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Dremsek P, Schwarz T, Weil B, Malashka A, Laccone F, Neesen J. Optical Genome Mapping in Routine Human Genetic Diagnostics-Its Advantages and Limitations. Genes (Basel) 2021; 12:1958. [PMID: 34946907 PMCID: PMC8701374 DOI: 10.3390/genes12121958] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 11/16/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/01/2022] Open
Abstract
In recent years, optical genome mapping (OGM) has developed into a highly promising method of detecting large-scale structural variants in human genomes. It is capable of detecting structural variants considered difficult to detect by other current methods. Hence, it promises to be feasible as a first-line diagnostic tool, permitting insight into a new realm of previously unknown variants. However, due to its novelty, little experience with OGM is available to infer best practices for its application or to clarify which features cannot be detected. In this study, we used the Saphyr system (Bionano Genomics, San Diego, CA, USA), to explore its capabilities in human genetic diagnostics. To this end, we tested 14 DNA samples to confirm a total of 14 different structural or numerical chromosomal variants originally detected by other means, namely, deletions, duplications, inversions, trisomies, and a translocation. Overall, 12 variants could be confirmed; one deletion and one inversion could not. The prerequisites for detection of similar variants were explored by reviewing the OGM data of 54 samples analyzed in our laboratory. Limitations, some owing to the novelty of the method and some inherent to it, were described. Finally, we tested the successful application of OGM in routine diagnostics and described some of the challenges that merit consideration when utilizing OGM as a diagnostic tool.
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Affiliation(s)
- Paul Dremsek
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090 Vienna, Austria; (T.S.); (B.W.); (A.M.); (F.L.); (J.N.)
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Shi X, Tang H, Lu J, Yang X, Ding H, Wu J. Prenatal genetic diagnosis of omphalocele by karyotyping, chromosomal microarray analysis and exome sequencing. Ann Med 2021; 53:1285-1291. [PMID: 34374610 PMCID: PMC8366676 DOI: 10.1080/07853890.2021.1962966] [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: 05/24/2021] [Accepted: 07/27/2021] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES The aim of this study is to share our experience in the prenatal diagnosis of omphalocele by karyotyping, chromosomal microarray analysis (CMA) and whole exome sequencing (WES). METHODS In this retrospective study, 81 cases of omphalocele were identified from 2015 to 2020. Associated anomalies and prenatal diagnosis based on karyotyping, CMA and WES were analysed. RESULTS Fifty-eight (71.6%) of the 81 foetuses had other ultrasound anomalies. Giant omphalocele was present in 11 cases (13.6%) and small omphalocele was present in 70 cases (86.4%). Chromosomal abnormalities were found in 24 foetuses (29.6%, 24/81), the most common of which were trisomy 18 (58.8%, 11/24) and trisomy 13 (29.2%, 7/24). Compared to isolated omphalocele, non-isolated omphalocele was accompanied by an increased prevalence of chromosomal abnormalities (4.3% (1/23) vs. 39.7% (23/58), χ2 = 8.226, p = .004). All chromosomal abnormalities were found in small omphalocele. Aside from aneuploidy, CMA showed one pathogenic copy number variants (CNVs) for a detection rate of 1.2%, one variants of unknown significance (VOUS) and one instance of loss of heterozygosity (LOH). WES was performed on 3 non-isolated cases, and one was found to have pathogenic variants. CONCLUSIONS The most common genetic cause of omphalocele is aneuploidy and the prevalence of chromosomal abnormalities is increased with non-isolated and small omphalocele. CMA and WES can be useful for providing further genetic information to assist in prenatal counselling and pregnancy management.
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Affiliation(s)
- Xiaomei Shi
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Hui Tang
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Jian Lu
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Xiue Yang
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Hongke Ding
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Jing Wu
- Gentic Medical Center, Guangdong Women and Children Hospital, Guangzhou, PR China
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de Oliveira Bustamante F, do Nascimento TH, Montenegro C, Dias S, do Vale Martins L, Braz GT, Benko-Iseppon AM, Jiang J, Pedrosa-Harand A, Brasileiro-Vidal AC. Oligo-FISH barcode in beans: a new chromosome identification system. Theor Appl Genet 2021; 134:3675-3686. [PMID: 34368889 DOI: 10.1007/s00122-021-03921-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7-15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.
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Affiliation(s)
- Fernanda de Oliveira Bustamante
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade do Estado de Minas Gerais, Unidade Divinópolis, Divinópolis, MG, Brazil
| | | | - Claudio Montenegro
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Sibelle Dias
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Lívia do Vale Martins
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Departamento de Biologia, Universidade Federal do Piauí, Teresina, PI, Brazil
| | | | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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Knytl M, Fornaini NR. Measurement of Chromosomal Arms and FISH Reveal Complex Genome Architecture and Standardized Karyotype of Model Fish, Genus Carassius. Cells 2021; 10:2343. [PMID: 34571992 PMCID: PMC8471844 DOI: 10.3390/cells10092343] [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: 08/01/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 11/23/2022] Open
Abstract
The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T); C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, 12843 Prague, Czech Republic;
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Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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Haley L, Parimi V, Jiang L, Pallavajjala A, Hardy M, Yonescu R, Morsberger L, Stinnett V, Long P, Zou YS, Gocke CD. Diagnostic Utility of Gene Fusion Panel to Detect Gene Fusions in Fresh and Formalin-Fixed, Paraffin-Embedded Cancer Specimens. J Mol Diagn 2021; 23:1343-1358. [PMID: 34358677 DOI: 10.1016/j.jmoldx.2021.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/28/2021] [Revised: 06/04/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
Somatic gene fusions are common in leukemias/lymphomas and solid tumors. The detection of gene fusions is crucial for diagnosis. NanoString fusion technology is a multiplexed hybridization method that interrogates hundreds of gene fusions in a single reaction. This study's objective was to determine the performance characteristics and diagnostic utility of NanoString fusion assay in a clinical diagnostics laboratory. Validation using 100 positive specimens and 15 negative specimens by a combined reference standard of fluorescence in situ hybridization (FISH)/RT-PCR/next-generation sequencing (NGS) assays achieved 100% sensitivity in leukemias/lymphomas and 95.0% sensitivity and 100% specificity in solid tumors. Subsequently, 214 consecutive clinical cases, including 73 leukemia/lymphoma specimens and 141 formalin-fixed, paraffin-embedded solid tumor specimens, were analyzed by gene fusion panels across 638 unique gene fusion transcripts. A variety of comparator tests, including FISH panels, conventional karyotyping, a DNA-based targeted NGS assay, and custom RT-PCR testing, were performed in parallel. The gene fusion assay detected 31 gene fusions, including 16 in leukemia/lymphoma specimens and 15 in solid tumor specimens. The overall sensitivity, specificity, and accuracy of gene fusions detected by the gene fusion panel in all 329 specimens (validation and consecutive clinical specimens) tested in this study were 94.8%, 100%, and 97.9%, respectively, compared with FISH/RT-PCR/NGS assays. The gene fusion panel is a reliable approach that maximizes molecular detection of fusions among both fresh and formalin-fixed, paraffin-embedded cancer specimens.
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Affiliation(s)
- Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Raluca Yonescu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Laura Morsberger
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Victoria Stinnett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Patty Long
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Cytogenetics Laboratory, Johns Hopkins University Hospital, Baltimore, Maryland.
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Chen WL, Mefford HC. Diagnostic Considerations in the Epilepsies-Testing Strategies, Test Type Advantages, and Limitations. Neurotherapeutics 2021; 18:1468-1477. [PMID: 34532824 PMCID: PMC8608977 DOI: 10.1007/s13311-021-01121-7] [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] [Accepted: 09/04/2021] [Indexed: 02/04/2023] Open
Abstract
The role of genetics in epilepsy has been recognized for a long time. Over the past decade, genome-wide technologies have identified numerous genes and variants associated with epilepsy. In the clinical setting, a myriad of genetic testing options are available, and a subset of specific genetic diagnoses have management implications. Furthermore, genetic testing can be a dynamic process. As a result, fundamental knowledge about genetics and genomics has become essential for all specialists. Here, we review current knowledge of the genetic contribution to various types of epilepsy, provide an overview of types of genetic variants, and discuss genetic testing options and their diagnostic yield. We also consider advantages and limitations of testing approaches.
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Affiliation(s)
- Wei-Liang Chen
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Current Location: Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Fan Z, Weng X, Pan Z, Fan Q, Long J, Lin G, Yang Q, Sun L. Molecular diagnosis of sex chromosome mosaics in fetal amniotic cells. Medicine (Baltimore) 2021; 100:e26331. [PMID: 34160397 PMCID: PMC8238360 DOI: 10.1097/md.0000000000026331] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/26/2021] [Indexed: 01/04/2023] Open
Abstract
Mosaicism can be observed in karyotype analyses of amniotic fluid cells. Differentiating between true mosaicism and pseudomosaicism and determining mosaic proportions can help avoid misjudgments by doctors and effectively reduce mental and physical harm to pregnant women. However, the detection of mosaicism and mosaic proportions via karyotype analysis and fluorescence in situ hybridization (FISH) is extremely complex. We have developed a novel approach, "segmental duplication quantitative fluorescent PCR" (SD-QF-PCR), to detect mosaicism and mosaic proportions.In this study, twenty control samples and fourteen mosaic samples were tested by first-line karyotype analysis; by second-line karyotype analysis, SD-QF-PCR and FISH were used to reassess fetal sex chromosome mosaicism and mosaic proportions.Detection of the 20 control samples by second-line karyotype analysis via FISH and SD-QF-PCR showed normal and consistent results. Among the 14 mosaic samples, the numbers of samples showing true mosaicism and pseudomosaicism detected by the three methods were 6 and 8, respectively.Our study demonstrates that SD-QF-PCR can be used as a complementary method to traditional cytogenetic analysis of amniotic fluid mosaics and has clinical application value.
