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Macorano E, Gentile M, Stellacci G, Manzionna M, Mele F, Calvano M, Leonardelli M, Duma S, De Gabriele G, Cristalli A, Minella R, Di Fazio A, Introna F. 'Compressed Baby Head': A New 'Abusive Head Trauma' Entity? CHILDREN (BASEL, SWITZERLAND) 2023; 10:1003. [PMID: 37371236 DOI: 10.3390/children10061003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Child abuse represents an important issue in the medico-legal and social context. In the last few decades, various aspects and mechanisms have been identified in child abuse case studies; however, constant research is needed in the field. With this paper, the authors will present a case of a new entity of Abusive Head Trauma that has come to the attention of medico-legal experts. DISCUSSION The trauma analysis performed on the cranio-encephalic district of the baby revealed quite peculiar lesions that led the authors to exclude that the injuries had been solely caused by violent shaking of the baby's head, as suggested by Shaken Baby Syndrome. Instead, the authors hypothesised that another lesion mechanism had been added to this one, namely latero-lateral cranial compression. The comprehensive and exhaustive analysis of the case led the authors to present a new possible entity in child abuse trauma, namely 'Compressed Baby Head'. CONCLUSIONS To the best of our knowledge, in the current literature, no similar clinical cases have ever been described. Thus, the case's uniqueness deserves to be brought to the attention of experts and the entire scientific community, as well as medical personnel, paediatricians, and reanimators. These professional figures are the first individuals who may encounter complex clinical cases such as the one presented in this paper; thus, they need to know how to properly manage the case and ensure protection for the abused infants and children.
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Affiliation(s)
- Enrica Macorano
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Mattia Gentile
- Medical Genetics, Maternal and Child Department, Hospital of Venus, 70012 Bari, Italy
| | | | - Mariano Manzionna
- Complex Operating Unit, Paediatric and Neonatology, San Paolo Hospital, ASL Bari, 70100 Bari, Italy
| | - Federica Mele
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Mariagrazia Calvano
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Mirko Leonardelli
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Stefano Duma
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Giovanni De Gabriele
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Alessandro Cristalli
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
| | - Raffaella Minella
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 5UX, UK
| | - Aldo Di Fazio
- Regional Complex Intercompany Institute of Legal Medicine, 85100 Potenza, Italy
| | - Francesco Introna
- Section of Legal Medicine, Interdisciplinary Department of Medicine, University of Bari 'Aldo Moro', 70124 Bari, Italy
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De Falco A, Iolascon A, Ascione F, Piscopo C. New Insights in 9q21.13 Microdeletion Syndrome: Genotype-Phenotype Correlation of 28 Patients. Genes (Basel) 2023; 14:genes14051116. [PMID: 37239476 DOI: 10.3390/genes14051116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
The implementation of array comparative genomic hybridisation (array-CGH) allows us to describe new microdeletion/microduplication syndromes which were previously not identified. 9q21.13 microdeletion syndrome is a genetic condition due to the loss of a critical genomic region of approximately 750kb and includes several genes, such as RORB and TRPM6. Here, we report a case of a 7-year-old boy affected by 9q21.13 microdeletion syndrome. He presents with global developmental delay, intellectual disability, autistic behaviour, seizures and facial dysmorphism. Moreover, he has severe myopia, which was previously reported in only another patient with 9q21.13 deletion, and brain anomalies which were never described before in 9q21.13 microdeletion syndrome. We also collect 17 patients from a literature search and 10 cases from DECIPHER database with a total number of 28 patients (including our case). In order to better investigate the four candidate genes RORB, TRPM6, PCSK5, and PRUNE2 for neurological phenotype, we make, for the first time, a classification in four groups of all the collected 28 patients. This classification is based both on the genomic position of the deletions included in the 9q21.3 locus deleted in our patient and on the different involvement of the four-candidate gene. In this way, we compare the clinical problems, the radiological findings, and the dysmorphic features of each group and of all the 28 patients in our article. Moreover, we perform the genotype-phenotype correlation of the 28 patients to better define the syndromic spectrum of 9q21.13 microdeletion syndrome. Finally, we propose a baseline ophthalmological and neurological monitoring of this syndrome.
