maturation, due to the interaction between the two causative genes derived from each of the hybrid parents. The interspecific hybrid of Nicotiana suaveolens × Nicotiana tabacum is a model plant used in studies on hybrid lethality. While most of the progeny produced from such a cross die, some individuals grow normally and mature. Separately, a technique for producing mature hybrids by artificial culture has been developed. However, the mechanism by which hybrids overcome lethality, either spontaneously or by artificial culture, remains unclear. In the present study, we found that some hybrids that overcome lethality, either spontaneously or by artificial culture, lack the distal part of the Q chromosome, a region that includes the gene responsible for lethality. Quantitative polymerase chain reaction results suggested that the distal deletion of the Q chromosome, detected in some hybrid seedlings that overcome lethality, is caused by reciprocal translocations between homoeologous chromosomes. The results showed that chromosomal instability during meiosis in amphidiploid N. tabacum as well as during artificial culturing of hybrid seedlings is involved in overcoming hybrid lethality in interspecific crosses of the genus Nicotiana.
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Affiliation(s)
- Kouki Nakata
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
| | - Hiroki Nagashima
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
| | - Natsuki Inaba
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
| | - Haruka Yamashita
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
- Division of Evolutionary Genetics, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Yoshihito Shinozaki
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
| | - Motoki Kanekatsu
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan
| | - Wataru Marubashi
- Faculty of Agricultural Science, Meiji University, Kanagawa, Japan
| | - Tetsuya Yamada
- Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, 183-0054, Japan.
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Hochstenbach R, Liehr T, Hastings RJ. Chromosomes in the genomic age. Preserving cytogenomic competence of diagnostic genome laboratories. Eur J Hum Genet 2021; 29:541-552. [PMID: 33311710 PMCID: PMC8115145 DOI: 10.1038/s41431-020-00780-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
Participation of clinical genetic laboratories in External Quality Assessment schemes (EQAs) is a powerful method to ascertain if any improvement or additional training is required in the diagnostic service. Here, we provide evidence from recent EQAs that the competence in recognizing and interpreting cytogenetic aberrations is variable and could impact patient management. We identify several trends that could affect cytogenomic competence. Firstly, as a result of the age distribution among clinical laboratory geneticists (CLGs) registered at the European Board of Medical Genetics, about 25-30% of those with experience in cytogenetics will retire during the next decade. At the same time, there are about twice as many molecular geneticists to cytogeneticists among the younger CLGs. Secondly, when surveying training programs for CLG, we observed that not all programs guarantee that candidates gather sufficient experience in clinical cytogenomics. Thirdly, we acknowledge that whole genome sequencing (WGS) has a great attraction to biomedical scientists that wish to enter a training program for CLG. This, with a larger number of positions available, makes a choice for specialization in molecular genetics logical. However, current WGS technology cannot provide a diagnosis in all cases. Understanding the etiology of chromosomal rearrangements is essential for appropriate follow-up and for ascertaining recurrence risks. We define the minimal knowledge a CLG should have about cytogenomics in a world dominated by WGS, and discuss how laboratory directors and boards of professional organizations in clinical genetics can uphold cytogenomic competence by providing adequate CLG training programs and attracting sufficient numbers of trainees.
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Affiliation(s)
- Ron Hochstenbach
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Clinical Genetics, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands.
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Rosalind J Hastings
- GenQA, Level 1, The Women's Centre, John Radcliffe Hospital, Oxford University Hospitals Foundation Trust, Headley Way, Headington, Oxford, OX3 9DU, UK
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Iannucci A, Makunin AI, Lisachov AP, Ciofi C, Stanyon R, Svartman M, Trifonov VA. Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq). Genes (Basel) 2021; 12:124. [PMID: 33478118 PMCID: PMC7835784 DOI: 10.3390/genes12010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/10/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023] Open
Abstract
The study of vertebrate genome evolution is currently facing a revolution, brought about by next generation sequencing technologies that allow researchers to produce nearly complete and error-free genome assemblies. Novel approaches however do not always provide a direct link with information on vertebrate genome evolution gained from cytogenetic approaches. It is useful to preserve and link cytogenetic data with novel genomic discoveries. Sequencing of DNA from single isolated chromosomes (ChromSeq) is an elegant approach to determine the chromosome content and assign genome assemblies to chromosomes, thus bridging the gap between cytogenetics and genomics. The aim of this paper is to describe how ChromSeq can support the study of vertebrate genome evolution and how it can help link cytogenetic and genomic data. We show key examples of ChromSeq application in the refinement of vertebrate genome assemblies and in the study of vertebrate chromosome and karyotype evolution. We also provide a general overview of the approach and a concrete example of genome refinement using this method in the species Anolis carolinensis.
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Affiliation(s)
- Alessio Iannucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Alexey I. Makunin
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK;
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia;
| | - Artem P. Lisachov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, 625003 Tyumen, Russia;
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Claudio Ciofi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Roscoe Stanyon
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy; (C.C.); (R.S.)
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
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Magatha LS, Scott JX, Subramaniam G, Chandrasekaran T, Paul SFD, Koshy T. Cytogenetic and Fluorescence in situ Hybridization Profile of Pediatric Acute Lymphoblastic Leukemia in a University Hospital in South India. Med Princ Pract 2021; 30:563-570. [PMID: 34348305 PMCID: PMC8739856 DOI: 10.1159/000518280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/04/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The purpose of this study was to evaluate the cytogenetic and fluorescent in situ hybridization (FISH) profile in children with acute lymphoblastic leukemia (ALL), referred to a university hospital in a 5-year 6-month period. SUBJECTS AND METHODS Cytogenetic analysis of the bone marrow aspirate specimens of 91 patients was performed by standard Giemsa (G)-banding and interphase FISH (iFISH). RESULTS The frequency of chromosomal abnormalities detected by G-banding was 29.5%, and the frequency of nonrandom abnormalities with independent prognostic significance identified by iFISH was 46.4%. The abnormality with the highest frequency was gain of RUNX1 (n = 18, 21.4%), followed by ETV6/RUNX1 fusion (n = 7, 8.3%), and gain of KMT2A (n = 6, 7.1%). Additionally, rarely reported gains of ETV6, PBX1, and ABL1 were observed at a frequency of 6% (n = 5), and the deletion of ETV6 and TCF3 was seen at a frequency of 3.6% (n = 3) and 2.3% (n = 2), respectively. A 10-year old with intrachromosomal amplification of chromosome 21 was also observed. CONCLUSIONS This study strengthens and widens the current knowledge of the cytogenetic landscape of pediatric ALL.