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Affiliation(s)
- Zuqian Fan
- Department of Clinical Laboratory, Qinzhou Maternal and Child Health Hospital, Guangxi
| | - Xunjin Weng
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
| | - Zhijian Pan
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
| | - Qiongying Fan
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
| | - Ju Long
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi
- Laboratory Animal Center, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, PR China
| | - Guixian Lin
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
| | - Qian Yang
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
| | - Lei Sun
- Qinzhou Key Laboratory of Molecular and Cell Biology on Endemic Diseases, Qinzhou, Guangxi
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Hospital, Guangxi
- Laboratory Animal Center, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, PR China
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Quessada J, Cuccuini W, Saultier P, Loosveld M, Harrison CJ, Lafage-Pochitaloff M. Cytogenetics of Pediatric Acute Myeloid Leukemia: A Review of the Current Knowledge. Genes (Basel) 2021; 12:genes12060924. [PMID: 34204358 PMCID: PMC8233729 DOI: 10.3390/genes12060924] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 05/12/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Pediatric acute myeloid leukemia is a rare and heterogeneous disease in relation to morphology, immunophenotyping, germline and somatic cytogenetic and genetic abnormalities. Over recent decades, outcomes have greatly improved, although survival rates remain around 70% and the relapse rate is high, at around 30%. Cytogenetics is an important factor for diagnosis and indication of prognosis. The main cytogenetic abnormalities are referenced in the current WHO classification of acute myeloid leukemia, where there is an indication for risk-adapted therapy. The aim of this article is to provide an updated review of cytogenetics in pediatric AML, describing well-known WHO entities, as well as new subgroups and germline mutations with therapeutic implications. We describe the main chromosomal abnormalities, their frequency according to age and AML subtypes, and their prognostic relevance within current therapeutic protocols. We focus on de novo AML and on cytogenetic diagnosis, including the practical difficulties encountered, based on the most recent hematological and cytogenetic recommendations.
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Affiliation(s)
- Julie Quessada
- Hematological Cytogenetics Laboratory, Timone Children’s Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille University, 13005 Marseille, France;
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France;
| | - Wendy Cuccuini
- Hematological Cytogenetics Laboratory, Saint-Louis Hospital, Assistance Publique des Hôpitaux de Paris (APHP), 75010 Paris, France;
- Groupe Francophone de Cytogénétique Hématologique (GFCH), 1 Avenue Claude Vellefaux, 75475 Paris, France
| | - Paul Saultier
- APHM, La Timone Children’s Hospital Department of Pediatric Hematology and Oncology, 13005 Marseille, France;
- Faculté de Médecine, Aix Marseille University, INSERM, INRAe, C2VN, 13005 Marseille, France
| | - Marie Loosveld
- Aix Marseille University, CNRS, INSERM, CIML, 13009 Marseille, France;
- Hematology Laboratory, Timone Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), 13005 Marseille, France
| | - Christine J. Harrison
- Leukaemia Research Cytogenetics Group Translational and Clinical Research Institute, Newcastle University Centre for Cancer Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Marina Lafage-Pochitaloff
- Hematological Cytogenetics Laboratory, Timone Children’s Hospital, Assistance Publique-Hôpitaux de Marseille (APHM), Faculté de Médecine, Aix Marseille University, 13005 Marseille, France;
- Groupe Francophone de Cytogénétique Hématologique (GFCH), 1 Avenue Claude Vellefaux, 75475 Paris, France
- Correspondence: ; Tel.: +33-4-91-38-76-41
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Tang Z, Kanagal-Shamanna R, Tang G, Patel K, Medeiros LJ, Toruner GA. Analytical and clinical performance of chromosomal microarrays compared with FISH panel and conventional karyotyping in patients with chronic lymphocytic leukemia. Leuk Res 2021; 108:106616. [PMID: 34022744 DOI: 10.1016/j.leukres.2021.106616] [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] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
In this single center retrospective analysis on 102 CLL patients, we assessed analytical and clinical performance of CMA against a targeted FISH panel (ATM, TP53, CEP12, D13S319 and LAMP1 loci) and karyotyping. CMA yielded additional information compared to karyotype in 39 cases (38 %). On the other hand, while CMA detected aberrations were also detected by FISH in all 31 cases (30 %), aberrations with low clonal size (<30 %) detected by FISH were missed by CMA. When evaluated with National Cancer Center Network (NCCN) guidelines, the capture rate of prognostic relevant cytogenetic information for FISH only, FISH + Chromosomes and FISH + CMA analyses were 95, 96 and 100 % respectively. With Cancer Cytogenomics Consortium (CGC) Criteria, these figures for FISH only, FISH + Chromosomes and FISH + CMA were 88 %, 92 and 100 % respectively. In conclusion, CMA provides additional analytical information to FISH and karyotyping, but this information has a clinical utility only in a small number of patients. Limit of detection (LOD) issues preclude replacement of FISH by CMA, but CMA may be a viable alternative to karyotyping. Further research is warranted.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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11
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Baudoin NC, Bloomfield M. Karyotype Aberrations in Action: The Evolution of Cancer Genomes and the Tumor Microenvironment. Genes (Basel) 2021; 12:558. [PMID: 33921421 PMCID: PMC8068843 DOI: 10.3390/genes12040558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/11/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of cellular evolution. For this cellular evolution to take place, a population of cells must contain functional heterogeneity and an assessment of this heterogeneity in the form of natural selection. Cancer cells from advanced malignancies are genomically and functionally very different compared to the healthy cells from which they evolved. Genomic alterations include aneuploidy (numerical and structural changes in chromosome content) and polyploidy (e.g., whole genome doubling), which can have considerable effects on cell physiology and phenotype. Likewise, conditions in the tumor microenvironment are spatially heterogeneous and vastly different than in healthy tissues, resulting in a number of environmental niches that play important roles in driving the evolution of tumor cells. While a number of studies have documented abnormal conditions of the tumor microenvironment and the cellular consequences of aneuploidy and polyploidy, a thorough overview of the interplay between karyotypically abnormal cells and the tissue and tumor microenvironments is not available. Here, we examine the evidence for how this interaction may unfold during tumor evolution. We describe a bidirectional interplay in which aneuploid and polyploid cells alter and shape the microenvironment in which they and their progeny reside; in turn, this microenvironment modulates the rate of genesis for new karyotype aberrations and selects for cells that are most fit under a given condition. We conclude by discussing the importance of this interaction for tumor evolution and the possibility of leveraging our understanding of this interplay for cancer therapy.
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Affiliation(s)
- Nicolaas C. Baudoin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mathew Bloomfield
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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12
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Sonek J, Muller R, Pfau R, Buchanan P. Detection of 69,XXX karyotype in circulating trophoblasts using fluorescence in-situ hybridization after enrichment using novel high-throughput microfluidic platform. Ultrasound Obstet Gynecol 2021; 57:650-651. [PMID: 33428295 DOI: 10.1002/uog.23586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Affiliation(s)
- J Sonek
- Wright State University, Obstetrics and Gynecology, Dayton, OH, USA
| | - R Muller
- BioFluidica, Inc., San Diego, CA, USA
| | - R Pfau
- Nationwide Children's Hospital, Institute for Genomic Medicine, Columbus, OH, USA
| | - P Buchanan
- The George Washington University, Department of Obstetrics and Gynecology, Washington, DC, USA
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13
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Viotti M, Victor AR, Barnes FL, Zouves CG, Besser AG, Grifo JA, Cheng EH, Lee MS, Horcajadas JA, Corti L, Fiorentino F, Spinella F, Minasi MG, Greco E, Munné S. Using outcome data from one thousand mosaic embryo transfers to formulate an embryo ranking system for clinical use. Fertil Steril 2021; 115:1212-1224. [PMID: 33685629 DOI: 10.1016/j.fertnstert.2020.11.041] [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: 07/11/2020] [Revised: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To study how the attributes of mosaicism identified during preimplantation genetic testing for aneuploidy relate to clinical outcomes, in order to formulate a ranking system of mosaic embryos for intrauterine transfer. DESIGN Compiled analysis. SETTING Multi-center. PATIENT(S) A total of 5,561 euploid blastocysts and 1,000 mosaic blastocysts used in clinical transfers in patients undergoing fertility treatment. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Implantation (gestational sac), ongoing pregnancy, birth, and spontaneous abortion (miscarriage before 20 weeks of gestation). RESULT(S) The euploid group had significantly more favorable rates of implantation and ongoing pregnancy/birth (OP/B) compared with the combined mosaic group or the mosaic group affecting only whole chromosomes (implantation: 57.2% vs. 46.5% vs. 41.8%; OP/B: 52.3% vs. 37.0% vs. 31.3%), as well as lower likelihood of spontaneous abortion (8.6% vs. 20.4% vs. 25%). Whole-chromosome mosaic embryos with level (percent aneuploid cells) <50% had significantly more favorable outcomes than the ≥50% group (implantation: 44.5% vs. 30.4%; OP/B: 36.1% vs. 19.3%). Mosaic type (nature of the aneuploidy implicated in mosaicism) affected outcomes, with a significant correlation between number of affected chromosomes and unfavorable outcomes. This ranged from mosaicism involving segmental abnormalities to complex aneuploidies affecting three or more chromosomes (implantation: 51.6% vs. 30.4%; OP/B: 43.1% vs. 20.8%). Combining mosaic level, type, and embryo morphology revealed the order of subcategories regarding likelihood of positive outcome. CONCLUSION(S) This compiled analysis revealed traits of mosaicism identified with preimplantation genetic testing for aneuploidy that affected outcomes in a statistically significant manner, enabling the formulation of an evidence-based prioritization scheme for mosaic embryos in the clinic.
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Affiliation(s)
- Manuel Viotti
- Zouves Foundation for Reproductive Medicine, Foster City, California; Zouves Fertility Center, Foster City, California.
| | - Andrea R Victor
- Zouves Foundation for Reproductive Medicine, Foster City, California
| | - Frank L Barnes
- Zouves Foundation for Reproductive Medicine, Foster City, California; Zouves Fertility Center, Foster City, California
| | - Christo G Zouves
- Zouves Foundation for Reproductive Medicine, Foster City, California; Zouves Fertility Center, Foster City, California
| | - Andria G Besser
- New York University Langone Fertility Center, New York, New York
| | - James A Grifo
- New York University Langone Fertility Center, New York, New York
| | | | - Maw-Sheng Lee
- Lee Women's Hospital, Taichung, Taiwan; Chung Shan Medical University, Institute of Medicine, Taichung, Taiwan
| | | | - Laura Corti
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Maria Giulia Minasi
- European Hospital, Centre For Reproductive Medicine, Rome, Italy; Villa Mafalda, Center For Reproductive Medicine, Rome, Italy
| | - Ermanno Greco
- European Hospital, Centre For Reproductive Medicine, Rome, Italy; Villa Mafalda, Center For Reproductive Medicine, Rome, Italy
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14
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Snyder EA, San Roman AK, Piña-Aguilar RE, Steeves MA, McNamara EA, Souter I, Hayes FJ, Levitsky LL, Lin AE. Genetic counseling for women with 45,X/46,XX mosaicism: Towards more personalized management. Eur J Med Genet 2021; 64:104140. [PMID: 33524610 DOI: 10.1016/j.ejmg.2021.104140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/27/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 01/06/2023]
Abstract
Despite numerous clinical series, consistent karyotype-phenotype correlations for Turner syndrome have not been established, although a lower level of 45,X is generally thought to be associated with a milder phenotype. This limits personalized counseling for women with 45,X/46,XX mosaicism. To better understand the phenotypic spectrum associated with various levels of 45,X/46,XX mosaicism, we compared patients evaluated in the Massachusetts General Hospital Turner Syndrome Clinic to determine if cardiac, renal, and thyroid abnormalities correlated with the percentage of 45,X cells present in a peripheral blood karyotype. of the 118 patients included in the study, 78 (66%) patients had non-mosaic 45,X and 40 (34%) patients had varying levels of 45,X/46,XX mosaicism. Patients with ≤70% 45,X compared with those with >70% 45,X had a significantly lower frequency of cardiac and renal anomalies. The presence of hypothyroidism was somewhat lower for the ≤70% 45,X group, but was not statistically significant. Supplemental tissue testing on another tissue type, typically buccal mucosa, was often useful in counseling patients with 45,X mosaicism. Given the modest sample size of patients with varying levels of mosaicism and the variability of Turner syndrome abnormalities, we hope this preliminary study will inspire a multicenter collaboration, which may lead to modification of clinical guidelines. Because several patients with ≤70% 45,X were ascertained from perinatal care referrals, we still advise women with 45,X mosaicism pursuing pregnancy to receive standard Turner syndrome cardiac surveillance. There is an opportunity to personalize counseling and surveillance for patients based on percentage of 45,X cells on chromosome analysis.
