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Smith AC, Hoischen A, Raca G. Cytogenetics Is a Science, Not a Technique! Why Optical Genome Mapping Is So Important to Clinical Genetic Laboratories. Cancers (Basel) 2023; 15:5470. [PMID: 38001730 PMCID: PMC10670395 DOI: 10.3390/cancers15225470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Karyotyping is a technique that has been used in clinical cytogenetic laboratories for more than 40 years [...].
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Affiliation(s)
- Adam C. Smith
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander Hoischen
- Department of Human Genetics and Department of Internal Medicine, Research Institute for Medical Innovation, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, 6525 Nijmegen, The Netherlands;
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
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2
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Wan Mohamad Zamri WN, Mohd Yunus N, Abdul Aziz AA, Zulkipli NN, Sulong S. Perspectives on the Application of Cytogenomic Approaches in Chronic Lymphocytic Leukaemia. Diagnostics (Basel) 2023; 13:964. [PMID: 36900108 PMCID: PMC10001075 DOI: 10.3390/diagnostics13050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a haematological malignancy characterised by the accumulation of monoclonal mature B lymphocytes (positive for CD5+ and CD23+) in peripheral blood, bone marrow, and lymph nodes. Although CLL is reported to be rare in Asian countries compared to Western countries, the disease course is more aggressive in Asian countries than in their Western counterparts. It has been postulated that this is due to genetic variants between populations. Various cytogenomic methods, either of the traditional type (conventional cytogenetics or fluorescence in situ hybridisation (FISH)) or using more advanced technology such as DNA microarrays, next generation sequencing (NGS), or genome wide association studies (GWAS), were used to detect chromosomal aberrations in CLL. Up until now, conventional cytogenetic analysis remained the gold standard in diagnosing chromosomal abnormality in haematological malignancy including CLL, even though it is tedious and time-consuming. In concordance with technological advancement, DNA microarrays are gaining popularity among clinicians as they are faster and better able to accurately diagnose the presence of chromosomal abnormalities. However, every technology has challenges to overcome. In this review, CLL and its genetic abnormalities will be discussed, as well as the application of microarray technology as a diagnostic platform.
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Affiliation(s)
| | - Nazihah Mohd Yunus
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ahmad Aizat Abdul Aziz
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ninie Nadia Zulkipli
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Terengganu 21300, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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3
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Fu F, Li R, Dang X, Yu Q, Xu K, Gu W, Wang D, Yang X, Pan M, Zhen L, Zhang Y, Li F, Jing X, Li F, Li D, Liao C. Prenatal diagnosis of 21 fetuses with balanced chromosomal abnormalities (BCAs) using whole-genome sequencing. Front Genet 2022; 13:951829. [PMID: 36186435 PMCID: PMC9520355 DOI: 10.3389/fgene.2022.951829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Balanced chromosomal abnormalities (BCAs) are the most common chromosomal abnormalities and the frequency of congenital abnormalities is approximately twice as high in newborns with a de novo BCA, but a prenatal diagnosis based on BCAs is subject to evaluation. To detect translocation breakpoints and conduct a prenatal diagnosis, we performed whole-genome sequencing (WGS) in 21 subjects who were found BCAs, 19 balanced chromosome translocations and two inversions, in prenatal screening. In 16 BCAs on non-N-masked regions (non-NMRs), WGS detected 13 (81.2%, 13/16) BCAs, including all the inversions. All the breakpoints of 12 (12/14) cases of sufficient DNA were confirmed by Sanger sequencing. In 13 interrupted genes, CACNA1E (in case 12) and STARD7 (in case 17) are known causative and PDCL was found in subject (case 11) with situs inversus for the first time. Case 12 with abnormal ultrasound reached a definitive genetic diagnosis of CACNA1E-disease, while STARD7 exon deletion has never been found causative in patients. WGS provides the possibility of prenatal diagnosis in fetuses with BCAs, and its clinical significance also lies in providing data for postnatal diagnosis.