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Affiliation(s)
- Latha Sneha Magatha
- Division of Pediatric Hemato-oncology, Department of Pediatrics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Julius Xavier Scott
- Division of Pediatric Hemato-oncology, Department of Pediatrics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Gayathri Subramaniam
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Thirugnanasambandan Chandrasekaran
- Division of Pediatric Hemato-oncology, Department of Pediatrics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | | | - Teena Koshy
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
- *Teena Koshy,
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Fu Q, Xie S, Chen J, Huang H. Modified Culture System and Combination of FICTION Could Increase the Detection Rate of Abnormalities in Multiple Myeloma. Ann Clin Lab Sci 2021; 51:61-72. [PMID: 33653782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
OBJECTIVE Conventional karyotyping of multiple myeloma (MM) is hampered by the low mitotic index of plasma cells (PCs), and low proportion of PCs in some specimens may lead to false negative results in fluorescence in situ hybridisation (FISH) detection. METHODS Bone marrow cells were cultured in an ordinary medium for 24 h or in a medium containing 10 ng/mL IL-6 and 40 ng/mL GM-CSF for 6 d. Fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms (FICTION) was also conducted, combining CD138 fluorescent immunophenotype and FISH. RESULTS Under modified culture conditions, the successful rate of culture and abnormality detection rate during karyotype analysis increased to 86.4% and 40.9%, respectively. The abnormality detection rate of FICTION (89.5%) was significantly higher than that of FISH (60.0%). The genetic abnormality detection rate increased to 92.3% when FICTION and karyotyping were conducted under modified culture conditions. CONCLUSION The established modified culture system could improve karyotyping quality in MM. Due to its obvious advantages compared with FISH, FICTION is recommended for detecting genetic abnormalities in MM.
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Affiliation(s)
- Qiang Fu
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shanzhen Xie
- Central Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jiadi Chen
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Huifang Huang
- Central Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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Siljak-Yakovlev S, Pustahija F, Vičić-Bočkor V, Robin O. Molecular Cytogenetics (Fluorescence In Situ Hybridization - FISH and Fluorochrome Banding): Resolving Species Relationships and Genome Organization. Methods Mol Biol 2021; 2222:363-379. [PMID: 33301102 DOI: 10.1007/978-1-0716-0997-2_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorochrome banding (chromomycin, Hoechst, and DAPI) and fluorescence in situ hybridization (FISH) are excellent molecular cytogenetic tools providing various possibilities in the study of chromosomal evolution and genome organization. The constitutive heterochromatin and rRNA genes are the most widely used FISH markers. The rDNA is organized into two distinct gene families (18S-5.8S-26S and 5S) whose number and location vary within the complex of closely related species. Therefore, they are widely used as chromosomal landmarks to provide valuable evidence concerning genome evolution at chromosomal levels.
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Affiliation(s)
- Sonja Siljak-Yakovlev
- University Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France.
| | - Fatima Pustahija
- Faculty of Forestry, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Vedrana Vičić-Bočkor
- Faculty of Science, Department of Molecular Biology, University of Zagreb, Zagreb, Croatia
| | - Odile Robin
- University Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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Abstract
Visualization of meiotic chromatin from pollen mother cells has become an essential technique to study meiosis in the model plant Arabidopsis thaliana. Here we present an advanced cytogenetic method that combines improved immunocytology with chromosome painting, thereby generating a tool to quantitatively analyze localization of proteins to any given genomic region. Proteins involved in different processes such as DNA double-strand break formation and recombinational repair can be visualized on meiotic chromatin with the additional feature of assessing their abundance at specific chromosomal locations.
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Affiliation(s)
- Jason Sims
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota St. Paul, St. Paul, MN, USA
| | - Peter Schlögelhofer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Marie-Therese Kurzbauer
- Max Perutz Labs, Department of Chromosome Biology, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria.
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30
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M'kacher R, Colicchio B, Marquet V, Borie C, Najar W, Hempel WM, Heidingsfelder L, Oudrhiri N, Al Jawhari M, Wilhelm-Murer N, Miguet M, Dieterlen A, Deschênes G, Tabet AC, Junker S, Grynberg M, Fenech M, Bennaceur-Griscelli A, Voisin P, Carde P, Jeandidier E, Yardin C. Telomere aberrations, including telomere loss, doublets, and extreme shortening, are increased in patients with infertility. Fertil Steril 2020; 115:164-173. [PMID: 33272625 DOI: 10.1016/j.fertnstert.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To test the hypothesis that telomere shortening and/or loss are risk factors for infertility. DESIGN Retrospective analysis of the telomere status in patients with infertility using conventional cytogenetic data collected prospectively. SETTING Academic centers. PATIENT(S) Cytogenetic slides with cultured peripheral lymphocytes from 50 patients undergoing fertility treatment and 150 healthy donors, including 100 donors matched for age. INTERVENTION(S) Cytogenetic slides were used to detect chromosomal and telomere aberrations. MAIN OUTCOME MEASURE(S) Telomere length and telomere aberrations were analyzed after telomere and centromere staining. RESULT(S) The mean telomere length of patients consulting for infertility was significantly less than that of healthy donors of similar age. Moreover, patients with infertility showed significantly more extreme telomere loss and telomere doublet formation than healthy controls. Telomere shortening and/or telomere aberrations were more pronounced in patients with structural chromosomal aberrations. Dicentric chromosomes were identified in 6/13 patients, with constitutional chromosomal aberrations leading to chromosomal instability that correlated with chromosomal end-to-end fusions. CONCLUSION(S) Our findings demonstrate the feasibility of analyzing telomere aberrations in addition to chromosomal aberrations, using cytogenetic slides. Telomere attrition and/or dysfunction represent the main common cytogenetic characteristic of patients with infertility, leading to potential implications for fertility assessment. Pending further studies, these techniques that correlate the outcome of assisted reproduction and telomere integrity status may represent a novel and useful diagnostic and/or prognostic tool for medical care in this field.
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Affiliation(s)
- Radhia M'kacher
- Cell Environment, DNA Damage Research & Development, Paris, France.