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Affiliation(s)
- Emma A Snyder
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | | | | | - Marcie A Steeves
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | - Erin A McNamara
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA
| | - Irene Souter
- Massachusetts General Hospital, Reproductive Endocrinology and Infertility, Boston, MA, USA
| | - Frances J Hayes
- Massachusetts General Hospital, Reproductive Endocrine Unit, Boston, MA, USA
| | - Lynne L Levitsky
- MassGeneral Hospital for Children, Pediatric Endocrinology, Boston, MA, USA
| | - Angela E Lin
- MassGeneral Hospital for Children, Medical Genetics, Department of Pediatrics, Boston, MA, USA.
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15
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Gug C, Burada F, Ioana M, Riza AL, Moldovan M, Mozos I, Ratiu A, Martiniuc V, Gorduza EV. Polyploidy in First and Second Trimester Pregnancies in Romania - a Retrospective Study. Clin Lab 2021; 66. [PMID: 32255304 DOI: 10.7754/clin.lab.2019.190649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Polyploidy is a rare lethal cytogenetic anomaly in pregnancies, generally leading to pregnancy termination. This study aims to compare first and second trimester polyploidy in pregnancies and describe the underlying mechanisms. METHODS A retrospective study was conducted in three medical genetics laboratories, collecting cases from Eastern, Southern, and Western Romania. The period of interest was January 2008 to December 2018. Prenatal samples (chorionic villi and amniotic fluid) and miscarriage samples were tested by standard karyotyping, as well as QF-PCR or FISH as complementary or alternative techniques. RESULTS In first trimester pregnancies, we report cytogenetic results of chorionic villi samples from miscarriages: 25 triploid cases and 13 tetraploid cases. In second trimester samples obtained by amniocentesis, cytogenetic findings were positive for 17 triploid cases. Maternal age, age of the pregnancy, and fetal gender identified by ultrasound were recorded in all cases and, additionally, data on biochemical risk and ultrasonographic findings for second trimester pregnancies. CONCLUSIONS Cytogenetic investigations of spontaneous abortions provide valuable information on the cause of abortion. This information is crucial for genetic counseling and may also contribute to prenatal diagnosis in subsequent pregnancies.
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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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17
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Matoulek D, Borůvková V, Ocalewicz K, Symonová R. GC and Repeats Profiling along Chromosomes-The Future of Fish Compositional Cytogenomics. Genes (Basel) 2020; 12:50. [PMID: 33396302 PMCID: PMC7823971 DOI: 10.3390/genes12010050] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.
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Affiliation(s)
- Dominik Matoulek
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Veronika Borůvková
- Faculty of Science, University of Hradec Kralove, 500 03 Hradec Králové, Czech Republic; (D.M.); (V.B.)
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, 80-309 Gdansk, Poland;
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 80333 Freising, Germany
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18
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Hao M, Li L, Zhang H, Li L, Liu R, Yu Y. The difference between karyotype analysis and chromosome microarray for mosaicism of aneuploid chromosomes in prenatal diagnosis. J Clin Lab Anal 2020; 34:e23514. [PMID: 32864771 PMCID: PMC7755766 DOI: 10.1002/jcla.23514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To compare karyotype and chromosomal microarray (CMA) analysis of aneuploid chromosome mosaicism in amniocentesis samples. MATERIALS AND METHODS A total of 2091 amniocentesis samples from pregnant women were collected from March 1, 2019, to January 31, 2020. Karyotype analysis was performed using G-banding and CMA analysis used the Affymetrix CytoScan 750K SNP microarray. RESULT Thirteen cases with aneuploid chromosome mosaicism were detected and compared between the karyotype and CMA methods. Seven of these cases were trisomic mosaicism, and the levels of mosaicism calculated from CMA were higher than those detected from karyotype analysis; noting three cases of trisomy mosaicism were not detected by karyotype analysis. Four cases exhibited monomeric mosaicism, and the levels of mosaicism detected in three of these cases were higher in karyotype compared with CMA analysis; one case had equivalent levels of monomeric mosaicism from both karyotype and CMA analysis. Two other cases from karyotype analysis were a mix of monosomic and trisomic mosaicism, whereas the CMA result was restricted to monosomic mosaicism for these cases. CONCLUSION Both karyotype and CMA analysis can be used to detect aneuploid chromosome mosaicism. However, the two methods produced different results. CMA and karyotype analysis have their own advantages in detecting aneuploid mosaicism, and the combination of these methods provides a more rigorous diagnosis.
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Affiliation(s)
- MengZhe Hao
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - LeiLei Li
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Han Zhang
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - LinLin Li
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Ruizhi Liu
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
| | - Yang Yu
- Center for Reproductive MedicineCenter for Prenatal DiagnosisThe First Hospital of Jilin UniversityChangchunChina
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19
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Biltueva LS, Prokopov DY, Romanenko SA, Interesova EA, Schartl M, Trifonov VA. Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon ( Acipenser baerii). Genes (Basel) 2020; 11:E1375. [PMID: 33233736 PMCID: PMC7699875 DOI: 10.3390/genes11111375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 01/05/2023] Open
Abstract
Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.
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Affiliation(s)
- Larisa S. Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave., 8/2, 630090 Novosibirsk, Russia; (L.S.B.); (S.A.R.); (V.A.T.)
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave., 8/2, 630090 Novosibirsk, Russia; (L.S.B.); (S.A.R.); (V.A.T.)
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave., 8/2, 630090 Novosibirsk, Russia; (L.S.B.); (S.A.R.); (V.A.T.)
| | - Elena A. Interesova
- Department of Ichthyology and Hydrobiology, Tomsk State University, Lenin Ave, 36, 634050 Tomsk, Russia;
| | - Manfred Schartl
- Developmental Biochemistry, University of Wuerzburg, Biocenter, Am Hubland, 97074 Wuerzburg, Germany;
- Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, 419 Centennial Hall, San Marcos, TX 78666-4616, USA
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave., 8/2, 630090 Novosibirsk, Russia; (L.S.B.); (S.A.R.); (V.A.T.)
- Novosibirsk State University, Novosibirsk, Pirogova, 2, 630090 Novosibirsk, Russia
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Jiang M, Wang S, Li F, Geng J, Ji Y, Li K, Jiang X. A novel 1p33p32.2 deletion involving SCP2, ORC1, and DAB1 genes in a patient with craniofacial dysplasia, short stature, developmental delay, and leukoencephalopathy: A case report. Medicine (Baltimore) 2020; 99:e23033. [PMID: 33157955 PMCID: PMC7647596 DOI: 10.1097/md.0000000000023033] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Microdeletion syndromes occur from deletion of 5Mb of a chromosome in approximately 5% of patients with unexplained intellectual disability. Interstitial microdeletions at bands 1p33 and 1p32.2 of the short arm of chromosome 1 are rare and have not been previously reported in relation to disease. PATIENT CONCERNS We present a case of a 39-month boy with Pierre Robin sequence, development delay/intellectual disability, growth retardation, short stature, leukoencephalopathy, craniofacial dysplasia, and speech delay. The child was referred to the Child health care department in October 2014 for his delayed language development and aggravated aggression. DIAGNOSIS Molecular diagnostic testing with G-band karyotyping was normal but clinical microarray analysis detected a 10 Mb microdeletion at 1p33p32.2. INTERVENTIONS The patient received rehabilitation. OUTCOMES Three candidate genes were pinpointed to the deleted area, including ORC1, SCP2, and DAB1. Phenotype-genotype analysis suggested that these three genes are likely to be responsible for the main phenotypes observed in the patient, such as microcephaly, growth retardation, short stature, leukoencephalopathy, and development delay/intellectual disability. CONCLUSIONS The spectrum of phenotypes this case presented with are likely to be caused by 1p33p32.2 deletion which could represent a new microdeletion syndrome.
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Affiliation(s)
- Maoying Jiang
- Hangzhou Children's Hospital, Behavioral Pediatric Department &Child Primary Care Department, Hangzhou
| | - Shanlin Wang
- Hangzhou Children's Hospital, Behavioral Pediatric Department &Child Primary Care Department, Hangzhou
| | - Fei Li
- Developmental and Behavioral Pediatric Department & Child Primary Care Department, MOE-Shanghai Key Lab for Children's Enviromental Health, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai
| | - Juan Geng
- Hangzhou Joingenome Diagnostics, Hangzhou
| | - Yiting Ji
- Developmental and Behavioral Pediatric Department, Shanghai Children's Hospital, Affiliated To Shanghai Jiaotong University School of Medicine& MOE-Shanghai Key Lab for Children's Environmental Health, Shanghai, China
| | - Ke Li
- Developmental and Behavioral Pediatric Department, Shanghai Children's Hospital, Affiliated To Shanghai Jiaotong University School of Medicine& MOE-Shanghai Key Lab for Children's Environmental Health, Shanghai, China
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Hilger AC, Dworschak GC, Reutter HM. Lessons Learned from CNV Analysis of Major Birth Defects. Int J Mol Sci 2020; 21:ijms21218247. [PMID: 33153233 PMCID: PMC7663563 DOI: 10.3390/ijms21218247] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022] Open
Abstract
The treatment of major birth defects are key concerns for child health. Hitherto, for the majority of birth defects, the underlying cause remains unknown, likely to be heterogeneous. The implicated mortality and/or reduced fecundity in major birth defects suggest a significant fraction of mutational de novo events among the affected individuals. With the advent of systematic array-based molecular karyotyping, larger cohorts of affected individuals have been screened over the past decade. This review discusses the identification of disease-causing copy-number variations (CNVs) among individuals with different congenital malformations. It highlights the differences in findings depending on the respective congenital malformation. It looks at the differences in findings of CNV analysis in non-isolated complex congenital malformations, associated with central nervous system malformations or intellectual disabilities, compared to isolated single organ-system malformations. We propose that the more complex an organ system is, and the more genes involved during embryonic development, the more likely it is that mutational de novo events, comprising CNVs, will confer to the expression of birth defects of this organ system.