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Affiliation(s)
- Alessandro De Falco
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare di Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy
| | - Achille Iolascon
- U.O.C. Genetica Medica, A.O.U. Federico II, 80131 Naples, Italy
- Dipartimento di Medicina Molecolare di Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80136 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Flora Ascione
- Hospital Directorate, A.O.R.N. "Antonio Cardarelli", 80100 Naples, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. "Antonio Cardarelli", 80100 Naples, Italy
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Lü Y, Jiang Y, Zhou X, Hao N, Lü G, Guo X, Guo R, Liu W, Xu C, Chang J, Li M, Zhang H, Zhou J, Zhang W(V, Qi Q. Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis. Diagnostics (Basel) 2023; 13:diagnostics13030560. [PMID: 36766665 PMCID: PMC9914714 DOI: 10.3390/diagnostics13030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. METHODS In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). RESULTS The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. CONCLUSION Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.
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Affiliation(s)
- Yan Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guizhen Lü
- AmCare Genomics Lab, Guangzhou 510335, China
| | | | - Ruidong Guo
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Wenjie Liu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Chenlu Xu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence: ; Tel.: +86-1851-066-6066
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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Zapata-García JA, Riveros-Magaña AR, Ortiz-Lazareno PC, Hernández-Flores G, Jave-Suárez LF, Aguilar-Lemarroy A. Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene. Diagnostics (Basel) 2022; 12:diagnostics12112788. [PMID: 36428851 PMCID: PMC9689318 DOI: 10.3390/diagnostics12112788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) in children or adults is characterized by structural and numeric aberrations in chromosomes; these anomalies strongly correlate with prognosis and clinical outcome. Therefore, this work aimed to identify the genes present in chromosomal gain regions found more frequently in patients with acute lymphoblastic leukemia (ALL) and ALL-derived cell lines using comparative genomic hybridization (CGH). In addition, validation of the genes found in these regions was performed utilizing RNAseq from JURKAT, CEM, and SUP-B15 cell lines, as well as expression microarrays derived from a MILE study. Chromosomes with common gain zones that were maintained in six or more samples were 14, 17, and 22, in which a total of 22 genes were identified. From them, NT5C3B, CNP, ACLY, and GNB1L maintained overexpression at the mRNA level in the cell lines and in patients with ALL. It is noteworthy that SALL2 showed very high expression in T-ALL, while JUP was highly expressed in B-ALL lineages. Interestingly, the latter correlated with worse survival in patients. This provided evidence that the measurement of these genes has high potential for clinical utility; however, their expressions should first be evaluated with a sensitive test in a more significant number of patients.
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Affiliation(s)
- Jessica Alejandra Zapata-García
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Alma Rocío Riveros-Magaña
- Centro Universitario del Sur, Universidad de Guadalajara, Ciudad Guzmán C.P. 49000, Mexico
- Hospital General Zona 9, Ciudad Guzmán C.P. 49000, Mexico
| | - Pablo Cesar Ortiz-Lazareno
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Georgina Hernández-Flores
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Luis Felipe Jave-Suárez
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
| | - Adriana Aguilar-Lemarroy
- Programa de Doctorado en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C.P. 44340, Mexico
- División de Inmunología, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara C.P. 44340, Mexico
- Correspondence: ; Tel.: +52-331-520-7625
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6
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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de Souza VS, da Cunha GCR, Versiani BR, de Oliveira CP, Rosa MTAS, de Oliveira SF, Moretti PN, Mazzeu JF, Pic-Taylor A. Characterization of Associated Nonclassical Phenotypes in Patients with Deletion in the WAGR Region Identified by Chromosomal Microarray: New Insights and Literature Review. Mol Syndromol 2022; 13:290-304. [PMID: 36158055 PMCID: PMC9421677 DOI: 10.1159/000518872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/03/2021] [Indexed: 01/03/2023] Open
Abstract
WAGR syndrome (Wilms' tumor, aniridia, genitourinary changes, and intellectual disability) is a contiguous gene deletion syndrome characterized by the joint deletion of PAX6 and WT1 genes, located in the short arm of chromosome 11. However, most deletions include other genes, leading to multiple associated phenotypes. Therefore, understanding how genes deleted together can contribute to other clinical phenotypes is still considered a challenge. In order to establish genotype-phenotype correlation in patients with interstitial deletions of the short arm of chromosome 11, we selected 17 patients with deletions identified by chromosomal microarray analysis: 4 new subjects and 13 subjects previously described in the literature with detailed clinical data. Through the analysis of deleted regions and the phenotypic changes, it was possible to suggest the contribution of specific genes to several nonclassical phenotypes, contributing to the accuracy of clinical characterization of the syndrome and emphasizing the broad phenotypic spectrum found in the patients. This study reports the first patient with a PAX6 partial deletion who does not present any eye anomaly thus opening a new set of questions about the functional activity of PAX6.