| | - Bruno Colicchio
- Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, Mulhouse, France
| | - Valentine Marquet
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l'Enfant, Centre hospitalo-universitaire Dupuytren, Limoges, France
| | - Claire Borie
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | - Wala Najar
- Cell Environment, DNA Damage Research & Development, Paris, France; Faculté de médecine Paris Centre, Université de Paris, Paris, France
| | - William M Hempel
- Cell Environment, DNA Damage Research & Development, Paris, France
| | | | - Noufissa Oudrhiri
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | | | - Nadège Wilhelm-Murer
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Marguerite Miguet
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Alain Dieterlen
- Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, Mulhouse, France
| | | | | | - Steffen Junker
- Institute of Biomedicine, University of Aarhus, Aarhus, Denmark
| | - Michael Grynberg
- Department of Reproductive Medicine and Fertility Preservation, Hôpital Antoine Béclère, Clamart, France
| | - Michael Fenech
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia; Genome Health Foundation, North Brighton, South Australia, Australia
| | - Annelise Bennaceur-Griscelli
- Assitance Pubique-Hopitaux de Paris (APHP)-Service d'hématologie-Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/INSERM 935, Villejuif, France
| | - Philippe Voisin
- Cell Environment, DNA Damage Research & Development, Paris, France
| | - Patrice Carde
- Department of Hematology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Eric Jeandidier
- Service de génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace, Mulhouse, France
| | - Catherine Yardin
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l'Enfant, Centre hospitalo-universitaire Dupuytren, Limoges, France; CNRS, XLIM, UMR 7252, University of Limoges, Limoges, France
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Ankathil R, Ismail SM, Mohd Yunus N, Sulong S, Husin A, Abdullah AD, Hassan R. Clinical implications of conventional cytogenetics, fluorescence in situ hybridization (FISH) and molecular testing in chronic myeloid leukaemia patients in the tyrosine kinase inhibitor era - A review. Malays J Pathol 2020; 42:307-321. [PMID: 33361712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chronic myeloid leukaemia (CML) provides an illustrative disease model for both molecular pathogenesis of cancer and rational drug therapy. Imatinib mesylate (IM), a BCR-ABL1 targeted tyrosine kinase inhibitor (TKI) drug, is the first line gold standard drug for CML treatment. Conventional cytogenetic analysis (CCA) can identify the standard and variant Philadelphia (Ph) chromosome, and any additional complex chromosome abnormalities at diagnosis as well as during treatment course. Fluorescence in situ hybridization (FISH) is especially important for cells of CML patients with inadequate or inferior quality metaphases or those with variant Ph translocations. CCA in conjunction with FISH can serve as powerful tools in all phases of CML including the diagnosis, prognosis, risk stratification and monitoring of cytogenetic responses to treatment. Molecular techniques such as reverse transcriptase-polymerase chain reaction (RT-PCR) is used for the detection of BCR-ABL1 transcripts at diagnosis whereas quantitative reverse transcriptase-polymerase chain reaction (qRTPCR) is used at the time of diagnosis as well as during TKI therapy for the quantitation of BCR-ABL1 transcripts to evaluate the molecular response and minimal residual disease (MRD). Despite the excellent treatment results obtained after the introduction of TKI drugs, especially Imatinib mesylate (IM), resistance to TKIs develops in approximately 35% - 40% of CML patients on TKI therapy. Since point mutations in BCR-ABL1 are a common cause of IM resistance, mutation analysis is important in IM resistant patients. Mutations are reliably detected by nested PCR amplification of the translocated ABL1 kinase domain followed by direct sequencing of the entire amplified kinase domain. The objective of this review is to highlight the importance of regular and timely CCA, FISH analysis and molecular testing in the diagnosis, prognosis, assessment of therapeutic efficacy, evaluation of MRD and in the detection of BCR-ABL1 kinase mutations which cause therapeutic resistance in adult CML patients.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Cytogenetic Analysis/methods
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/genetics
- Humans
- Imatinib Mesylate/therapeutic use
- In Situ Hybridization, Fluorescence
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Molecular Targeted Therapy/methods
- Mutation
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Reverse Transcriptase Polymerase Chain Reaction/methods
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Affiliation(s)
- R Ankathil
- Human Genome Centre, School of Medical Sciences, Health campus, Universiti Sains Malaysia, 16150 Kubang kerian, Kelantan, Malaysia.
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Coluccia E, Deidda F, Lobina C, Melis R, Porcu C, Agus B, Salvadori S. Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation. Genes (Basel) 2020; 11:genes11111319. [PMID: 33172170 PMCID: PMC7694744 DOI: 10.3390/genes11111319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022] Open
Abstract
The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using species-specific 5S rDNA probes; in addition, two-colour FISH was performed to investigate the possible association with the 45S ribosomal gene family. Multiple 5S rDNA clusters, located either in species-specific or in possibly homoeologous chromosomes, were found. Either a syntenic or different chromosomal location of the two ribosomal genes was detected. Our results revealed variability in the number and location of 5S rDNA clusters and confirmed a substantial conservation of the number and location of the 45S rDNA.
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Lindquist A, Hui L, Poulton A, Kluckow E, Hutchinson B, Pertile MD, Bonacquisto L, Gugasyan L, Kulkarni A, Harraway J, Howden A, McCoy R, Da Silva Costa F, Menezes M, Palma-Dias R, Nisbet D, Martin N, Bethune M, Poulakis Z, Halliday J. State-wide utilization and performance of traditional and cell-free DNA-based prenatal testing pathways: the Victorian Perinatal Record Linkage (PeRL) study. Ultrasound Obstet Gynecol 2020; 56:215-224. [PMID: 31625225 DOI: 10.1002/uog.21899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/02/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVES To perform individual record linkage of women undergoing screening with cell-free DNA (cfDNA), combined first-trimester screening (CFTS), second-trimester serum screening (STSS), and/or prenatal and postnatal cytogenetic testing with the aim to (1) obtain population-based estimates of utilization of prenatal screening and invasive diagnosis, (2) analyze the performance of different prenatal screening strategies, and (3) report the residual risk of any major chromosomal abnormality following a low-risk aneuploidy screening result. METHODS This was a retrospective study of women residing in the state of Victoria, Australia, who underwent prenatal screening or invasive prenatal diagnosis in 2015. Patient-funded cfDNA referrals from multiple providers were merged with state-wide results for government-subsidized CFTS, STSS and invasive diagnostic procedures. Postnatal cytogenetic results from products of conception and infants up to 12 months of age were obtained to ascertain cases of false-negative screening results and atypical chromosomal abnormalities. Individual record linkage was performed using LinkageWizTM . RESULTS During the study period, there were 79 140 births and 66 166 (83.6%) women underwent at least one form of aneuploidy screening. Linkage data were complete for 93.5% (n = 61 877) of women who underwent screening, and of these, 73.2% (n = 45 275) had CFTS alone, 20.2% (n = 12 486) had cfDNA alone; 5.3% (n = 3268) had STSS alone, 1.3% (n = 813) had both CFTS and cfDNA, and < 0.1% (n = 35) had both STSS and cfDNA. CFTS had a combined sensitivity for trisomies 21 (T21), 18 (T18) and 13 (T13) of 89.57% (95% CI, 82.64-93.93%) for a screen-positive rate (SPR) of 2.94%. There were 12 false-negative results in the CFTS pathway, comprising 10 cases of T21, one of T18 and one of T13. cfDNA had a combined sensitivity for T21, T18 and T13 of 100% (95% CI, 95.00-100%) for a SPR of 1.21%. When high-risk cfDNA results for any chromosome (including the sex chromosomes) and failed cfDNA tests were treated as screen positives, the SPR for cfDNA increased to 2.42%. The risk of any major chromosomal abnormality (including atypical abnormalities) detected on prenatal or postnatal diagnostic testing after a low-risk screening result was 1 in 1188 for CFTS (n = 37) and 1 in 762 for cfDNA (n = 16) (P = 0.13). The range of chromosomal abnormalities detected after a low-risk cfDNA result included pathogenic copy-number variants (n = 6), triploidy (n = 3), rare autosomal trisomies (n = 3) and monosomy X (n = 2). CONCLUSIONS Our state-wide record-linkage analysis delineated the utilization and clinical performance of the multitude of prenatal screening pathways available to pregnant women. The sensitivity of cfDNA for T21, T18 and T13 was clearly superior to that of CFTS. While there was no statistically significant difference in the residual risk of any major chromosomal abnormality after a low-risk CFTS or cfDNA result, there were fewer live infants diagnosed with a major chromosomal abnormality in the cfDNA cohort. These data provide valuable population-based evidence to inform practice recommendations and health policies. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- A Lindquist