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Affiliation(s)
- Alina Christine Hilger
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Gabriel Clemens Dworschak
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Heiko Martin Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
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22
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Schwabkey ZI, Al Ali N, Chan O, Sallman DA, Padron E, Kuykendall AT, Talati C, Sweet K, Lancet JE, Komrokji RS. Fluorescence in Situ Hybridization (FISH) Utility for Risk Score Assessment in Patients With MDS With Normal Metaphase Karyotype. Clin Lymphoma Myeloma Leuk 2020; 21:e52-e56. [PMID: 33093008 DOI: 10.1016/j.clml.2020.08.012] [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] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Cytogenetic profile is an essential parameter in myelodysplastic syndromes (MDS) risk stratification by both International Prognostic Symptom Score (IPSS) and Revised (R)-IPSS. Almost one-half of patients with MDS have normal cytogenetics by metaphase karyotype. Here we report the yield of MDS fluorescence in situ hybridization (FISH) panel detecting cytogenetic abnormalities in these patients and its impact on risk stratification. PATIENTS AND METHODS Among patients with normal metaphase karyotype, we assessed those patients who had cytogenetic abnormalities detected by an MDS FISH panel, which included probes for del (5), del (7), del (20), trisomy 8, and del (17p). Risk stratification was calculated by both IPSS and R-IPSS. RESULTS Of 1600 patients with MDS with normal metaphase karyotype, 53 (3%) patients had cytogenetic abnormality detected by MDS FISH panel. Integrating the MDS FISH panel cytogenetics (IPSS + FISH restaging) resulted in upstaging the score, where 53% of low-risk IPSS were upstaged to intermediate (int)-1, 56% of int-1 were upstaged to int-2, and 78% of int-2 were upstaged to high risk. Based on the R-IPSS, 61% of very low-risk patients, all low-risk patients, 92% of intermediate-risk patients, and 50% of high-risk patients with FISH abnormalities were upstaged, respectively. CONCLUSION The yield of MDS FISH panel detecting cytogenetic abnormalities in patients with normal karyotype by G-banding is low and may not warrant ordering the panel in all patients. Among the 3% of patients with normal karyotype who had cytogenetic abnormality detected by FISH, the risk score assignment by IPSS and R-IPSS was upstaged.
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Affiliation(s)
- Zaker I Schwabkey
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Najla Al Ali
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Onyee Chan
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - David A Sallman
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Eric Padron
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | | | - Chetasi Talati
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Kendra Sweet
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Jeffrey E Lancet
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL
| | - Rami S Komrokji
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL.
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Viana PF, Ezaz T, Cioffi MDB, Liehr T, Al-Rikabi A, Tavares-Pinheiro R, Bertollo LAC, Feldberg E. Revisiting the Karyotype Evolution of Neotropical Boid Snakes: A Puzzle Mediated by Chromosomal Fissions. Cells 2020; 9:cells9102268. [PMID: 33050432 PMCID: PMC7601083 DOI: 10.3390/cells9102268] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 11/16/2022] Open
Abstract
The Boidae family is an ancient group of snakes widely distributed across the Neotropical region, where several biogeographic events contributed towards shaping their evolution and diversification. Most species of this family have a diploid number composed of 2n = 36; however, among Booidea families, the Boidae stands out by presenting the greatest chromosomal diversity, with 2n ranging between 36 and 44 chromosomes and an undifferentiated XY sex chromosome system. Here, we applied a comparative chromosome analysis using cross-species chromosome paintings in five species representing four Boidae genera, to decipher the evolutionary dynamics of some chromosomes in these Neotropical snakes. Our study included all diploid numbers (2n = 36, 40, and 44) known for this family and our comparative chromosomal mappings point to a strong evolutionary relationship among the genera Boa, Corallus, Eunectes, and Epicrates. The results also allowed us to propose the cytogenomic diversification that had occurred in this family: a process mediated by centric fissions, including fission events of the putative and undifferentiated XY sex chromosome system in the 2n = 44 karyotype, which is critical in solving the puzzle of the karyotype evolution of boid snakes.
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Affiliation(s)
- Patrik F. Viana
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra 12 2616, ACT, Australia;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
- Correspondence: ; Tel.: +49-3641-9396850
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Rodrigo Tavares-Pinheiro
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Herpetologia, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Eliana Feldberg
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
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24
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Toren A, Alpern S, Berkenstadt M, Bar-Yosef O, Pras E, Katorza E. Chromosomal Microarray Evaluation of Fetal Ventriculomegaly. Isr Med Assoc J 2020; 22:639-644. [PMID: 33070489] [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: 06/11/2023]
Abstract
BACKGROUND Fetal ventriculomegaly is one of the more common fetal anomalies detected during prenatal screening. OBJECTIVES To assess the rate of genetic aberrations as the cause for ventriculomegaly in these fetuses. METHODS A historic cohort study was conducted on 164 fetuses with sonographic diagnosis of ventriculomegaly. All cases were analyzed for karyotype and 41 cases were further analyzed by chromosomal microarray (CMA). The study group was subdivided by laterality, severity, and whether the ventriculomegaly was an isolated finding or not. Subgroups were compared and the study group was compared to a control group of 209 fetuses. RESULTS Karyotype aberrations were more common among fetuses with ventriculomegaly (6.6%) compared to controls (0%, P < 0.001). CMA aberrations were more common in the non-isolated ventriculomegaly cases (24.1%) compared to controls (6.2%, P = 0.031). The rate of genetic aberrations was not associated with the degree of dilatation or laterality. CONCLUSIONS It is equivocal whether CMA testing should be conducted on every amniotic fluid sample taken from fetuses with isolated ventriculomegaly. However, if more anomalies are detected during an anatomical survey, CMA analysis should be conducted to decrease oversights of genetic diagnoses.
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Affiliation(s)
- Arik Toren
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Alpern
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Berkenstadt
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elon Pras
- Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eldad Katorza
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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25
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Imamura H, Monsieurs P, Jara M, Sanders M, Maes I, Vanaerschot M, Berriman M, Cotton JA, Dujardin JC, Domagalska MA. Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Sci Rep 2020; 10:15043. [PMID: 32929126 PMCID: PMC7490275 DOI: 10.1038/s41598-020-71882-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 02/21/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a pilot study paving the way for further single cell genomics studies in Leishmania. First, the performances of two commercially available kits for Whole Genome Amplification (WGA), PicoPLEX and RepliG were compared on small amounts of Leishmania donovani DNA, testing their ability to preserve specific genetic variations, including aneuploidy levels and SNPs. We show here that the choice of WGA method should be determined by the planned downstream genetic analysis, PicoPLEX and RepliG performing better for aneuploidy and SNP calling, respectively. This comparison allowed us to evaluate and optimize corresponding bio-informatic methods. As PicoPLEX was shown to be the preferred method for studying single cell aneuploidy, this method was applied in a second step, on single cells of L. braziliensis, which were sorted by fluorescence activated cell sorting (FACS). Even sequencing depth was achieved in 28 single cells, allowing accurate somy estimation. A dominant karyotype with three aneuploid chromosomes was observed in 25 cells, while two different minor karyotypes were observed in the other cells. Our method thus allowed the detection of aneuploidy mosaicism, and provides a solid basis which can be further refined to concur with higher-throughput single cell genomic methods.
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Affiliation(s)
- Hideo Imamura
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Pieter Monsieurs
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Marlene Jara
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | | | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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26
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Weng BH, Shen XY, Xu YL, Ying J, Xu W, Zou DB, He LM, Jin K, Li LJ. A Novel External Quality Assessment of Chromosomal Karyotype Analysis Based on Chimera Image Assembly. Ann Clin Lab Sci 2020; 50:674-680. [PMID: 33067215] [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 This study aimed to establish a new external quality assessment (EQA) of chromosomal karyotype analysis. METHODS Chimeric assembly A1 was established by collecting chimeric chromosome images prepared artificially from chromosomally abnormal amniocytes remaining after prenatal diagnosis. Chimeric assembly B1 and nonchimeric assembly C1 were constructed through the collection of chimeric and nonchimeric chromosome images from prenatal diagnosis, respectively. Then, chromosome images were selected randomly from assemblies A1, B1, or C1 to send to 20 technicians via email to verify the validity of a new EQA of chromosomal karyotype analysis. RESULTS According to the EQA of 20 technicians, 47,XX,+mar from assembly A was easily misdiagnosed as 47,XX,+19 or 47,XXY, and 45,XX,t(13;22) (q10;q10) was misdiagnosed as 45,XX,13S+,-22. The total misdiagnosis rate was 3.8%. For assembly B, 46,X,+mar and 46,X,idic(Y) were easily misdiagnosed as 46,XY and 46,X,+mar, respectively. In addition, some testers missed 47,XXX in 47,XXX[2]/46,XX[48], as well as 47,XX,+18 in 46,XX [47]/47,XX,+18[3], and 45,X and 47,XXX in 46,XX[47]/45,X[2]/47,XXX[1]. The total misdiagnosis rate was 4.2%. All karyo-types from assembly C were correctly diagnosed, although incorrect descriptions used for 4% of cases. CONCLUSION The quality of chromosome karyotype analysis can be comprehensively evaluated by a new EQA based on assembly A1 or B1.