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Affiliation(s)
- Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Guangzhou Medical University, Guangzhou, China
- *Correspondence: Fang Fu, ; Can Liao,
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Xiao Dang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Qiuxia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Ke Xu
- Chigene (Beijing) Translational Medical Research Center Co,. Ltd., Beijing, China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co,. Ltd., Beijing, China
| | - Dan Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Yongling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Fatao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | | | - Fucheng Li
- Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- Guangzhou Medical University, Guangzhou, China
- *Correspondence: Fang Fu, ; Can Liao,
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Paneque M, Serra Juhé C, Melegh B, Carreira I, Moog U, Liehr T. Erratum zu: Über die Notwendigkeit der Anerkennung von sog. Kernberufsgruppen innerhalb der genetischen Gesundheitsversorgung in Europa. MED GENET-BERLIN 2022. [DOI: 10.1515/medgen-2022-2122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Milena Paneque
- i3S – Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
- IBMC – Institute for Molecular and Cell Biology , Universidade do Porto , Porto , Portugal
- Centre for Predictive and Preventive Genetics (CGPP) , Universidade do Porto , Porto , Portugal
| | - Clara Serra Juhé
- U705 CIBERER, Genetics Department, Hospital de la Santa Creu i Sant Pau , Universitat Autònoma de Barcelona , Barcelona , Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) , Madrid , Spain
| | - Bela Melegh
- Department of Medical Genetics , University of Pécs, School of Medicine , Pécs , Hungary
| | - Isabel Carreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Ute Moog
- Institut für Humangenetik , Universität Heidelberg , Heidelberg , Germany
| | - Thomas Liehr
- Universitätsklinik Jena , Friedrich Schiller Universität, Institut für Human Genetik , Jena , Germany
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Paneque M, Liehr T, Serra Juhé C, Moog U, Melegh B, Carreira I. The need for recognition of core professional groups in genetics healthcare services in Europe. Eur J Hum Genet 2022; 30:639-640. [PMID: 35283482 DOI: 10.1038/s41431-022-01080-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Milena Paneque
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IBMC-Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal. .,Centre for Predictive and Preventive Genetics (CGPP), Universidade do Porto, Porto, Portugal.
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Clara Serra Juhé
- U705 CIBERER, Genetics Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Bela Melegh
- Department of Medical Genetics, University of Pécs, School of Medicine, Pécs, Hungary
| | - Isabel Carreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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Paneque M, Serra Juhé C, Melegh B, Carreira I, Moog U, Liehr T. Über die Notwendigkeit der Anerkennung von sog. Kernberufsgruppen innerhalb der genetischen Gesundheitsversorgung in Europa. MED GENET-BERLIN 2022. [DOI: 10.1515/medgen-2022-2116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Milena Paneque
- i3S – Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
- IBMC – Institute for Molecular and Cell Biology , Universidade do Porto , Porto , Portugal
- Centre for Predictive and Preventive Genetics (CGPP) , Universidade do Porto , Porto , Portugal
| | - Clara Serra Juhé
- U705 CIBERER, Genetics Department, Hospital de la Santa Creu i Sant Pau , Universitat Autònoma de Barcelona , Barcelona , Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) , Madrid , Spain
| | - Bela Melegh
- Department of Medical Genetics , University of Pécs, School of Medicine , Pécs , Hungary
| | - Isabel Carreira
- Cytogenetics and Genomics Laboratory, CACC, iCBR/CIMAGO, CIBB, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Ute Moog
- Institut für Humangenetik , Universität Heidelberg , Heidelberg , Germany
| | - Thomas Liehr
- Universitätsklinik Jena , Friedrich Schiller Universität, Institut für Human Genetik , Jena , Germany
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Chehimi SN, Almeida VT, Nascimento AM, Zanardo ÉA, de Oliveira YG, Carvalho GFDS, Wolff BM, Montenegro MM, de Assunção NA, Kim CA, Kulikowski LD. Novel rearrangements between different chromosomes with direct impact on the diagnosis of 5p- syndrome. Clinics (Sao Paulo) 2022; 77:100045. [PMID: 35640457 PMCID: PMC9160337 DOI: 10.1016/j.clinsp.2022.100045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Copy Number Variations (CNVs) in the human genome account for common populational variations but can also be responsible for genetic syndromes depending on the affected region. Although a deletion in 5p is responsible for a syndrome with highly recognizable phenotypical features, other chromosomal abnormalities might overlap phenotypes, especially considering that most studies in 5p use traditional cytogenetic techniques and not molecular techniques. METHODS The authors have investigated 29 patients with clinical suspicion of 5p- syndrome using Chromosomal Microarray (CMA), and have gathered information on previous tests, clinical signs, symptoms, and development of the patients. RESULTS The results showed 23 pure terminal deletions, one interstitial deletion, one deletion followed by a 3 Mb duplication in 5p, three cases of 5p deletion concomitant to duplications larger than 20 Mb in chromosomes 2, 9, and 18, and one 5p deletion with a chromosome Y deletion. CMA showed relevant CNVs not typically associated with 5p- that may have contributed to the final phenotype in these patients. CONCLUSIONS The authors have identified three novel rearrangements between chromosomes 5 and 2 (Patient 27), 5 and 18 (Patient 11), and 5 and Y (Patient 22), with breakpoints and overlapped phenotypes that were not previously described. The authors also highlight the need for further molecular investigation using CMA, in different chromosomes beyond chromosome 5 (since those cases did not show only the typical deletion expected for the 5p- syndrome) to explain discordant chromosomal features and overlapped phenotypes to unravel the cause of the syndrome in atypical cases.