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Obstetrics, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
| | - L Hui
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Obstetrics, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- The Northern Hospital, Epping, Victoria, Australia
| | - A Poulton
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - E Kluckow
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - B Hutchinson
- Department of Obstetrics, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - M D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - L Bonacquisto
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - L Gugasyan
- Cytogenetics, Monash Pathology, Monash Medical Centre, Clayton, Victoria, Australia
| | - A Kulkarni
- Cytogenetics, Monash Pathology, Monash Medical Centre, Clayton, Victoria, Australia
| | - J Harraway
- Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia
| | - A Howden
- Department of Cytogenetics, Melbourne Pathology, Collingwood, Victoria, Australia
| | - R McCoy
- Molecular Genetics, Australian Clinical Labs, Clayton, Victoria, Australia
| | - F Da Silva Costa
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia
| | - M Menezes
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Monash Ultrasound for Women, Richmond, Victoria, Australia
| | - R Palma-Dias
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Women's Ultrasound Melbourne, East Melbourne, Victoria, Australia
- Ultrasound Services, Royal Women's Hospital, Parkville, Victoria, Australia
| | - D Nisbet
- Women's Ultrasound Melbourne, East Melbourne, Victoria, Australia
- Ultrasound Services, Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Medicine and Radiology, University of Melbourne, Parkville, Victoria, Australia
| | - N Martin
- Virtus Diagnostics and Pathology Services, Spring Hill, Queensland, Australia
| | - M Bethune
- Specialist Women's Ultrasound, Box Hill, Victoria, Australia
- Department of Radiology, University of Melbourne, Parkville, Victoria, Australia
| | - Z Poulakis
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Victorian Infant Hearing Screening Program, Centre for Community Child Health, Royal Children's Hospital, Parkville, Victoria, Australia
- Prevention Innovation Group, Population Health, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - J Halliday
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
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34
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Al-Eitan LN, Omari IO, Alkhatib RQ, Aljamal HA. The investigation of the in vivo cytogenetic effects of psychotropic drugs in human lymphocyte cultures. Pak J Pharm Sci 2020; 33:1503-1510. [PMID: 33583780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The connection of nearly all current antipsychotic drugs to their in vivo cytogenetic activity has not been yet fully investigated. Fluvoxamine, Valproic acid (VA) and Haloperidol (HLP) are three universally common consumed psychotic drugs whereas used to treat several psychiatric disorders. This study aims to investigate the cytogenetic effects of these three psychotropic drugs by evaluating the frequency of Sister Chromatid Exchanges (SCEs) and the Proliferation Rate Index (PRI) in cultured lymphocytes. Fifteen patients with psychiatric disorders (i.e. depression, bipolar and schizophrenia) consisting of smokers and non-smokers were included. Estimation of SCEs was used as a sensitive biomarker of the potential cytotoxicity, while PRI was used as a valuable marker of cytostatic activity. A significant increase of SCEs in the cultured lymphocyte of the smoker controls (P= 0.013) was found in compared to the non-smoker controls. This study found that there is no difference in the average of SCEs values in lymphocytes isolated from the smoker and non-smoker patients treated with Fluvoxamine, Valproic acid and Haloperidol (P> 0.05). A significant difference of PRI (P= 0.036) in the lymphocytes of smoker controls compared to those of the non-smoker controls were detected. This study also found a significant difference with respect to PRI between the three patient groups (P= 0.017). These results illustrated that treatment (monotherapy) of psychiatric patients with Fluvoxamine, Valproic acid, and Haloperidol exerts a significant cytostatic but not cytotoxic effect on their lymphocytes whereas these effects are intensified by smoking.
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Affiliation(s)
- Laith Naser Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan/Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Israa Othman Omari
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Rami Qassim Alkhatib
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan/Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Hanan Abdulraheem Aljamal
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan
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35
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Azawi S, Liehr T, Rincic M, Manferrari M. Molecular Cytogenomic Characterization of the Murine Breast Cancer Cell Lines C-127I, EMT6/P and TA3 Hauschka. Int J Mol Sci 2020; 21:ijms21134716. [PMID: 32630352 PMCID: PMC7369978 DOI: 10.3390/ijms21134716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND To test and introduce effective and less toxic breast cancer (BC) treatment strategies, animal models, including murine BC cell lines, are considered as perfect platforms. Strikingly, the knowledge on the genetic background of applied BC cell lines is often sparse though urgently necessary for their targeted and really justified application. METHODS In this study, we performed the first molecular cytogenetic characterization for three murine BC cell lines C-127I, EMT6/P and TA3 Hauschka. Besides fluorescence in situ hybridization-banding, array comparative genomic hybridization was also applied. Thus, overall, an in silico translation for the detected imbalances and chromosomal break events in the murine cell lines to the corresponding homologous imbalances in humans could be provided. The latter enabled a comparison of the murine cell line with human BC cytogenomics. RESULTS All three BC cell lines showed a rearranged karyotype at different stages of complexity, which can be interpreted carefully as reflectance of more or less advanced tumor stages. CONCLUSIONS Accordingly, the C-127I cell line would represent the late stage BC while the cell lines EMT6/P and TA3 Hauschka would be models for the premalignant or early BC stage and an early or benign BC, respectively. With this cytogenomic information provided, these cell lines now can be applied really adequately in future research studies.
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Affiliation(s)
- Shaymaa Azawi
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747 Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747 Jena, Germany
| | - Martina Rincic
- Croatian Institute for Brain Research, School of Medicine University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Mattia Manferrari
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747 Jena, Germany
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36
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Horne GA, Stobo J, Kelly C, Mukhopadhyay A, Latif AL, Dixon-Hughes J, McMahon L, Cony-Makhoul P, Byrne J, Smith G, Koschmieder S, BrÜmmendorf TH, Schafhausen P, Gallipoli P, Thomson F, Cong W, Clark RE, Milojkovic D, Helgason GV, Foroni L, Nicolini FE, Holyoake TL, Copland M. A randomised phase II trial of hydroxychloroquine and imatinib versus imatinib alone for patients with chronic myeloid leukaemia in major cytogenetic response with residual disease. Leukemia 2020; 34:1775-1786. [PMID: 31925317 PMCID: PMC7224085 DOI: 10.1038/s41375-019-0700-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022]
Abstract
In chronic-phase chronic myeloid leukaemia (CP-CML), residual BCR-ABL1+ leukaemia stem cells are responsible for disease persistence despite TKI. Based on in vitro data, CHOICES (CHlorOquine and Imatinib Combination to Eliminate Stem cells) was an international, randomised phase II trial designed to study the safety and efficacy of imatinib (IM) and hydroxychloroquine (HCQ) compared with IM alone in CP-CML patients in major cytogenetic remission with residual disease detectable by qPCR. Sixty-two patients were randomly assigned to either arm. Treatment 'successes' was the primary end point, defined as ≥0.5 log reduction in 12-month qPCR level from trial entry. Selected secondary study end points were 24-month treatment 'successes', molecular response and progression at 12 and 24 months, comparison of IM levels, and achievement of blood HCQ levels >2000 ng/ml. At 12 months, there was no difference in 'success' rate (p = 0.58); MMR was achieved in 80% (IM) vs 92% (IM/HCQ) (p = 0.21). At 24 months, the 'success' rate was 20.8% higher with IM/HCQ (p = 0.059). No patients progressed. Seventeen serious adverse events, including four serious adverse reactions, were reported; diarrhoea occurred more frequently with combination. IM/HCQ is tolerable in CP-CML, with modest improvement in qPCR levels at 12 and 24 months, suggesting autophagy inhibition maybe of clinical value in CP-CML.