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Affiliation(s)
- Bing-Huan Weng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical College, Zhejiang University, Hangzhou
- The Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Department of Obstetrics and Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou
| | - Xiao-Yun Shen
- Department of Experimental Research, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou
| | - Ya-Li Xu
- Department of Clinical Laboratory, Shulan Hospital, Zhejiang University, Hangzhou
| | - Jun Ying
- Department of Clinical Laboratory, Shulan Hospital, Zhejiang University, Hangzhou
| | - Wei Xu
- Department of Clinical Laboratory, Shulan Hospital, Zhejiang University, Hangzhou
| | - Duo-Bing Zou
- Department of Prenatal Diagnosis, Ningbo First Hospital, Ningbo, Zhejiang
| | - Li-Mei He
- Department of Clinical Laboratory, Shanghai Changning Maternity and Infant Health Hospital, Shanghai
| | - Keqin Jin
- Department of Genetics laboratory, Jinhua Women & Children Hospital, Zhejiang, JinHua, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical College, Zhejiang University, Hangzhou
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27
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Moura MN, Cardoso DC, Lima Baldez BC, Cristiano MP. Intraspecific variation in the karyotype length and genome size of fungus-farming ants (genus Mycetophylax), with remarks on procedures for the estimation of genome size in the Formicidae by flow cytometry. PLoS One 2020; 15:e0237157. [PMID: 32760102 PMCID: PMC7410318 DOI: 10.1371/journal.pone.0237157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
Ants (Formicidae) present considerable diversity in chromosome numbers, which vary from n = 1 to n = 60, although this variation is not proportional to that in genome size, for which estimates range from 0.18 pg to 0.77 pg. Intraspecific variation in the chromosome number and karyotype structure has been reported among species, although the variation among populations of the same species has received much less attention, and there are few data on genome size. Here, we studied the karyotype length and genome size of different populations of the fungus-farming ants Mycetophylax conformis (Mayr, 1884) and Mycetophylax morschi (Emery, 1888). We also provide remarks on procedure for the estimation of ant genome size by Flow Cytometry (FCM) analysis. Chromosome number and morphology did not vary among the populations of M. conformis or the cytotypes of M. morschi, but karyotype length and genome size were significantly distinct among the populations of these ants. Our results on the variation in karyotype length and genome size among M. morschi and M. conformis populations reveal considerable diversity that would be largely overlooked by more traditional descriptions of karyotypes, which were also supported by the estimates of genome size obtained using flow cytometry. Changes in the amount of DNA reflect variation in the fine structure of the chromosomes, which may represent the first steps of karyotype evolution and may occur previously to any changes in the chromosome number.
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Affiliation(s)
- Mariana Neves Moura
- Programa de Pós-graduação em Ecologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Danon Clemes Cardoso
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Brenda Carla Lima Baldez
- Programa de Pós-graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
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28
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Roodgar M, Babveyh A, Nguyen LH, Zhou W, Sinha R, Lee H, Hanks JB, Avula M, Jiang L, Jian R, Lee H, Song G, Chaib H, Weissman IL, Batzoglou S, Holmes S, Smith DG, Mankowski JL, Prost S, Snyder MP. Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. Gigascience 2020; 9:giaa069. [PMID: 32649757 PMCID: PMC7350979 DOI: 10.1093/gigascience/giaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/25/2019] [Revised: 02/27/2020] [Accepted: 06/02/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. RESULTS To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. CONCLUSIONS These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.
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Affiliation(s)
- Morteza Roodgar
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA
| | - Afshin Babveyh
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
| | - Lan H Nguyen
- Institute for computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Wenyu Zhou
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA
| | - Hayan Lee
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
| | - John B Hanks
- Stanford Research Computing Center, Stanford University, Stanford, CA 94305, USA
| | - Mohan Avula
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
| | - Lihua Jiang
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
| | - Hoyong Lee
- School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea
| | - Giltae Song
- School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea
| | - Hassan Chaib
- Stanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA
| | - Irv L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, 265 Campus Dr., Stanford University, Stanford, CA 94305, USA
| | - Serafim Batzoglou
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - David G Smith
- California National Primate Research Center, University of California, Davis, CA 95616, USA
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg 25, 60325 Frankfurt am Main, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Michael P Snyder
- Department of Genetics, 300 Pasteur Dr, Stanford University, Stanford, CA 94305, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, 3165 Porter Dr. Palo Alto, CA 94305, USA
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29
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Xie X, Tan W, Li F, Carrano E, Ramirez P, DiAdamo A, Grommisch B, Amato K, Chai H, Wen J, Li P. Diagnostic cytogenetic testing following positive noninvasive prenatal screening results of sex chromosome abnormalities: Report of five cases and systematic review of evidence. Mol Genet Genomic Med 2020; 8:e1297. [PMID: 32383339 PMCID: PMC7336728 DOI: 10.1002/mgg3.1297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 03/19/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Follow-up cytogenetic analysis has been recommended for cases with positive noninvasive prenatal screening (NIPS) results. This study of five cases with numerical and structural sex chromosomal abnormalities (SCA) and a review of large case series of NIPS provided guidance to improve prenatal diagnosis for SCA. METHODS Following positive NIPS results for SCA, karyotype analysis, chromosomal microarray analysis (CMA), fluorescence in situ hybridization (FISH), and locus-specific quantitative PCR were performed on cultured amniocytes, chorionic villi cells, and stimulated lymphocytes. Review of large case series was performed to evaluate the NIPS positive rate, follow-up rate of cytogenetic analysis, positive predictive value (PPV) for major types of SCA, and relative frequencies of subtypes of major SCA. RESULTS Of the five cases with positive NIPS for SCA, case 1 showed a mosaic pattern of monosomy X and isodicentric Y; case 2 showed a mosaic pattern of monosomy X confined to the placenta; cases 3 and 4 had an isochromosome of Xq, and case 5 showed a derivative chromosome 14 from a Yq/14p translocation of maternal origin. Review of literature showed that mean positive rate of NIPS for SCA was 0.61%, follow-up rate of cytogenetics analysis was 76%, and mean PPV for SCA was 48%. Mosaic patterns and structural rearrangements involving sex chromosomes were estimated in 3%-20% and 3% of SCA cases, respectively. CONCLUSION These five cases further demonstrated the necessity to pursue follow-up cytogenetic analysis to characterize mosaic patterns and structural abnormalities involving sex chromosomes and their value for prenatal genetic counseling. A workflow showing the performance of current NIPS and cytogenetic analysis for SCA was summarized. These results could facilitate an evidence-based approach to guide prenatal diagnosis of SCA.
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Affiliation(s)
- Xiaolei Xie
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Prenatal Diagnosis CenterThe Sixth Affiliated Hospital of Guangzhou Medical UniversityQingyuan People’s HospitalQingyuanGuangdongChina
| | - Weihe Tan
- Prenatal Diagnosis CenterThe Sixth Affiliated Hospital of Guangzhou Medical UniversityQingyuan People’s HospitalQingyuanGuangdongChina
| | - Fuguang Li
- Prenatal Diagnosis CenterThe Sixth Affiliated Hospital of Guangzhou Medical UniversityQingyuan People’s HospitalQingyuanGuangdongChina
| | - Eric Carrano
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Diagnostic Genetics Sciences ProgramUniversity of ConnecticutStorrsCTUSA
| | - Paola Ramirez
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Diagnostic Genetics Sciences ProgramUniversity of ConnecticutStorrsCTUSA
| | - Autumn DiAdamo
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | | | - Katherine Amato
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - Hongyan Chai
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - Jiadi Wen
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - Peining Li
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
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30
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Abstract
Tumors of the central nervous system (CNS) have been historically classified according to their morphologic and immunohistochemical features. In 2016, updates to the classification of tumors of the CNS by the World Health Organization revolutionized this paradigm. For the first time, genomic findings, whether whole-arm chromosomal aberrations or single nucleotide variants, represent a necessary and critical component of diagnosis, contributing or superseding histologic findings. These updates stem from decades of technical innovation and genomic discovery. During this time, there has been a dramatic expansion and evolution in clinical genomic assays for these tumors, informing diagnosis and guiding therapeutic management.
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Affiliation(s)
- Adrian M Dubuc
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
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31
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Jacobson JD, Willig LK, Gatti J, Strickland J, Egan A, Saunders C, Farrow E, Heckert LL. High Molecular Diagnosis Rate in Undermasculinized Males with Differences in Sex Development Using a Stepwise Approach. Endocrinology 2020; 161:5721303. [PMID: 32010941 DOI: 10.1210/endocr/bqz015] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022]
Abstract
Differences of sex development (DSDs) are a constellation of conditions that result in genital ambiguity or complete sex reversal. Although determining the underlying genetic variants can affect clinical management, fewer than half of undermasculinized males ever receive molecular diagnoses. Next-generation sequencing (NGS) technology has improved diagnostic capabilities in several other diseases, and a few small studies suggest that it may improve molecular diagnostic capabilities in DSDs. However, the overall diagnostic rate that can be achieved with NGS for larger groups of patients with DSDs remains unknown. In this study, we aimed to implement a tiered approach to genetic testing in undermasculinized males seen in an interdisciplinary DSD clinic to increase the molecular diagnosis rate in this group. We determined the diagnosis rate in patients undergoing all clinically available testing. Patients underwent a stepwise approach to testing beginning with a karyotype and progressing through individual gene testing, microarray, panel testing, and then to whole-exome sequencing (WES) if no molecular cause was found. Deletion/duplication studies were also done if deletions were suspected. Sixty undermasculinized male participants were seen in an interdisciplinary DSD clinic from 2008 to 2016. Overall, 37/60 (62%) of patients with Y chromosomes and 46% of those who were 46XY received molecular diagnoses. Of the 46,XY patients who underwent all available genetic testing, 18/28 (64%) achieved molecular diagnoses. This study suggests that the addition of WES testing can result in a higher rate of molecular diagnoses compared to genetic panel testing.