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Affiliation(s)
- Samar Nasser Chehimi
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil; Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil.
| | - Vanessa Tavares Almeida
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Amom Mendes Nascimento
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil; Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil
| | - Évelin Aline Zanardo
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Yanca Gasparini de Oliveira
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | | | - Beatriz Martins Wolff
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Marilia Moreira Montenegro
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Nilson Antônio de Assunção
- Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil; Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Chong Ae Kim
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil
| | - Leslie Domenici Kulikowski
- Laboratório de Citogenômica, Departmento de Patologia, Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil; Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HCFMUSP), São Paulo, SP, Brazil
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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9
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Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
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Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
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McNeill A. What's new in EJHG in April. Eur J Hum Genet 2021; 29:539-540. [PMID: 33837296 PMCID: PMC8035134 DOI: 10.1038/s41431-021-00841-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
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Szczerbal I, Switonski M. Clinical Cytogenetics of the Dog: A Review. Animals (Basel) 2021; 11:947. [PMID: 33801756 PMCID: PMC8066086 DOI: 10.3390/ani11040947] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
The dog is an important companion animal and has been recognized as a model in biomedical research. Its karyotype is characterized by a high chromosome number (2n = 78) and by the presence of one-arm autosomes, which are mostly small in size. This makes the dog a difficult subject for cytogenetic studies. However, there are some chromosome abnormalities that can be easily identified, such as sex chromosome aneuploidies, XX/XY leukocyte chimerism, and centric fusions (Robertsonian translocations). Fluorescence in situ hybridization (FISH) with the use of whole-chromosome painting or locus-specific probes has improved our ability to identify and characterize chromosomal abnormalities, including reciprocal translocations. The evaluation of sex chromosome complement is an important diagnostic step in dogs with disorders of sex development (DSD). In such cases, FISH can detect the copy number variants (CNVs) associated with the DSD phenotype. Since cancers are frequently diagnosed in dogs, cytogenetic evaluation of tumors has also been undertaken and specific chromosome mutations for some cancers have been reported. However, the study of meiotic, gamete, and embryo chromosomes is not very advanced. Knowledge of canine genome organization and new molecular tools, such as aCGH (array comparative genome hybridization), SNP (single nucleotide polymorphism) microarray, and ddPCR (droplet digital PCR) allow the identification of chromosomal rearrangements. It is anticipated that the comprehensive use of chromosome banding, FISH, and molecular techniques will substantially improve the diagnosis of chromosome abnormalities in dogs.
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Affiliation(s)
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland;
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Liehr T. About classical molecular genetics, cytogenetic and molecular cytogenetic data not considered by Genome Reference Consortium and thus not included in genome browsers like UCSC, Ensembl or NCBI. Mol Cytogenet 2021; 14:20. [PMID: 33743766 PMCID: PMC7981792 DOI: 10.1186/s13039-021-00540-7] [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: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background The Genome Reference Consortium (GRC) has according to its own statement the “mission to improve the human reference genome assembly, correcting errors and adding sequence to ensure it provides the best representation of the human genome to meet basic and clinical research needs”. Data from GRC is included in genome browsers like UCSC (University of California, Santa Cruz), Ensembl or NCBI (National Center for Biotechnology Information) and are thereby bases for scientific and diagnostically working human genetic community.
Method Here long standing knowledge deriving from classical molecular genetic, cytogenetic and molecular cytogenetic data, not being considered yet by GRC was revisited. Results There were three major points identified: (1) GRC missed to including three chromosomal subbands, each, for 1q32.1, 2p21, 5q13.2, 6p22.3 and 6q21, which were defined by International System for Human Cytogenetic Nomenclature (ISCN) already back in 1980s; instead GRC included additional 6 subbands not ever recognized by ISCN. (2) GRC defined 34 chromosomal subbands of 0.1 to 0.9 Mb in size, while it is general agreement of cytogeneticists that it unlikely to detect chromosomal aberrations below 1–2 Mb in size by GTG-banding. And (3): still all sequences used in molecular cytogenetic routine diagnostics to detect heterochromatic and/ or pericentromeric satellite DNA sequences within the human genome are not included yet into human reference genome. For those sequences, localization and approximate sizes have been determined in the 1970s to 1990, and if included at least ~ 100 Mb of the human genome sequence could be added to the genome browsers. Conclusion Overall, taking into account the here mentioned points and correcting and including the data will definitely provide to the still not being completely finished mapping of the human genome. Supplementary Information The online version contains supplementary material available at 10.1186/s13039-021-00540-7.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany.
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