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MESH Headings
- Aged
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Cytogenetic Analysis/methods
- Female
- Follow-Up Studies
- Fusion Proteins, bcr-abl/genetics
- Humans
- Hydroxychloroquine/administration & dosage
- Imatinib Mesylate/administration & dosage
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Male
- Middle Aged
- Prognosis
- Retrospective Studies
- Survival Rate
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Affiliation(s)
- G A Horne
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - J Stobo
- Cancer Research UK Clinical Trials Unit, University of Glasgow, Glasgow, UK
| | - C Kelly
- Cancer Research UK Clinical Trials Unit, University of Glasgow, Glasgow, UK
| | - A Mukhopadhyay
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - A L Latif
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - J Dixon-Hughes
- Cancer Research UK Clinical Trials Unit, University of Glasgow, Glasgow, UK
| | - L McMahon
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - P Cony-Makhoul
- Haematology department, CH Annecy-Genevois, Pringy, France
| | - J Byrne
- Department of Haematology, Nottingham City Hospital, Nottingham, UK
| | - G Smith
- Department of Haematology, St James's University Hospital, Leeds, UK
| | - S Koschmieder
- Department of Medicine (Hematology Oncology, Hemostaseology, and Stem Cell Transplantation), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - T H BrÜmmendorf
- Department of Medicine (Hematology Oncology, Hemostaseology, and Stem Cell Transplantation), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - P Schafhausen
- Department of Internal Medicine, University Medical Center Hamburg, Hamburg, Germany
| | - P Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - F Thomson
- Experimental therapeutics, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - W Cong
- Experimental therapeutics, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - R E Clark
- Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - D Milojkovic
- Department of Haematology, Hammersmith Hospital, London, UK
| | - G V Helgason
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - L Foroni
- Department of Haematology, Imperial College London, London, UK
| | - F E Nicolini
- Hématologie Clinique and INSERM U1052, CRCL, Centre Léon Bérard, Lyon, France
| | - T L Holyoake
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - M Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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Wu M, Leung J, Liu L, Kam C, Chan KYK, Li RA, Feng S, Chen S. A Small-Molecule AIE Chromosome Periphery Probe for Cytogenetic Studies. Angew Chem Int Ed Engl 2020; 59:10327-10331. [PMID: 32163217 PMCID: PMC7318220 DOI: 10.1002/anie.201916718] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Indexed: 01/12/2023]
Abstract
The chromosome periphery (CP) is a complex network that covers the outer surface of chromosomes. It acts as a carrier of nucleolar components, helps maintain chromosome structure, and plays an important role in mitosis. Current methods for fluorescence imaging of CP largely rely on immunostaining. We herein report a small-molecule fluorescent probe, ID-IQ, which possesses aggregation-induced emission (AIE) property, for CP imaging. By labelling the CP, ID-IQ sharply highlighted the chromosome boundaries, which enabled rapid segmentation of touching and overlapping chromosomes, direct identification of the centromere, and clear visualization of chromosome morphology. ID-IQ staining was also compatible with fluorescence in situ hybridization and could assist the precise location of the gene in designated chromosome. Altogether, this study provides a versatile cytogenetic tool for improved chromosome analysis, which greatly benefits the clinical diagnostic testing and genomic research.
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Affiliation(s)
- Ming‐Yu Wu
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Jong‐Kai Leung
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Li Liu
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Chuen Kam
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
| | - Kelvin Yuen Kwong Chan
- Department of Obstetrics and GynaecologyQueen Mary HospitalHong KongChina
- Prenatal Diagnostic LaboratoryTsan Yuk HospitalHong KongChina
| | - Ronald A. Li
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- Dr. Li Dak-Sum Research CentreThe University of Hong KongHong KongChina
| | - Shun Feng
- School of Life Science and EngineeringSouthwest Jiaotong UniversityChengduSichuan610031China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative MedicineKarolinska InstitutetHong KongChina
- Dr. Li Dak-Sum Research CentreThe University of Hong KongHong KongChina
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Zhang H, Li G, Chang J, Wang H. Myelodysplastic Syndrome with t(1;14),t(1;17),t(1;19) Transforms to AML-M5: A Case Report and Literature Review. Ann Clin Lab Sci 2020; 50:401-403. [PMID: 32581034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chromosomal aberrations play an important role in the incidence of myelodysplastic syndromes (MDS) and development to acute myeloid leukemia (AML). We report a case of a 62-year-old male patient diagnosed with MDS with excess blasts. The karyotype was 45, XY,+1,+1,-7,-10,-22,t(1;14) (q21;q32),t(1;17)(q21;p13),t(1;19)(q21;p13). The patient and his family refused treatment for financial reasons. After 2 months, the patient's MDS transformed into acute myeloid monocytic leukemia (AML-M5). This case of MDS with poor prognosis shows that patients with chromosomal numerical abnormality and balanced translocations should be treated early to prevent transition to AML. Further study of this case will reveal the molecular mechanism of MDS-to-AML transformation and identify new leukemic fusion genes.
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Affiliation(s)
- Huayue Zhang
- Institute of Hematology, the Second Hospital of Shanxi Medical University, China
| | - Guoxia Li
- Institute of Hematology, the Second Hospital of Shanxi Medical University, China
| | - Jianmei Chang
- Institute of Hematology, the Second Hospital of Shanxi Medical University, China
| | - Hongwei Wang
- Institute of Hematology, the Second Hospital of Shanxi Medical University, China
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39
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Chen X, Liu K, Hu J, Fan J, Huo Q, Yin J. Rare Case of Diffuse Large B-Cell Lymphoma Mimicking Acute Monocytic Leukemia, Associated with Complex Karyotype. Ann Clin Lab Sci 2020; 50:397-400. [PMID: 32581033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Diffuse Large B-Cell Lymphoma (DLBCL), NOS, constitutes 25-35% of adult non-Hodgkin lymphomas in developed countries, and a higher percentage in developing countries; older people are prone to the disease. Three frequent morphological variants have been recognized, including centroblastic, immunoblastic, and anaplastic variants. However, there are still other rare morphological variants of DLBCL, presenting challenge in diagnosis and treatment. CASE PRESENTATION A 62-year-old woman sought medical attention with a previous 6-month history of intermittent fever and leukocytosis. Bone marrow (BM) aspiration presented AML with acute monocytic leukemia-like morphologic features. The results of the immunophenotypic analysis suggested mature B cell lymphoma without obvious subtype characteristics. Lymph node biopsy indicated DLBCL of non-germinal centre B-cell subtype (n-GCB). Cytogenetic analysis of the BM cells revealed a 46,XX, trp(1)(q21q32),del(7)(q32q36),t(9;14)(p13;q32) [4]/46,XX [16] karyotype. The patient was diagnosed with EBV-positive DLBCL, NOS based on the combination of lymph node biopsy, clinical, cytological, immunophenotypic, and cytogenetic analyses. CONCLUSION To date, no case reports of a patient diagnosed with DLBCL mimicking acute monocytic leukemia with complex karyotype have been reported. We present the case given its rarity, easy misdiagnosis, and poor prognosis. The case highlights the importance of awareness about the rare morphological variant to laboratory staff and hematologists.