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Affiliation(s)
- Jill D Jacobson
- Division of Endocrinology and Diabetes, Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Laurel K Willig
- Division of Nephrology, Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
- Center for Pediatric Genomic Medicine Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - John Gatti
- Division of Urology, Department of Surgery, Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Julie Strickland
- Division of Pediatric and Adolescent Gynecology, Department of Surgery, Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Anna Egan
- Developmental and Behavioral Sciences, Department of Pediatrics, Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Carol Saunders
- Center for Pediatric Genomic Medicine Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Emily Farrow
- Center for Pediatric Genomic Medicine Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Leslie L Heckert
- Department of Molecular and Integrative Physiology, University of Kansas School of Medicine, Kansas City, Kansas
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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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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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Sember A, Pelikánová Š, de Bello Cioffi M, Šlechtová V, Hatanaka T, Do Doan H, Knytl M, Ráb P. Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae). Genes (Basel) 2020; 11:E479. [PMID: 32354012 PMCID: PMC7291238 DOI: 10.3390/genes11050479] [Citation(s) in RCA: 5] [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: 02/26/2020] [Revised: 03/31/2020] [Accepted: 04/24/2020] [Indexed: 11/30/2022] Open
Abstract
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping of multigene families and telomeric repeats. Both species shared (i) a diploid chromosome number 2n = 48 and the karyotype structure, (ii) low amount of constitutive heterochromatin, (iii) the absence of interstitial telomeric sites (ITSs), (iv) a single pair of 5S rDNA loci adjacent to one major rDNA cluster, and (v) a single pair of co-localized U1/U2 snDNA tandem repeats. Both species, on the other hand, differed in (i) the presence/absence of remarkable interstitial block of constitutive heterochromatin on the largest acrocentric pair 11 and (ii) the number of major (CMA3-positive) rDNA sites. Additionally, we applied here, for the first time, the conventional cytogenetics in H. harmandi, a species considered extinct in the wild and/or extensively cross-hybridized with H. molitrix. Its 2n and karyotype description match those found in the previous two species, while silver staining showed differences in distribution of major rDNA. The bighead carps thus represent another case of taxonomic diversity not associated with gross karyotype differentiation, where 2n and karyotype structure cannot help in distinguishing between genomes of closely related species. On the other hand, we demonstrated that two cytogenetic characters (distribution of constitutive heterochromatin and major rDNA) may be useful for diagnosis of pure species. The universality of these markers must be further verified by analyzing other pure populations of bighead carps.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Hiep Do Doan
- Research Institute of Aquaculture No. 1, Dinh Bang, Tu Son, Bac Ninh 16000, Vietnam
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 2-128-43 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
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Li L, He Z, Huang X, Lin S, Wu J, Huang L, Wan Y, Fang Q. Chromosomal abnormalities detected by karyotyping and microarray analysis in twins with structural anomalies. Ultrasound Obstet Gynecol 2020; 55:502-509. [PMID: 30977228 DOI: 10.1002/uog.20287] [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] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/19/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVES To evaluate the incidence and types of chromosomal abnormalities detected in twins with structural anomalies and compare their distribution according to chorionicity and amnionicity and by structural-anomaly type. The added value of chromosomal microarray analysis (CMA) over conventional karyotyping in twins was also estimated. METHODS This was a single-center, retrospective analysis of 534 twin pregnancies seen over an 11-year period, in which one or both fetuses were diagnosed with congenital structural anomalies on ultrasound. The ultrasound findings and invasive prenatal diagnostic results were reviewed. Twin pregnancies were categorized as monochorionic monoamniotic (MCMA), monochorionic diamniotic (MCDA) or dichorionic diamniotic (DCDA). Chromosomal abnormalities detected by G-banding karyotyping and/or CMA were analyzed by chorionicity and amnionicity and by structural-anomaly type. RESULTS The 534 twin pairs analyzed comprised 25 pairs of MCMA, 112 pairs of MCDA and 397 pairs of DCDA twins. Of the 549 fetuses affected by structural anomalies, 432 (78.7%) underwent invasive prenatal testing and cytogenetic results were obtained. The incidence of overall chromosomal abnormalities in the DCDA fetuses (25.4%) was higher than that in the MCMA (3.7%) and MCDA (15.3%) fetuses. The incidence of aneuploidy was significantly higher in the DCDA group (22.8%) than in the MCMA (0.0%) and MCDA (12.4%) groups. The incidence of chromosomal abnormalities detected in fetuses, with anomalies of the cardiovascular, faciocervical, musculoskeletal, genitourinary and gastrointestinal systems, was higher in the DCDA group than in the MCDA group. In both the DCDA and MCDA groups, hydrops fetalis was associated with the highest incidence of chromosomal abnormality; of these fetuses, 67.6% had Turner syndrome (45,X). Pathogenic copy-number variations (CNVs) undetectable by karyotyping were identified by CMA in five (2.0%; 95% CI, 0.3-3.7%) DCDA fetuses. No pathogenic CNVs were found in MCMA and MCDA twins. CONCLUSIONS Dichorionic twins with structural anomalies have a higher risk of chromosomal abnormalities, especially aneuploidies, than do monochorionic twins. The incremental diagnostic yield of CMA over karyotyping seems to be lower (2.0%) in twins than that reported in singleton pregnancy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- L Li
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Z He
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - X Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - S Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - J Wu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - L Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Y Wan
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Q Fang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Harshini V, Kumarasamy P, Karthickeyan SMK, Cauveri D, Gowri M, Rangasamy S. Ascertaining the paternal lineage in crossbred calves. J Genet 2020; 99:27. [PMID: 32482916] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Karyotyping is one among the culling parameter used for taking up culling decisions. Cytogenetic screening of breeding bulls has been recommended to screen for chromosomal abnormalities before semen production in artificial insemination. The chromosomal analysis of a Holstein Friesian crossbred bull revealed the presence of acrocentric Y-chromosome, which was further confirmed by CBG banding. The shape of the Y-chromosome determining that male line used for crossbreeding was from indigenous origin. Karyotyping is a best and reliable technique for the identification of crossbred calves born to the indigenous bulls.
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Affiliation(s)
- V Harshini
- Department of Animal Genetics and Breeding, Madras Veterinary College, Chennai 600 007, India.
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Boro N, Nabis Das B. Karyomorphology in two species of the genus Phlogacanthus Nees of Assam: some new karyological insights. J Genet 2020; 99:76. [PMID: 33168791] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The genus Phlogacanthus Nees belongs to the family Acanthaceae and is represented by herbs or shrubs species. The present work shows detailed karyomorphological studies in two species, Phlogacanthus quadrangularis (Hook.) Heine and Phlogacanthus guttatus Nees. Both the species grow as undergrowth vegetation. The conservation status of both the species are yet to be determined. The somatic chromosome counts of both the mentioned species are available for the first time, 2n = 40 for P. quadrangularis and 2n = 34 for P. guttatus. The karyomorphological observations showed that both plant species show dominance of sub-telocentric chromosomes with a few metacentric chromosomes. P. quadrangularis have telocentric chromosomes which is absent in the other species. The range of length of chromosomes in P. quadrangularis is from 0.340 lm to 1.32 lm and that of P. guttatus is from 0.560 lm to 1.878 lm. The karyotype type of the two species are classified as 3B type. But the dispersion index (DI) value of both the species are different. P. guttatus shows higher value of DI than P. quadrangularis. Higher the DI value more specialized is the karyotype. By comparing the chromosome length, size, DI value and idiogram of both the species, it is concluded that the karyotype of P. guttatus is more asymmetric and advanced than karyotype of P. quadrangularis. The karyomorphological findings of the present study will aid in determining the importance and utility, ex-situ conservation, protection, preservation and regeneration of germplasm.
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Affiliation(s)
- Neetumalata Boro
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141 004, India.
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Méndez-Rosado LA, Quiñones-Masa O, Vaglio A, Quadrelli R, Sanchez-Peñarate D, Soriano-Torres M, Cerrillo-Hinojosa M, Escobedo-Aguirre F, Gutiérrez-Nájar A, Venegas-Barbosa P, Barrios-Martinez A, Echavarría-Estenoz D, Carbonell-de la Torre P, Pimentel-Benitez HI, González-Salé O, Hernádez-Gil J, de la Torre-Santos ME, Alonso-García Y, Cedeño-Aparicio N, Torriani-Mendoza P, Morales-Rodríguez E, Martín-García D, Cuétara-Lugo E, González-Domínguez N. Antenatal Diagnosis of De Novo Balanced Structural Chromosome Aberrations in Latin America. MEDICC Rev 2019; 20:27-34. [PMID: 31242169 DOI: 10.37757/mr2018.v20.n4.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
INTRODUCTION The consequences of de novo balanced structural chromosome aberrations diagnosed antenatally are unpredictable, and, as a result, they introduce uncertainty into genetic counseling decisions. OBJECTIVE Describe de novo balanced structural aberrations present at antenatal diagnosis in samples from pregnant women in five Latin American countries and determine their effect on carrier individuals. METHODS This was a retrospective observational study based on analysis of 109,011 antenatal tests conducted from January 1981 to December 2016 in Cuba, Uruguay, Costa Rica, Mexico, and Colombia. Thirteen cytogenetic laboratories provided information that included the cases analyzed during the study period; number of de novo balanced structural aberrations diagnosed antenatally; number of diagnoses with de novo balanced structural aberrations that resulted in termination of pregnancy; detailed descriptions of the karyotypes of de novo balanced structural aberration carriers, and descriptions of the form of diagnosis, including types of samples used (amniotic fluid, chorionic villus or fetal blood). Each laboratory also provided pathology reports and genetic counseling at time of diagnosis. Postnatal followup for pregnancies carried to term continued for at least two years. RESULTS Of the 109,011 antenatal tests studied, 72 (0.07%) showed de novo balanced structural aberrations. These events primarily involved chromosomes 1, 2, 7, 14, 18, and 20. Of the 79 breakpoints identified, the most common were 5p15.3, 7q11.2, 7q22, and 14q24. We identified three breakpoints corresponding to 3.8% (3q13.1, 3q13.2, and 9p12) that were not reported in other studies of de novo balanced structural aberrations diagnosed antenatally in patients from other geographic regions or in studies of chromosomal fragile sites. Two of these breakpoints (3q13.1 and 3q13.2) were associated with high risk of phenotypic abnormalities. Information on antenatal or postnatal followup was available for 62 (86%) of de novo balanced structural aberration carriers; of the 44 carriers with postnatal followup, 10 had phenotypic abnormalities. CONCLUSIONS Three new de novo breakpoints were identified, presumably related to genetic admixture characteristics in Latin America. Since some diseases associated with de novo balanced structural aberrations detected antenatally have a late onset, followup for at least two years is recommended for carriers of these aberrations. The information in this study is useful in genetic counseling for pregnant women in Latin America.
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Tay Za K, Shanmugam H, Chin EFM. A new complex translocation (8;22;21)(q22;q12;q22) in RUNX1/RUNX1T1 acute myeloid leukaemia. Malays J Pathol 2019; 41:333-338. [PMID: 31901918] [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: 06/10/2023]
Abstract
INTRODUCTION Acute myeloid leukaemia (AML) with t(8;21)(q22;q22) producing RUNX1-RUNX1T1 rearrangement is a distinct sub-type which is usually associated with a favourable clinical outcome. Variant forms of t(8;21) are rare. Herein we describe a novel variant of t(8;21) AML in a 25-year-old pregnant woman who presented with intermittent fever. CASE REPORT Her peripheral smear and bone marrow aspirate showed many myeloblasts. Chromosomal study revealed t(8;22;21)(q22;q12;q22) and loss of X chromosome. Fluorescence in situ hybridization (FISH) using whole chromosome painting probes confirmed the three-way translocation involving chromosomes 8, 21 and 22. RUNX1-RUNX1T1 rearrangement was identified in FISH and reverse transcriptase polymerase chain reaction confirming the diagnosis of AML with variant t(8;21). The patient was treated with standard chemotherapy. She achieved morphological remission one month after induction chemotherapy. DISCUSSION Although the clinical significance of variant t(8;21) is not well delineated, the evaluation of 31 such cases suggests patients with variant t(8;21) have similar prognosis to those with classical t(8;21).
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Affiliation(s)
- K Tay Za
- University Malaya Medical Centre, Department of Pathology, Division of Laboratory Medicine, Kuala Lumpur, Malaysia.