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Affiliation(s)
- Vanessa Sodré de Souza
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil
| | - Gabriela Corassa Rodrigues da Cunha
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil
| | - Beatriz R. Versiani
- Hospital de Apoio de Brasília, Secretária de Estado de Saúde do Distrito Federal, Brasília, Brazil,Hospital Universitário, Universidade de Brasília, Brasília, Brazil
| | - Claudiner Pereira de Oliveira
- Hospital de Apoio de Brasília, Secretária de Estado de Saúde do Distrito Federal, Brasília, Brazil,Hospital Universitário, Universidade de Brasília, Brasília, Brazil
| | - Maria Teresa Alves Silva Rosa
- Hospital Universitário, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil
| | - Silviene F. de Oliveira
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Patricia N. Moretti
- Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil
| | - Juliana F. Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil,Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil,*Juliana F. Mazzeu,
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil,**Aline Pic-Taylor,
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Perovic D, Damnjanovic T, Jekic B, Dusanovic-Pjevic M, Grk M, Djuranovic A, Rasic M, Novakovic I, Maksimovic N. Chromosomal microarray in postnatal diagnosis of congenital anomalies and neurodevelopmental disorders in Serbian patients. J Clin Lab Anal 2022; 36:e24441. [PMID: 35441737 PMCID: PMC9169173 DOI: 10.1002/jcla.24441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Background Array‐based genomic analysis is a gold standard for the detection of copy number variations (CNVs) as an important source of benign as well as pathogenic variations in humans. The introduction of chromosomal microarray (CMA) has led to a significant leap in diagnostics of genetically caused congenital malformations and neurodevelopmental disorders, with an average diagnostic yield of 15%. Here, we present our experience from a single laboratory perspective in four years’ postnatal clinical CMA application. Methods DNA samples of 430 patients with congenital anomalies and/or neurodevelopmental disorders were analyzed by comparative genome hybridization using oligonucleotide‐based microarray platforms. Interpretation of detected CNVs was performed according to current guidelines. The detection rate (DR) of clinically significant findings (pathogenic/likely pathogenic CNVs) was calculated for the whole cohort and isolated or combined phenotypic categories. Results A total of 140 non‐benign CNVs were detected in 113/430 patients (26.5%). In 70 patients at least one CNV was considered clinically significant thus reaching a diagnostic yield of 16.3%. The more complex the phenotype, including developmental delay/intellectual disability (DD/ID) as a prevailing feature, the higher the DR of clinically significant CNVs is obtained. Isolated congenital anomalies had the lowest, while the “dysmorphism plus” category had the highest diagnostic yield. Conclusion In our study, CMA proved to be a very useful method in the diagnosis of genetically caused congenital anomalies and neurodevelopmental disorders. DD/ID and dysmorphism stand out as important phenotypic features that significantly increase the diagnostic yield of the analysis.
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Affiliation(s)
- Dijana Perovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Tatjana Damnjanovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Biljana Jekic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Milka Grk
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ana Djuranovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Milica Rasic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Nela Maksimovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
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9
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Zhang X, Huang Q, Yu Z, Wu H. Copy number variation characterization and possible candidate genes in miscarriage and stillbirth by next-generation sequencing analysis. J Gene Med 2021; 23:e3383. [PMID: 34342101 PMCID: PMC9285438 DOI: 10.1002/jgm.3383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 12/17/2022] Open
Abstract
Background The present study aimed to explore the etiological relationship between miscarriage and stillbirth and copy number variations (CNVs), as well as provide useful genetic guidance for high‐risk pregnancy. Methods In total, 659 fetal samples were recruited and subjected to DNA extraction and CNV sequencing (CNV‐seq), relevant medical records were collected. Results There were 322 cases (48.86%) with chromosomal abnormalities, including 230 with numerical abnormalities and 92 with structural abnormalities. Chromosomal monosomy variations mainly occurred on sex chromosomes and trisomy variations mainly occurred on chromosomes 16, 22, 21, 18, 13 and 15. In total, 41 pathogenic CNVs (23 microdeletions and 18 microduplications) were detected in 27 fetal tissues. The rates of numerical chromosomal abnormalities were 29.30% (109/372), 32.39% (57/176) and 57.66% (64/111) in < 30‐year‐old, 30–34‐year‐old and ≥ 35‐year‐old age pregnant women, respectively, and increased with an increasing age (p < 0.001). There was statistically significant difference (χ2 = 7.595, p = 0.022) in the rates of structural chromosomal abnormalities in these groups (13.71%, 18.75% and 7.21%, respectively). The rates of numerical chromosomal abnormalities were 45.44% (219/482), 7.80% (11/141) and 0% (0/36) in the ≤ 13 gestational weeks, 14–27 weeks and ≥ 28 weeks groups, respectively, and decreased with respect to the increasing gestational age of the fetuses (p < 0.001). Conclusions The present study has obtained useful and accurate genetic etiology information that will provide useful genetic guidance for high‐risk pregnancies.