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Affiliation(s)
- Xueyan Chen
- Department of Clinical Laboratory, The People's Hospital of Longhua, Shenzhen, Guangdong Province, China
| | - Keyu Liu
- Department of Clinical Laboratory, Affiliated Hospital of Engineering University of Hebei, Handan, Hebei Province, China
| | - Jintian Hu
- Department of Clinical Laboratory, Affiliated Hospital of Engineering University of Hebei, Handan, Hebei Province, China
| | - Jie Fan
- Department of Clinical Laboratory, Affiliated Hospital of Engineering University of Hebei, Handan, Hebei Province, China
| | - Qingyan Huo
- Department of Clinical Laboratory, Affiliated Hospital of Engineering University of Hebei, Handan, Hebei Province, China
| | - Junping Yin
- Department of Clinical Laboratory, Affiliated Hospital of Engineering University of Hebei, Handan, Hebei Province, China
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40
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M’kacher R, Colicchio B, Borie C, Junker S, Marquet V, Heidingsfelder L, Soehnlen K, Najar W, Hempel WM, Oudrhiri N, Wilhelm-Murer N, Miguet M, Arnoux M, Ferrapie C, Kerbrat W, Plesch A, Dieterlen A, Girinsky T, Voisin P, Deschenes G, Tabet AC, Yardin C, Bennaceur-Griscelli A, Fenech M, Carde P, Jeandidier E. Telomere and Centromere Staining Followed by M-FISH Improves Diagnosis of Chromosomal Instability and Its Clinical Utility. Genes (Basel) 2020; 11:genes11050475. [PMID: 32349350 PMCID: PMC7291161 DOI: 10.3390/genes11050475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022] Open
Abstract
Dicentric chromosomes are a relevant marker of chromosomal instability. Their appearance is associated with telomere dysfunction, leading to cancer progression and a poor clinical outcome. Here, we present Telomere and Centromere staining followed by M-FISH (TC+M-FISH) for improved detection of telomere dysfunction and the identification of dicentric chromosomes in cancer patients and various genetic syndromes. Significant telomere length shortening and significantly higher frequencies of telomere loss and deletion were found in the peripheral lymphocytes of patients with cancer and genetic syndromes relative to similar age-matched healthy donors. We assessed our technique against conventional cytogenetics for the detection of dicentric chromosomes by subjecting metaphase preparations to both approaches. We identified dicentric chromosomes in 28/50 cancer patients and 21/44 genetic syndrome patients using our approach, but only 7/50 and 12/44, respectively, using standard cytogenetics. We ascribe this discrepancy to the identification of the unique configuration of dicentric chromosomes. We observed significantly higher frequencies of telomere loss and deletion in patients with dicentric chromosomes (p < 10−4). TC+M-FISH analysis is superior to classical cytogenetics for the detection of chromosomal instability. Our approach is a relatively simple but useful tool for documenting telomere dysfunction and chromosomal instability with the potential to become a standard additional diagnostic tool in medical genetics and the clinic.
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Affiliation(s)
- Radhia M’kacher
- Cell Environment, DNA Damage R&D, 75020 Paris, France; (K.S.); (W.N.); (W.M.H.); (P.V.)
- Correspondence:
| | - Bruno Colicchio
- IRIMAS, Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, 68093 Mulhouse, France; (B.C.); (A.D.)
| | - Claire Borie
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Steffen Junker
- Institute of Biomedicine, University of Aarhus, DK-8000 Aarhus, Denmark;
| | - Valentine Marquet
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l’Enfant, CHU Dupuytren, 87042 Limoges, France; (V.M.); (C.Y.)
| | | | - Kevin Soehnlen
- Cell Environment, DNA Damage R&D, 75020 Paris, France; (K.S.); (W.N.); (W.M.H.); (P.V.)
| | - Wala Najar
- Cell Environment, DNA Damage R&D, 75020 Paris, France; (K.S.); (W.N.); (W.M.H.); (P.V.)
- IRIMAS, Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, 68093 Mulhouse, France; (B.C.); (A.D.)
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
- Institute of Biomedicine, University of Aarhus, DK-8000 Aarhus, Denmark;
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l’Enfant, CHU Dupuytren, 87042 Limoges, France; (V.M.); (C.Y.)
- MetaSystems GmbH, Robert-Bosch-Str., 6 D-68804 Altlussheim, Germany; (L.H.); (A.P.)
- Faculté de Médicine, Université Paris Descartes, 75005 Paris, France
| | - William M. Hempel
- Cell Environment, DNA Damage R&D, 75020 Paris, France; (K.S.); (W.N.); (W.M.H.); (P.V.)
| | - Noufissa Oudrhiri
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Nadège Wilhelm-Murer
- Service de Génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace Mulhouse, 68070 Mulhouse, France; (N.W.-M.); (M.M.); (E.J.)
| | - Marguerite Miguet
- Service de Génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace Mulhouse, 68070 Mulhouse, France; (N.W.-M.); (M.M.); (E.J.)
| | - Micheline Arnoux
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Catherine Ferrapie
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Wendy Kerbrat
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Andreas Plesch
- MetaSystems GmbH, Robert-Bosch-Str., 6 D-68804 Altlussheim, Germany; (L.H.); (A.P.)
| | - Alain Dieterlen
- IRIMAS, Institut de Recherche en Informatique, Mathématiques, Automatique et Signal, Université de Haute-Alsace, 68093 Mulhouse, France; (B.C.); (A.D.)
| | - Theodore Girinsky
- Department of Radiation Oncology, Gustave Roussy Cancer Campus, 94800 Villejuif, France;
| | - Philippe Voisin
- Cell Environment, DNA Damage R&D, 75020 Paris, France; (K.S.); (W.N.); (W.M.H.); (P.V.)
| | - Georges Deschenes
- Nephrology Department, APHP-Hopital Robert Debré, 75019 Paris, France;
| | - Anne-Claude Tabet
- Cytogenetic Laboratory, APHP-Hopital Robert Debré, 75019 Paris, France;
| | - Catherine Yardin
- Service de Cytogénétique, Génétique Médicale, et Biologie de la Reproduction Hôpital de la Mère et de l’Enfant, CHU Dupuytren, 87042 Limoges, France; (V.M.); (C.Y.)
| | - Annelise Bennaceur-Griscelli
- APHP-Service D’hématologie Oncohématologie Moléculaire et Cytogénétique Hôpital Paul Brousse Université Paris Saclay/ Inserm UMR 935, 94800 Villejuif, France; (C.B.); (N.O.); (M.A.); (C.F.); (W.K.); (A.B.-G.)
| | - Michael Fenech
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia;
- Genome Health Foundation, North Brighton, SA 5048, Australia
| | - Patrice Carde
- Department of Hematology, Gustave Roussy Cancer Campus, 94800 Villejuif, France;
| | - Eric Jeandidier
- Service de Génétique Groupe Hospitalier de la Région de Mulhouse et Sud Alsace Mulhouse, 68070 Mulhouse, France; (N.W.-M.); (M.M.); (E.J.)