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40
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He Y, Liu YH, Xie RG, Liu SA, Li DZ. Rare autosomal trisomies on non-invasive prenatal testing: not as adverse as expected. Ultrasound Obstet Gynecol 2019; 54:838-839. [PMID: 30887590 DOI: 10.1002/uog.20264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Y He
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - Y-H Liu
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - R-G Xie
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - S-A Liu
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - D-Z Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Castro JP, Hattori RS, Yoshinaga TT, Silva DMZDA, Ruiz-Ruano FJ, Foresti F, Santos MH, de Almeida MC, Moreira-Filho O, Artoni RF. Differential Expression of Genes Related to Sexual Determination Can Modify the Reproductive Cycle of Astyanax scabripinnis (Characiformes: Characidae) in B Chromosome Carrier Individuals. Genes (Basel) 2019; 10:E909. [PMID: 31717315 PMCID: PMC6896079 DOI: 10.3390/genes10110909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 10/04/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
The species complex Astyanax scabripinnis is one of the most studied with respect to origin, distribution, and frequency of B chromosomes, and is considered a model organism for evolutionary studies. Research using population inferences about the occurrence and frequency of the B chromosome shows seasonal variation between sexes, which is associated with the presence of this supernumerary element. We hypothesized that the B chromosome could influence the sex ratio of these animals. Based on this assumption, the present work aimed to investigate if differences exist among levels of gene expression with qRT-PCR of the amh (associated with testicular differentiation) and foxl2a (associated with ovarian differentiation) genes between B-carrier and non-B-carrier individuals. The results showed that for the amh gene, the difference in expression between animals with B chromosomes was not accentuated compared to that in animals without this chromosome. Expression of foxl2a in B-carrier females, however, was reduced by 73.56% compared to females that lacked the B chromosome. Males had no difference in expression of the amh and foxl2a genes between carriers and non-carriers of the B chromosome. Results indicate that the presence of B chromosomes is correlated with the differential expression of sex-associated genes. An analysis of these results integrated with data from other studies on the reproductive cycle in the same species reveals that this difference in expression may be expanding the reproductive cycle of the species.
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Affiliation(s)
- Jonathan Pena Castro
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
| | - Ricardo Shohei Hattori
- Estação Experimental de Salmonicultura de Campos do Jordão, UPD-CJ (APTA/SAA), Campos do Jordão, São Paulo, SP 12460-000, Brazil;
| | - Túlio Teruo Yoshinaga
- Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Departamento de Cirurgia, Universidade de São Paulo, Butantã, Rua Professor Orlando Marque Paiva, São Paulo, SP 05508-270, Brazil;
| | - Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP 18618-970, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Francisco J. Ruiz-Ruano
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP 18618-970, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
| | - Mara Cristina de Almeida
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
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Qin Y, Wen J, Zheng H, Huang X, Yang J, Song N, Zhu YM, Wu L, Yang GZ. Varifocal-Net: A Chromosome Classification Approach Using Deep Convolutional Networks. IEEE Trans Med Imaging 2019; 38:2569-2581. [PMID: 30908259 DOI: 10.1109/tmi.2019.2905841] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chromosome classification is critical for karyotyping in abnormality diagnosis. To expedite the diagnosis, we present a novel method named Varifocal-Net for simultaneous classification of chromosome's type and polarity using deep convolutional networks. The approach consists of one global-scale network (G-Net) and one local-scale network (L-Net). It follows three stages. The first stage is to learn both global and local features. We extract global features and detect finer local regions via the G-Net. By proposing a varifocal mechanism, we zoom into local parts and extract local features via the L-Net. Residual learning and multi-task learning strategies are utilized to promote high-level feature extraction. The detection of discriminative local parts is fulfilled by a localization subnet of the G-Net, whose training process involves both supervised and weakly supervised learning. The second stage is to build two multi-layer perceptron classifiers that exploit features of both two scales to boost classification performance. The third stage is to introduce a dispatch strategy of assigning each chromosome to a type within each patient case, by utilizing the domain knowledge of karyotyping. The evaluation results from 1909 karyotyping cases showed that the proposed Varifocal-Net achieved the highest accuracy per patient case (%) of 99.2 for both type and polarity tasks. It outperformed state-of-the-art methods, demonstrating the effectiveness of our varifocal mechanism, multi-scale feature ensemble, and dispatch strategy. The proposed method has been applied to assist practical karyotype diagnosis.
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Gökpınar İli E, Altıner Ş, Karabulut HG. Cytogenetic, Molecular, and Phenotypic Characterization of a Patient with de novo Derivative Chromosome 18 and Review of the Literature. Cytogenet Genome Res 2019; 159:74-80. [PMID: 31658462 DOI: 10.1159/000503574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 11/19/2022] Open
Abstract
We present a patient with a de novo derivative chromosome 18 which includes a terminal deletion of 18p and a terminal duplication of 18q accompanied by a cryptic duplication of 18p. The girl had mild dysmorphic features such as micro-retrognathia, upslanted palpebral fissures, bilateral epicanthus, high palate, low-set ears, short neck, and full cheeks. She also had an H-type tracheoesophageal fistula which required surgery. Her cognitive and motor skills were delayed. Karyotype analysis showed an additional segment on the short arm of chromosome 18. Chromosomal microarray revealed a 7.3-Mb terminal loss from 18p11.32 to 18p11.23, a 22.2-Mb terminal gain from 18q21.31 to 18q23, and a 3.9-Mb interstitial gain from 18p11.22 to 18p11.21. We hypothesize that the mother has gonadal mosaicism for normal chromosome 18, der(18)dup(p11.22p11.21), and der(18)dup(p11. 22p11.21)inv(18)(p11.22q21.31), or both the terminal del/dup and the interstitial duplication occurred simultaneously.
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Manhães VDC, de Miranda FD, Clarindo WR, Carrijo TT. Genetic diversity and karyotype of Pitcairnia azouryi: an endangered species of Bromeliaceae endemic to Atlantic Forest inselbergs. Mol Biol Rep 2019; 47:179-189. [PMID: 31587186 DOI: 10.1007/s11033-019-05118-6] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Abstract
Plant species of various families, such as those of Bromeliaceae, occur on inselbergs where they are subject to geographic isolation and environmental conditions that can lead to genetic erosion. This, in turn, can result in the loss of natural populations due to homozygosis, or changes in ploidy that may lead to reproductive isolation. The genetic diversity of five natural populations of Pitcairnia azouryi was measured using nine microsatellite markers transferred from P. albiflos and P. geyskesii. Chromosome numbers and nuclear DNA content were also evaluated. The results indicated moderate genetic differentiation among populations (FST = 0.188), and significant gene flow (Nm = 1.073) in four of the five populations. P. azouryi has, predominantly, 2n = 50 chromosomes and DNA content of 2C = 1.16 pg, but the tetraploid condition was found (2n = 100 and 2C = 2.32 pg) in seedlings of an individual of the most geographically isolated population. The moderate level of genetic structuring observed for P. azouryi seems to be related to its disjoint geographical distribution and the locally aggregated spatial structure of the populations, which are isolated from each other, hindering the inter and intrapopulational gene flow. This interpretation was also evidenced by the mantel test (r = 0.777, P < 0.05). The occurrence of diploid individuals with tetraploid seedlings is indicative of events of eupolyploidization, possibly due to the environmental conditions of this geographically isolated population.
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Affiliation(s)
- Vitor da Cunha Manhães
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil.
- Programa de Pós-graduação em Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, Rio De Janeiro, Rio de Janeiro, 20940-040, Brazil.
| | - Fábio Demolinari de Miranda
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
| | - Wellington Ronildo Clarindo
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
| | - Tatiana Tavares Carrijo
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
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Guterman S, Beneteau C, Redon S, Dupont C, Missirian C, Jaeger P, Herve B, Jacquin C, Douet-Guilbert N, Till M, Tabet AC, Moradkhani K, Malan V, Doco-Fenzy M, Vialard F. Prenatal findings in 1p36 deletion syndrome: New cases and a literature review. Prenat Diagn 2019; 39:871-882. [PMID: 31172545 DOI: 10.1002/pd.5498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/19/2018] [Revised: 03/21/2019] [Accepted: 05/18/2019] [Indexed: 11/12/2022]
Abstract
OBJECTIVE/METHOD 1p36 deletion syndrome is considered to be the most common deletion after 22q11.2 deletion. It is characterized by specific facial features, developmental delay, and organ defects. The primary objective of the present multicenter study was to survey all the cases of 1p36 deletion diagnosed prenatally by French cytogenetics laboratories using a chromosomal microarray. We then compared these new cases with the literature data. RESULTS Ten new cases were reported. On average, the 1p36 deletion was diagnosed at 19 weeks of gestation. The size of the deletion ranged from 1.6 to 16 Mb. The 1p36 deletion was the only chromosomal abnormality in eight cases and was associated with a complex chromosome 1 rearrangement in the two remaining cases. The invasive diagnostic procedure had always been prompted by abnormal ultrasound findings: elevated nuchal translucency, structural brain abnormality, retrognathia, or a cardiac defect. Multiple anomalies were present in all cases. DISCUSSION We conclude that 1p36 deletion is not associated with any specific prenatal signs. We suggest that a prenatal observation of ventriculomegaly, congenital heart defect, or facial dysmorphism should prompt the clinician to consider a diagnosis of 1p36 deletion syndrome.