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Affiliation(s)
- Xia Zhang
- Center for Prenatal Disgnosis, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Heming Wu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
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10
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Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. Genes (Basel) 2021; 12:genes12071071. [PMID: 34356087 PMCID: PMC8305509 DOI: 10.3390/genes12071071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past 20 years, analyses of single brain cell genomes have revealed that the brain is composed of cells with myriad distinct genomes: the brain is a genomic mosaic, generated by a host of DNA sequence-altering processes that occur somatically and do not affect the germline. As such, these sequence changes are not heritable. Some processes appear to occur during neurogenesis, when cells are mitotic, whereas others may also function in post-mitotic cells. Here, we review multiple forms of DNA sequence alterations that have now been documented: aneuploidies and aneusomies, smaller copy number variations (CNVs), somatic repeat expansions, retrotransposons, genomic cDNAs (gencDNAs) associated with somatic gene recombination (SGR), and single nucleotide variations (SNVs). A catch-all term of DNA content variation (DCV) has also been used to describe the overall phenomenon, which can include multiple forms within a single cell’s genome. A requisite step in the analyses of genomic mosaicism is ongoing technology development, which is also discussed. Genomic mosaicism alters one of the most stable biological molecules, DNA, which may have many repercussions, ranging from normal functions including effects of aging, to creating dysfunction that occurs in neurodegenerative and other brain diseases, most of which show sporadic presentation, unlinked to causal, heritable genes.
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11
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Huebner T, Scholl C, Steffens M. Cytogenetic and Biochemical Genetic Techniques for Personalized Drug Therapy in Europe. Diagnostics (Basel) 2021; 11:diagnostics11071169. [PMID: 34206978 PMCID: PMC8303692 DOI: 10.3390/diagnostics11071169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with drugs centrally approved in the European Union (EU). We identified several methods and combinations of techniques registered in the Genetic Testing Registry (GTR), which can be used to guide therapy with drugs for which pharmacogenomic-related information is provided in the European public assessment reports. Although this registry provides information on genetic tests offered worldwide, we identified limitations regarding standard techniques applied in clinical practice and the information on test validity rarely provided in the according sections.
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12
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Identification of copy number variants by NGS-based NIPT at low sequencing depth. Eur J Obstet Gynecol Reprod Biol 2020; 256:297-301. [PMID: 33310305 DOI: 10.1016/j.ejogrb.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/20/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To explore the clinical utility of detecting chromosome copy number variants (CNVs) in the fetus by noninvasive prenatal testing (NIPT) using the low-pass whole-genome sequencing. METHODS Eight hundred and seventy-three singleton pregnancies with chromosomal microarray analysis (CMA) available between January 2017 to December 2019 and stored enough plasma sample for NIPT testing were included in this study. The CMA results show that forty-eight pregnancies with CNVs and eight hundred and twenty-five pregnancies are normal. Each pregnancy's plasma sample was blindly tested with NIPT at a depth of 0.51-1.19x for CNVs detection. The performance of the NIPT method for CNVs detection compared with the CMA method is evaluated. RESULTS A total of fifty-two CNVs ranging from 0.1-47.3 Mb identified in forty-eight samples were identified by NIPT, of which thirty-four CNVs were consistent with CMA results. Additionally, eighteen CNVs were missed by NIPT. The overall sensitivity and specificity for the detection of CNVs were 65.38% (95% CI: 51.76%-76.89%) and 97.45% (95% CI: 96.12%-98.35%), respectively. However, for the detection of CNVs larger than 2 Mb and CNVs less than 2Mb, the sensitivities were 81.58% (95% CI: 66.27%-91.09%) and 21.43% (95% CI: 6.84%-48.32%), respectively. CONCLUSION Our study demonstrated that the NIPT might be an alternative method for screening CNVs comparable with other studies. However, CNVs less than 2Mb in length shows poor sensitivity by NIPT. Noninvasive CNVs detection based on the NIPT method still needs more clinical validation studies and technical improvement to achieve clinically acceptable accuracy.