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41
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Sakamoto K, Takeuchi K. Cytogenetics of Blastic Plasmacytoid Dendritic Cell Neoplasm: Chromosomal Rearrangements and DNA Copy-Number Alterations. Hematol Oncol Clin North Am 2020; 34:523-538. [PMID: 32336417 DOI: 10.1016/j.hoc.2020.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a skin-tropic hematopoietic malignancy. Approximately 60% of cases with analyzable karyotyping results show complex karyotypes. Losses are more frequently found than copy-number gains. Recurrently deleted regions include tumor suppressor genes. No specific chromosomal abnormalities have been demonstrated in BPDCN, but genomic rearrangements involving the MYB family genes and MYC were identified. One-third of cases of BPDCN harbor the 8q24 rearrangement, most frequently with 6p21 harboring RUNX2, which is associated with immunoblastoid cytomorphology and MYC expression. MYB rearrangement is detected in 20% of patients with BPDCN. We review copy-number alterations and chromosomal rearrangements.
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Affiliation(s)
- Kana Sakamoto
- Pathology Project for Molecular Targets, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo 135-8550, Japan; Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo 135-8550, Japan; Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Clinical Pathology Center, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.
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M. Weerakoon-Ratnayake K, Vaidyanathan S, Larkey N, Dathathreya K, Hu M, Jose J, Mog S, August K, K. Godwin A, L. Hupert M, A. Witek M, A. Soper S. Microfluidic Device for On-Chip Immunophenotyping and Cytogenetic Analysis of Rare Biological Cells. Cells 2020; 9:E519. [PMID: 32102446 PMCID: PMC7072755 DOI: 10.3390/cells9020519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 01/09/2023] Open
Abstract
The role of circulating plasma cells (CPCs) and circulating leukemic cells (CLCs) as biomarkers for several blood cancers, such as multiple myeloma and leukemia, respectively, have recently been reported. These markers can be attractive due to the minimally invasive nature of their acquisition through a blood draw (i.e., liquid biopsy), negating the need for painful bone marrow biopsies. CPCs or CLCs can be used for cellular/molecular analyses as well, such as immunophenotyping or fluorescence in situ hybridization (FISH). FISH, which is typically carried out on slides involving complex workflows, becomes problematic when operating on CLCs or CPCs due to their relatively modest numbers. Here, we present a microfluidic device for characterizing CPCs and CLCs using immunofluorescence or FISH that have been enriched from peripheral blood using a different microfluidic device. The microfluidic possessed an array of cross-channels (2-4 µm in depth and width) that interconnected a series of input and output fluidic channels. Placing a cover plate over the device formed microtraps, the size of which was defined by the width and depth of the cross-channels. This microfluidic chip allowed for automation of immunofluorescence and FISH, requiring the use of small volumes of reagents, such as antibodies and probes, as compared to slide-based immunophenotyping and FISH. In addition, the device could secure FISH results in <4 h compared to 2-3 days for conventional FISH.
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Affiliation(s)
- Kumuditha M. Weerakoon-Ratnayake
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Swarnagowri Vaidyanathan
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Bioengineering, The University of Kansas, Lawrence, KS 66045, USA
| | - Nicholas Larkey
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Kavya Dathathreya
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Mengjia Hu
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Jilsha Jose
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Shalee Mog
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Keith August
- Children’s Mercy Hospital, Kansas City, MO 64108, USA;
| | - Andrew K. Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Mateusz L. Hupert
- Biofluidica Inc., BioFluidica Research Laboratory, Lawrence, KS 66047, USA
| | - Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA; (K.M.W.-R.); (K.D.); (S.M.)
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66045, USA; (S.V.); (N.L.); (M.H.); (J.J.)
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
- Biofluidica Inc., BioFluidica Research Laboratory, Lawrence, KS 66047, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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43
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Muys J, Blaumeiser B, Janssens K, Loobuyck P, Jacquemyn Y. Chromosomal microarray analysis in prenatal diagnosis: ethical considerations of the Belgian approach. J Med Ethics 2020; 46:104-109. [PMID: 31527144 DOI: 10.1136/medethics-2018-105186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/25/2019] [Accepted: 09/01/2019] [Indexed: 06/10/2023]
Abstract
Detection of genetic aberrations in prenatal samples, obtained through amniocentesis or chorion villus biopsy, is increasingly performed using chromosomal microarray (CMA), a technique that can uncover both aneuploidies and copy number variants throughout the genome. Despite the obvious benefits of CMA, the decision on implementing the technology is complicated by ethical issues concerning variant interpretation and reporting. In Belgium, uniform guidelines were composed and a shared database for prenatal CMA findings was established. This Belgian approach sparks discussion: it is evidence-based, prevents inconsistencies and avoids parental anxiety, but can be considered paternalistic. Here, we reflect on the cultural and moral bases of the Belgian reporting system of prenatally detected variants.
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Affiliation(s)
- Joke Muys
- Department of Obstetrics and Gynaecology, Universitair Ziekenhuis Antwerpen, Edegem, Belgium
- Center for Medical Genetics, Universiteit Antwerpen, Edegem, Belgium
| | - Bettina Blaumeiser
- Center for Medical Genetics, Universiteit Antwerpen, Edegem, Belgium
- Department of Medical Genetics, Universitair Ziekenhuis Antwerpen, Edegem, Belgium
| | - Katrien Janssens
- Center for Medical Genetics, Universiteit Antwerpen, Edegem, Belgium
| | | | - Yves Jacquemyn
- Department of Obstetrics and Gynaecology, Universitair Ziekenhuis Antwerpen, Edegem, Belgium
- Global Health Institute, Universiteit Antwerpen, Edegem, Belgium
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44
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Heitkam T. Balancing Retrospection and Visions: The Cytogenetics Group of the Society of Plant Breeding (GPZ) Came Together in Dresden. Cytogenet Genome Res 2020; 159:163-168. [PMID: 31931500 DOI: 10.1159/000505280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2019] [Indexed: 11/19/2022] Open
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45
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Iannuzzi A, Braun M, Genualdo V, Perucatti A, Reinartz S, Proios I, Heppelmann M, Rehage J, Hülskötter K, Beineke A, Metzger J, Distl O. Clinical, cytogenetic and molecular genetic characterization of a tandem fusion translocation in a male Holstein cattle with congenital hypospadias and a ventricular septal defect. PLoS One 2020; 15:e0227117. [PMID: 31923267 PMCID: PMC6953810 DOI: 10.1371/journal.pone.0227117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
Hypospadias, disorder of sex development (DSD), is a sporadic congenital abnormality of the genital region in male ruminants, which is characterized by a non-fused urethra during fetal development. Detailed clinical examination classified the hypospadias phenotype of a male Holstein calf studied here as the perineal type. In combined use of cytogenetic analysis and whole genome sequencing, a non-mosaic, pseudo-monosomy 59, XY + tan(18;27) was detected. This chromosomal aberration had its origin in a tandem fusion translocation of the bovine autosomes (BTA) 18 and 27 with an accompanying loss of genomic sequences mainly in the distal end of BTA 18 and the proximal end of BTA 27. The resulting phenotype included hypospadias, growth retardation and ventricular septal defect.