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Affiliation(s)
- Sarah Guterman
- Fédération de Génétique, Centre Hospitalier Intercommunal Poissy-St-Germain-en-Laye, Poissy, France
- EA-7404-GIG, UFR des Sciences de la santé Simone VEIL, UVSQ, Montigny le Bretonneux, France
| | - Claire Beneteau
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Sylvia Redon
- Laboratoire de Génétique Moléculaire, CHU de Brest, Brest, France
| | - Céline Dupont
- Unité de Cytogénétique, Hôpital Robert Debré, Paris, France
| | - Chantal Missirian
- Unité de Génétique Clinique, CHU Marseille-Hôpital de la Timone, Marseille, France
| | - Pauline Jaeger
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - Berenice Herve
- Fédération de Génétique, Centre Hospitalier Intercommunal Poissy-St-Germain-en-Laye, Poissy, France
- EA-7404-GIG, UFR des Sciences de la santé Simone VEIL, UVSQ, Montigny le Bretonneux, France
| | | | | | - Marianne Till
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | | | | | - Valérie Malan
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Martine Doco-Fenzy
- Service de Génétique, CHU de Reims, Reims, France
- EA3801, SFR CAP Santé, Reims, France
| | - François Vialard
- Fédération de Génétique, Centre Hospitalier Intercommunal Poissy-St-Germain-en-Laye, Poissy, France
- EA-7404-GIG, UFR des Sciences de la santé Simone VEIL, UVSQ, Montigny le Bretonneux, France
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Soares AR, Soares G, Mota-Freitas M, Oliva-Teles N, Fortuna AM. Subtelomeric Rearrangements: Presentation of 21 Probands with Emphasis on Familial Cases. ACTA MEDICA PORT 2019; 32:529-535. [PMID: 31445533 DOI: 10.20344/amp.11466] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Intellectual disability affects 2% - 3% of the general population, with a chromosomal abnormality being found in 4% - 28% of these patients and a cryptic subtelomeric abnormality in 3% - 16%. In most cases, these subtelomeric rearrangements are submicroscopic, requiring techniques other than conventional karyotype for detection. They may be de novo or inherited from an affected parent or from a healthy carrier of a balanced chromosomal abnormality. The aim of this study was to characterize patients from our medical genetics center, in whom both a deletion and duplication in subtelomeric regions were found. MATERIAL AND METHODS Clinical and cytogenetic characterization of 21 probands followed at our center, from 1998 until 2017, with subtelomeric rearrangements. RESULTS There were 21 probands from 19 families presenting with intellectual disability and facial dysmorphisms. Seven had behavior changes, five had epilepsy and 14 presented with some other sign or symptom. Four had chromosomal abnormalities detected by conventional karyotype and four were diagnosed by array-comparative genomic hybridization. In four cases, parental studies were not possible. The online mendelian inheritance in man classification was provided whenever any of the phenotypes (deletion or duplication syndrome) was dominant. DISCUSSION Patients and relevant family members were clinically and cytogenetically characterized. Although rare, subtelomeric changes are a substantial cause of syndromic intellectual disability with important familial repercussions. It is essential to remember that a normal array-comparative genomic hybridization result does not exclude a balanced rearrangement in the parents. CONCLUSION Parental genetic studies are essential not only for a complete characterization of the rearrangement, but also for accurate genetic counselling and screening of family members at risk for recurrence.
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Affiliation(s)
- Ana Rita Soares
- Unidade de Genética Médica. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. Portugal
| | - Gabriela Soares
- Unidade de Genética Médica. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. Portugal
| | - Manuela Mota-Freitas
- Unidade de Citogenética. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. Unidade Multidisciplinar de Investigação Biomédica. Instituto de Ciências Biomédicas Abel Salazar. Universidade do Porto. Porto. Portugal
| | - Natália Oliva-Teles
- Unidade de Citogenética. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. 3. Unidade Multidisciplinar de Investigação Biomédica. Instituto de Ciências Biomédicas Abel Salazar. Universidade do Porto. Porto. Portugal
| | - Ana Maria Fortuna
- Unidade de Genética Médica. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. Unidade de Citogenética. Centro de Genética Médica Jacinto Magalhães. Centro Hospitalar Universitário do Porto. Porto. Portugal
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Iannucci A, Altmanová M, Ciofi C, Ferguson-Smith M, Milan M, Pereira JC, Pether J, Rehák I, Rovatsos M, Stanyon R, Velenský P, Ráb P, Kratochvíl L, Johnson Pokorná M. Conserved sex chromosomes and karyotype evolution in monitor lizards (Varanidae). Heredity (Edinb) 2019; 123:215-227. [PMID: 30670841 PMCID: PMC6781170 DOI: 10.1038/s41437-018-0179-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 09/15/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022] Open
Abstract
Despite their long history with the basal split dating back to the Eocene, all species of monitor lizards (family Varanidae) studied so far share the same chromosome number of 2n = 40. However, there are differences in the morphology of the macrochromosome pairs 5-8. Further, sex determination, which revealed ZZ/ZW sex microchromosomes, was studied only in a few varanid species and only with techniques that did not test their homology. The aim of this study was to (i) test if cryptic interchromosomal rearrangements of larger chromosomal blocks occurred during the karyotype evolution of this group, (ii) contribute to the reconstruction of the varanid ancestral karyotype, and (iii) test homology of sex chromosomes among varanids. We investigated these issues by hybridizing flow sorted chromosome paints from Varanus komodoensis to metaphases of nine species of monitor lizards. The results show that differences in the morphology of the chromosome pairs 5-8 can be attributed to intrachromosomal rearrangements, which led to transitions between acrocentric and metacentric chromosomes in both directions. We also documented the first case of spontaneous triploidy among varanids in Varanus albigularis. The triploid individual was fully grown, which demonstrates that polyploidization is compatible with life in this lineage. We found that the W chromosome differs between species in size and heterochromatin content. The varanid Z chromosome is clearly conserved in all the analyzed species. Varanids, in addition to iguanas, caenophidian snakes, and lacertid lizards, are another squamate group with highly conserved sex chromosomes over a long evolutionary time.
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Affiliation(s)
- Alessio Iannucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Marie Altmanová
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Claudio Ciofi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Malcolm Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Jorge Claudio Pereira
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, United Kingdom
| | - James Pether
- Reptilandia Park, Galdar, 35460, Gran Canaria, Spain
| | - Ivan Rehák
- Prague Zoological Garden, U Trojského zámku 120/3, 171 00, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy
| | - Petr Velenský
- Prague Zoological Garden, U Trojského zámku 120/3, 171 00, Prague, Czech Republic
| | - Petr Ráb
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic.
| | - Martina Johnson Pokorná
- Department of Ecology, Charles University, Viničná 7, 128 00, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
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Lapresa Alcalde MV, Cubo AM, Martín Seisdedos MC, Cortejoso Hernández J, Doyague Sanchez MJ, Sayagués JM. Ductus Venosus Agenesis as a Marker of Pallister-Killian Syndrome. ACTA ACUST UNITED AC 2019; 55:medicina55070374. [PMID: 31311125 PMCID: PMC6681314 DOI: 10.3390/medicina55070374] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/02/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
The ductus venosus (DV) is a shunt that allows the direct flow of well-oxygenated blood from the umbilical vein (UV) to the coronary and cerebral circulation through the foramen ovale. Its agenesis has been associated with chromosomal abnormalities and rare genetic syndromes, structural defects, intrauterine growth restriction (IUGR) and even antepartum fetal demise. Pallister–Killian Syndrome (PKS) is a rare sporadic disorder with specific tissue mosaic distribution of an extra 12p isochromosome (i(12p)). Its main clinical features are moderate to severe intellectual disability/neuromotor delay, skin pigmentation abnormalities, typical facial appearance, variable association with multiple congenital malformations and epilepsy. Though prenatal findings (including congenital diaphragmatic hernia, ventriculomegaly, congenital heart disease, polyhydramnios, and rhizomelic shortening) have been described in literature, prenatal diagnosis is difficult as there are no associated identification signs no distinctive or pathognomonic signs, and some of these malformations are hard to identify prenatally. The tissue mosaicism linked to this syndrome and the decrease of the abnormal clone carrier of the i(p12) after successive trypsinizations of cultured cells makes the diagnosis even more challenging. We present the case of a 27.5 weeks pregnant woman with a fetal ductus venosus agenesis (DVA) as the main guide marker. To our knowledge this is the first case published in literature reporting a DVA as a guide sign to diagnose a complex condition as Pallister–Killian syndrome. We also underscore the key role of new genetic techniques as microarrays to avoid misdiagnosis when only a subtle sonographic sign is present in complex conditions like this.
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Affiliation(s)
- María Victoria Lapresa Alcalde
- Department of Obstetrics and Gynecology, University Hospital of Salamanca and IBSAL, Paseo San Vicente 58-182, 37007 Salamanca, Spain
| | - Ana María Cubo
- Department of Obstetrics and Gynecology, University Hospital of Salamanca and IBSAL, Paseo San Vicente 58-182, 37007 Salamanca, Spain.
| | | | - Javier Cortejoso Hernández
- Department of Obstetrics and Gynecology, University Hospital of Valladolid, Calle Rondilla Sta. Teresa, s/n, 47010 Valladolid, Spain
| | - María José Doyague Sanchez
- Department of Obstetrics and Gynecology, University Hospital of Salamanca and IBSAL, Paseo San Vicente 58-182, 37007 Salamanca, Spain
| | - José María Sayagués
- Department of Hematology, University Hospital of Salamanca and IBSAL, Paseo San Vicente 58-182, 37007 Salamanca, Spain
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Tidrenczel Z, Tardy EP, Pikó H, Sarkadi E, Böjtös I, Demeter J, Simon J, Kósa JP, Beke A. Prenatal Diagnosis of 4q Terminal Deletion and Review of the Literature. Cytogenet Genome Res 2019; 158:63-73. [PMID: 31261151 DOI: 10.1159/000500735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2019] [Indexed: 12/13/2022] Open
Abstract
Terminal deletion of chromosome 4 (4q deletion syndrome) is a rare genetic condition that is characterized by a broad clinical spectrum and phenotypic variability. Diagnosis of the distinct condition can be identified by conventional chromosome analysis and small deletions by novel molecular cytogenetic methods such as microarray comparative genome hybridization (aCGH). Prenatal diagnosis is challenging; to date 10 cases have been described. We report a prenatally diagnosed case of de novo 4q deletion syndrome confirmed by conventional karyotyping and FISH due to an elevated combined risk for Down syndrome and prenatal ultrasound findings. aCGH validated the diagnosis and offered exact characterization of the disorder. Cytogenetic and microarray results described a 4q32.1qter terminal deletion of the fetus. Prenatal ultrasound detected multiple nonstructural findings (micrognathia, choroid plexus cysts, echogenic fetal bowel, short femur, and cardiac axis deviation). Pregnancy was terminated at 20 weeks. In addition to the index patient, we reviewed the 10 prenatally published cases of 4q deletion syndrome in the literature and compared these with our results. We summarize the patients' characteristics and prenatal clinical findings. Alterations of maternal serum biochemical factors, an elevated combined risk for trisomies, and distinct ultrasonographic findings can often be observed in cases of prenatal 4q deletion syndrome and may facilitate the otherwise difficult prenatal diagnosis.
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50
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Santos W, Carneiro MS, do Amaral WN. Prenatal diagnosis of Pallister-Killian syndrome. Ultrasound Obstet Gynecol 2019; 54:137-138. [PMID: 30125405 DOI: 10.1002/uog.20092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Affiliation(s)
- W Santos
- Morgana Potrich University, Setor Mundinho, Mineiros/GO, Brazil
- Schola Fértile Medical Training, Setor Marista, Goiânia/GO, Brazil
| | - M S Carneiro
- Morgana Potrich University, Setor Mundinho, Mineiros/GO, Brazil
- Schola Fértile Medical Training, Setor Marista, Goiânia/GO, Brazil
| | - W N do Amaral
- Morgana Potrich University, Setor Mundinho, Mineiros/GO, Brazil
- Schola Fértile Medical Training, Setor Marista, Goiânia/GO, Brazil
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