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13
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Advances in Genetic Characterization and Genotype-Phenotype Correlation of Duchenne and Becker Muscular Dystrophy in the Personalized Medicine Era. J Pers Med 2020; 10:jpm10030111. [PMID: 32899151 PMCID: PMC7565713 DOI: 10.3390/jpm10030111] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Currently, Duchenne muscular dystrophy (DMD) and the related condition Becker muscular dystrophy (BMD) can be usually diagnosed using physical examination and genetic testing. While BMD features partially functional dystrophin protein due to in-frame mutations, DMD largely features no dystrophin production because of out-of-frame mutations. However, BMD can feature a range of phenotypes from mild to borderline DMD, indicating a complex genotype–phenotype relationship. Despite two mutational hot spots in dystrophin, mutations can arise across the gene. The use of multiplex ligation amplification (MLPA) can easily assess the copy number of all exons, while next-generation sequencing (NGS) can uncover novel or confirm hard-to-detect mutations. Exon-skipping therapy, which targets specific regions of the dystrophin gene based on a patient’s mutation, is an especially prominent example of personalized medicine for DMD. To maximize the benefit of exon-skipping therapies, accurate genetic diagnosis and characterization including genotype–phenotype correlation studies are becoming increasingly important. In this article, we present the recent progress in the collection of mutational data and optimization of exon-skipping therapy for DMD/BMD.
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14
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Efficacy of emicizumab in a pediatric patient with type 3 von Willebrand disease and alloantibodies. Blood Adv 2020; 3:2748-2750. [PMID: 31540901 DOI: 10.1182/bloodadvances.2019000656] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/10/2019] [Indexed: 11/20/2022] Open
Abstract
Key Points
Type 3 von Willebrand disease with alloantibodies is a rare clinical entity with few treatment options. Emicizumab prophylaxis in such patients may result in improved hemarthrosis control, lower cost, and enhanced quality of life.
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15
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Dubucs C, Chassaing N, Sergi C, Aubert-Mucca M, Attié-Bitach T, Lacombe D, Thauvin-Robinet C, Arpin S, Perez MJ, Cabrol C, Chen CP, Aziza J, Colin E, Martinovic J, Calvas P, Plaisancié J. Re-focusing on Agnathia-Otocephaly complex. Clin Oral Investig 2020; 25:1353-1362. [PMID: 32643087 DOI: 10.1007/s00784-020-03443-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 07/03/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Agnathia-otocephaly complex is a rare condition characterized by mandibular hypoplasia or agnathia, ear anomalies (melotia/synotia) and microstomia with aglossia. This severe anomaly of the first branchial arch is most often lethal. The estimated incidence is less than 1 in 70.000 births, with etiologies linked to both genetic and teratogenic factors. Most of the cases are sporadic. To date, two genes have been described in humans to be involved in this condition: OTX2 and PRRX1. Nevertheless, the overall proportion of mutated cases is unknown and a significant number of patients remain without molecular diagnosis. Thus, the involvement of other genes than OTX2 and PRRX1 in the agnathia-otocephaly complex is not unlikely. Heterozygous mutations in Cnbp in mice are responsible for mandibular and eye defects mimicking the agnathia-otocephaly complex in humans and appear as a good candidate. Therefore, in this study, we aimed (i) to collect patients presenting with agnathia-otocephaly complex for screening CNBP, in parallel with OTX2 and PRRX1, to check its possible implication in the human phenotype and (ii) to compare our results with the literature data to estimate the proportion of mutated cases after genetic testing. MATERIALS AND METHODS In this work, we describe 10 patients suffering from the agnathia-otocephaly complex. All of them benefited from array-CGH and Sanger sequencing of OTX2, PRRX1 and CNBP. A complete review of the literature was made using the Pubmed database to collect all the patients described with a phenotype of agnathia-otocephaly complex during the 20 last years (1998-2019) in order (i) to study etiology (genetic causes, iatrogenic causes…) and (ii), when genetic testing was performed, to study which genes were tested and by which type of technologies. RESULTS In our 10 patients' cohort, no point mutation in the three tested genes was detected by Sanger sequencing, while array-CGH has allowed identifying a 107-kb deletion encompassing OTX2 responsible for the agnathia-otocephaly complex phenotype in 1 of them. In 4 of the 70 cases described in the literature, a toxic cause was identified and 22 out the 66 remaining cases benefited from genetic testing. Among those 22 patients, 6 were carrying mutation or deletion in the OTX2 gene and 4 in the PRRX1 gene. Thus, when compiling results from our