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Affiliation(s)
- Alessandra Iannuzzi
- Institute for the Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), Naples, Italy
| | - Marina Braun
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Viviana Genualdo
- Institute for the Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), Naples, Italy
| | - Angela Perucatti
- Institute for the Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), Naples, Italy
| | - Sina Reinartz
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ioannis Proios
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Maike Heppelmann
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jürgen Rehage
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kirsten Hülskötter
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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46
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Mora-Calderón J, Scott-Moraga K, Bolaños-Villegas P. Analysis of Meiosis in Nonmodel Tropical Plants: The Case of Carica papaya Linn. Methods Mol Biol 2020; 2061:131-139. [PMID: 31583657 DOI: 10.1007/978-1-4939-9818-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To develop plants that are more tolerant to drought, marginal soil fertility, and diseases and that satisfy demands for high yield, new cultivars of the tropical fruit papaya (Carica papaya L.) are needed. Nonetheless, in many cases, these traits are available in only wild relatives found throughout Latin America. Understanding meiotic progression may facilitate the introgression of desirable traits into commercial cultivars that maintain high fertility. In this protocol, we describe a practical and simple method to effectively isolate male meiocytes in order to document the behavior of papaya meiotic chromosomes.
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Affiliation(s)
- José Mora-Calderón
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
| | - Kalani Scott-Moraga
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
| | - Pablo Bolaños-Villegas
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica.
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47
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Mursalimov SR, Sidorchuk YV, Deineko EV. Cytological Techniques to Study Cytomixis in Plant Male Meiosis. Methods Mol Biol 2020; 2061:117-129. [PMID: 31583656 DOI: 10.1007/978-1-4939-9818-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
In this chapter we describe cytological techniques to study cytomixis, a process of nuclear migration between plant cells, in squashed plant male meiocytes of Nicotiana tabacum and Secale cereale. To perform immunostaining or fluorescence in situ hybridization (FISH) on meiotic cells involved in cytomixis common protocols are modified. During preparation of specimens for subsequent cytological analysis, it is necessary not only to make DNA and proteins accessible to DNA probes and antibodies, but also to preserve cell cytoplasm. There are also some important modifications in the protocols applied for meiocytes of different plant species. Here we describe protocols for immunostaining and FISH in rigid tobacco male meiocytes with dense cytoplasm and thick callose wall, that tolerate hard squashing, and in soft rye male meiocytes, that are easily damaged upon squashing, both to study cytomixis.
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Affiliation(s)
- Sergey R Mursalimov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russian Federation.
| | - Yuriy V Sidorchuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russian Federation
| | - Elena V Deineko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russian Federation
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48
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Nugis VY, Kozlova MG, Nadejina NM, Galstyan IA, Nikitina VA, Khvostunov IK, Golub EV. CYTOGENETIC BIODOSIMETRY OF ACCIDENTAL EXPOSURES IN THE LONG TERMS AFTER IRRADIATION. Radiat Prot Dosimetry 2019; 186:31-36. [PMID: 31321440 DOI: 10.1093/rpd/ncz040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/16/2019] [Accepted: 03/06/2019] [Indexed: 06/10/2023]
Abstract
The group of radiation victims who had received radiation injures similar to those of Chernobyl accident victims was evaluated in terms of retrospective cytogenetic biodosimetry in the long term period of from 17 y up to 50 y after irradiation. Based on the existing results of the long-term cytogenetic examination of the victims injured after the Chernobyl accident, an original method was developed. This method of retrospective dose recovery was based on the use of a special computer program, the time elapsed after irradiation and the frequency of atypical chromosomes. Both patient groups were examined using conventional cytogenetic analysis. The new method of a retrospective biodosimetry was tested on the non-Chernobyl group. As a result the multiple regression equations which included frequency atypical chromosomes produced better results because the majority of the estimates of the retrospective doses fell into the 95%-prediction intervals for the reference group of the Chernobyl victims.
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Affiliation(s)
- V Yu Nugis
- Center of Biomedical Technology of State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - M G Kozlova
- Center of Biomedical Technology of State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - N M Nadejina
- Center of Biomedical Technology of State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - I A Galstyan
- Center of Biomedical Technology of State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - V A Nikitina
- Center of Biomedical Technology of State Research Center-Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - I K Khvostunov
- Laboratory of Radiation Cytogenetics of A. Tsyb Medical Radiological Research Center-branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - E V Golub
- Laboratory of Radiation Cytogenetics of A. Tsyb Medical Radiological Research Center-branch of the National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
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49
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Furukawa A. THE PROJECT OF ANOTHER LOW-COST METAPHASE FINDER (SECOND REPORT-APPLICATION OF ARTIFICIAL INTELLIGENCE). Radiat Prot Dosimetry 2019; 186:37-41. [PMID: 30806467 DOI: 10.1093/rpd/ncz012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/04/2019] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Biological dosimetry is used to estimate individual absorbed radiation dose by quantifying an appropriate biological marker. The most popular gold-standard marker is the appearance of dicentric chromosomes in metaphase. The metaphase finder is a tool for biological dosimetry that finds metaphase cells on glass slides. The author and a software company have designed a new system and are now preparing to produce the system commercially. The metaphase finder consists of an automated microscope, a camera, and a computer. To enhance the accuracy of the system, an artificial intelligence (AI) with deep learning was tested. A total of 1709 images of the metaphase finder detected as 'metaphases' were read into a nine-layer artificial neural network to detect true metaphases. A total of 456 images were used for training, and the rest of the images were used for validation. The accuracy of AI was 0.89 for metaphases and 0.90 for non-metaphases.
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Affiliation(s)
- Akira Furukawa
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, Japan
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50
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Li Y, Shirley BC, Wilkins RC, Norton F, Knoll JHM, Rogan PK. RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE DICENTRIC CHROMOSOME ASSAY. Radiat Prot Dosimetry 2019; 186:42-47. [PMID: 30624749 DOI: 10.1093/rpd/ncy282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/15/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Accuracy of the automated dicentric chromosome (DC) assay relies on metaphase image selection. This study validates a software framework to find the best image selection models that mitigate inter-sample variability. Evaluation methods to determine model quality include the Poisson goodness-of-fit of DC distributions for each sample, residuals after calibration curve fitting and leave-one-out dose estimation errors. The process iteratively searches a pool of selection model candidates by modifying statistical and filter cut-offs to rank the best candidates according to their respective evaluation scores. Evaluation scores minimize the sum of squared errors relative to the actual radiation dose of the calibration samples. For one laboratory, the minimum score for the curve fit residual method was 0.0475 Gy2, compared to 1.1975 Gy2 without image selection. Application of optimal selection models using samples of unknown exposure produced estimated doses within 0.5 Gy of physical dose. Model optimization standardizes image selection among samples and provides relief from manual DC scoring, improving accuracy and consistency of dose estimation.
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Affiliation(s)
- Yanxin Li
- CytoGnomix, Inc., POB 27052, 60 N. Centre Rd, London, ON, Canada
| | - Ben C Shirley
- CytoGnomix, Inc., POB 27052, 60 N. Centre Rd, London, ON, Canada
| | - Ruth C Wilkins
- Health Canada, Environmental and Radiation and Health Sciences Directorate, Ottawa, ON, Canada
| | - Farrah Norton
- Canadian Nuclear Laboratories, 286 Plant Rd, Chalk River, ON, Canada
| | - Joan H M Knoll
- CytoGnomix, Inc., POB 27052, 60 N. Centre Rd, London, ON, Canada
- Department of Pathology and Laboratory Medicine, University of Western Ontario, 1151 Richmond St., London, ON, Canada
| | - Peter K Rogan
- CytoGnomix, Inc., POB 27052, 60 N. Centre Rd, London, ON, Canada
- Department of Biochemistry, University of Western Ontario, 1151 Richmond St., London, ON, Canada
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