cohort and the literature, a total of 32 patients benefited from genetic testing, with only 34% (11/32) of patients having a mutation in one of the two known genes, OTX2 or PRRX1. CONCLUSIONS From our work and the literature review, only mutations in OTX2 and PRRX1 have been found to date in patients, explaining around one third of the etiologies after genetic testing. Thus, agnathia-otocephaly complex remains unexplained in the majority of the patients, which indicates that other factors might be involved. Although involved in first branchial arch defects, no mutation in the CNBP gene was found in this study. This suggests that mutations in CNBP might not be involved in such phenotype in humans or that, unlike in mice, a compensatory effect might exist in humans. Nevertheless, given that agnathia-otocephaly complex is a rare phenotype, more patients have to be screened for CNBP mutations before we definitively conclude about its potential implication. Therefore, this work presents the current state of knowledge on agnathia-otocephaly complex and underlines the need to expand further the understanding of the genetic bases of this disorder, which remains largely unknown. CLINICAL RELEVANCE We made here an update and focus on the clinical and genetic aspects of agnathia-otocephaly complex as well as a more general review of craniofacial development.
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Affiliation(s)
- C Dubucs
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,Département d'Anatomie et de Cytologie Pathologiques, Institut Universitaire du cancer de Toulouse, Toulouse, France
| | - N Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, Université Toulouse III, Toulouse, France
| | - C Sergi
- Department of Lab. Med. & Pathology (5B4.09), University of Alberta, Edmonton, AB, Canada
| | - M Aubert-Mucca
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - T Attié-Bitach
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (APHP), Paris, France.,Institut Imagine, INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - D Lacombe
- Service de Génétique Médicale, CRMR, CHU de Bordeaux, Bordeaux, France.,INSERM U1211, Université de Bordeaux, 33076, Bordeaux, France
| | - C Thauvin-Robinet
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Dijon, Bourgogne, France.,Centre de Référence maladies rares "Anomalies du Développement et syndromes malformatifs," Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - S Arpin
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - M J Perez
- Department of Medical Genetics, Reference Center for Developmental Abnormalities and Constitutional Bone Diseases, CHRU, Montpellier, France
| | - C Cabrol
- Centre de Génétique Humaine, Centre Hospitalier Universitaire, Université de Franche-Comté, Besançon, France
| | - C P Chen
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City, Taiwan
| | - J Aziza
- Département d'Anatomie et de Cytologie Pathologiques, Institut Universitaire du cancer de Toulouse, Toulouse, France
| | - E Colin
- Department de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France.,UMR CNRS 6214-INSERM 1083 and PREMMI, Université d'Angers, Angers, France
| | - J Martinovic
- Unit of Fetal Pathology, AP-HP Antoine Béclère Hospital, Clamart, France
| | - P Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, Université Toulouse III, Toulouse, France
| | - Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France. .,INSERM U1056, Université Toulouse III, Toulouse, France.
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16
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Thomas R, Pontius JU, Borst LB, Breen M. Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers. Vet Sci 2020; 7:vetsci7030088. [PMID: 32645884 PMCID: PMC7560183 DOI: 10.3390/vetsci7030088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT,TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA;
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27606, USA
- Correspondence:
| | - Joan U Pontius
- Laboratory of Genomic Diversity, Basic Research Program, Science Applications International Corporation-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702, USA;
- Present address: JP Solutions, Ellicott City MD 21042, USA
| | - Luke B Borst
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA;
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA;
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27606, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27607, USA
- Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27514, USA
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17
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Wen G, Dang J, Xie Z, Wang J, Jiang P, Guo Q, Liang G. Molecular karyotypes of loquat ( Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity. PLANT METHODS 2020; 16:22. [PMID: 32123538 PMCID: PMC7041098 DOI: 10.1186/s13007-020-00568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. RESULTS Based on this imbalance in chromosome dosage, a new approach (referred to as 'SSR-qPCR') combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. CONCLUSION SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.
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Affiliation(s)
- Guo Wen
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Zhongyi Xie
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Jinying Wang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Pengfei Jiang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science for Southern Mountain Regions of Ministry of Education; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei, Chongqing, China
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18
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Scala M, Bianchi A, Bisulli F, Coppola A, Elia M, Trivisano M, Pruna D, Pippucci T, Canafoglia L, Lattanzi S, Franceschetti S, Nobile C, Gambardella A, Michelucci R, Zara F, Striano P. Advances in genetic testing and optimization of clinical management in children and adults with epilepsy. Expert Rev Neurother 2020; 20:251-269. [PMID: 31941393 DOI: 10.1080/14737175.2020.1713101] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Epileptic disorders are a heterogeneous group of medical conditions with epilepsy as the common denominator. Genetic causes, electro-clinical features, and management significantly vary according to the specific condition.Areas covered: Relevant diagnostic advances have been achieved thanks to the advent of Next Generation Sequencing (NGS)-based molecular techniques. These revolutionary tools allow to sequence all coding (whole exome sequencing, WES) and non-coding (whole genome sequencing, WGS) regions of human genome, with a potentially huge impact on patient care and scientific research.Expert opinion: The application of these tests in children and adults with epilepsy has led to the identification of new causative genes, widening the knowledge on the pathophysiology of epilepsy and resulting in therapeutic implications. This review will explore the most recent advancements in genetic testing and provide up-to-date approaches for the choice of the correct test in patients with epilepsy.
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Affiliation(s)
- Marcello Scala
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Amedeo Bianchi
- Division of Neurology, Hospital San Donato Arezzo, Arezzo, Italy
| | - Francesca Bisulli
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Bologna, Italy; Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Antonietta Coppola
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Maurizio Elia
- Unit of Neurology and Clinical Neurophysiopathology, IRCCS Oasi Research Institute, Troina, Italy
| | - Marina Trivisano
- Neurology Unit, Department of Neuroscience, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Clinic of Nervous System Diseases, University of Foggia, Foggia, Italy
| | - Dario Pruna
- Epilepsy Unit, A. Cao Hospital, Cagliari, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant' Orsola-Malpighi University Hospital, Bologna, Italy
| | | | - Simona Lattanzi
- Neurological Clinic, Department of Experimental and Clinical Medicine, Marche Polytechnic University, Ancona, Italy
| | | | - Carlo Nobile
- CNR-Neuroscience Institute and Department of Biomedical Sciences (C.N.), University of Padua, Padua, Italy
| | - Antonio Gambardella
- Dipartimento Di Scienze Mediche E Chirurgiche, Università Della Magna Graecia, Catanzaro, Istituto Di Scienze Neurologiche CNR Mangone, Cosenza, Italy
| | - Roberto Michelucci
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Ospedale Bellaria, Bologna, Italy
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
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19
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McClain L, Segreti AM, Nau S, Shaw P, Finegold DN, Pan LA, Peters DG. Chromosome 15q13.3 microduplications are associated with treatment refractory major depressive disorder. GENES BRAIN AND BEHAVIOR 2019; 19:e12628. [PMID: 31828948 DOI: 10.1111/gbb.12628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/18/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022]
Abstract
Major depressive disorder (MDD) affects approximately 15 million Americans. Approximately 2 million of these are classified as being refractory to treatment (TR-MDD). Because of the lack of available therapies for TR-MDD, and the high risk of suicide, there is interest in identifying new treatment modalities and diagnostic methods. Understanding of the impact of genomic copy number variation in the etiology of a variety of neuropsychiatric phenotypes is increasing. Low copy repeat elements at 15q13.3 facilitate non-allelic homologous recombination, resulting in recurrent copy number variants (CNVs). Numerous reports have described association between microdeletions in this region and a variety of neuropsychiatric phenotypes, with CHRNA7 implicated as a candidate gene. However, the pathogenicity of 15q13.3 duplications is less clear. As part of an ongoing study, in which we have identified a number of metabolomic anomalies in spinal fluid from TR-MDD patients, we also evaluated genomic copy number variation in patients (n = 125) and controls (n = 26) via array-based copy number genomic hybridization (CGH); the case frequency was compared with frequencies reported in a prior study as well as a larger population-sized cohort. We identified five TR-MDD patients with microduplications involving CHRNA7. CHRNA7 duplications are the most common CNVs identified by clinical CGH in this cohort. Therefore, this study provides insight into the potential involvement of CHRNA7 duplications in the etiology of TR-MDD and informs those involved with care of affected individuals.
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Affiliation(s)
- Lora McClain
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anna M Segreti
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sharon Nau
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patricia Shaw
- Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania
| | - David N Finegold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lisa A Pan
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David G Peters
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Magee-Womens Research Institute and Foundation, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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20
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Chau MHK, Cao Y, Kwok YKY, Chan S, Chan YM, Wang H, Yang Z, Wong HK, Leung TY, Choy KW. Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis. Am J Obstet Gynecol 2019; 221:493.e1-493.e11. [PMID: 31207233 DOI: 10.1016/j.ajog.2019.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution, and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications. OBJECTIVES The aim was to investigate the spectrum and characteristics of pathogenic copy number variants in prenatal genetic diagnosis and to provide recommendations for expanding the scope of noninvasive prenatal screening for microdeletions and microduplications. STUDY DESIGN This was a retrospective study of 1510 pregnant women who underwent invasive prenatal diagnostic testing by chromosomal microarray analysis. Prenatal samples were retrieved by amniocentesis or chorionic villus sampling and sent to our prenatal genetic diagnosis laboratory for chromosomal microarray analysis. The risk of carrying a fetus with pathogenic copy number variants is stratified by the patients' primary indication for invasive testing. We searched the literature for published prenatal chromosomal microarray data to generate a large cohort of 23,865 fetuses. The characteristics and spectrum of pathogenic copy number variants including the type of aberrations (gains or losses), genomic loci, sizes, and the mode of inheritance were studied. RESULTS Overall, 375 of 23,865 fetuses (1.6%) carried pathogenic copy number variants for any indication for invasive testing, and 44 of them (11.7%) involve 2 or more pathogenic copy number variants. A total of 428 pathogenic copy number variants were detected in these fetuses, of which 280 were deletions and 148 were duplications. Three hundred sixty (84.1%) were less than 5 Mb in size and 68 (15.9%) were between 5 and 10 Mb. The incidence of carrying a pathogenic copy number variant in the high-risk group is 1 in 36 and the low-risk group is 1 in 125. Parental inheritance study results were available for 311 pathogenic copy number variants, 71 (22.8%) were maternally inherited, 36 (11.6%) were paternally inherited, and 204 (65.6%) occurred de novo. CONCLUSION Collectively, pathogenic copy number variants are common in pregnancies. High-risk pregnancies should be offered invasive testing with chromosomal microarray analysis for the most comprehensive investigation. Detection limits on size, parental inheritance, and genomic distribution should be carefully considered before implementing copy number variant screening in expanded noninvasive prenatal screening.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne Ka Yin Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Samantha Chan
- Warwick Medical School at the University of Warwick, Coventry, United Kingdom
| | - Yiu Man Chan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Huilin Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research, and Transformation Team, Shenzhen, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenjun Yang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hoi Kin Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China.
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Zhang W, Li J, Salena B, Li Y. A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions. Chemistry 2019; 26:592-596. [PMID: 31475757 DOI: 10.1002/chem.201903536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/28/2019] [Indexed: 01/24/2023]
Abstract
DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.
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Affiliation(s)
- Wenqing Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Bruno Salena
- Department of Medicine, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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Balajee AS, Hande MP. History and evolution of cytogenetic techniques: Current and future applications in basic and clinical research. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:3-12. [PMID: 30389159 DOI: 10.1016/j.mrgentox.2018.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022]
Abstract
Chromosomes are the vehicles of genes, which are the functional units of a cell's nucleus. In humans, there are more than 20,000 genes that are distributed among 46 chromosomes in somatic cells. The study of chromosome structure and function is known as cytogenetics which is historically a field of hybrid science encompassing cytology and genetics. The field of cytogenetics has undergone rapid developments over the last several decades from classical Giemsa staining of chromosomes to 3-dimensional spatial organization of chromosomes with a high resolution mapping of gene structure at the nucleotide level. Improved molecular cytogenetic techniques have opened up exciting possibilities for understanding the chromosomal/molecular basis of various human diseases including cancer and tissue degeneration. This review summaries the history and evolution of various cytogenetic techniques and their current and future applications in diverse areas of basic research and medical diagnostics.
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Affiliation(s)
- Adayabalam S Balajee
- Cytogenetics Biodosimetry Laboratory, Radiation Emergency Assistance Center and Training Site, Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, 1299, Bethel Valley Road, Oak Ridge, TN 37830, USA.
| | - M Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine and Tembusu College, National University of Singapore, 117593, Singapore.
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