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Quinodoz M, Kaminska K, Cancellieri F, Han JH, Peter VG, Celik E, Janeschitz-Kriegl L, Schärer N, Hauenstein D, György B, Calzetti G, Hahaut V, Custódio S, Sousa AC, Wada Y, Murakami Y, Fernández AA, Hernández CR, Minguez P, Ayuso C, Nishiguchi KM, Santos C, Santos LC, Tran VH, Vaclavik V, Scholl HPN, Rivolta C. Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads. Am J Hum Genet 2024; 111:701-713. [PMID: 38531366 PMCID: PMC11023916 DOI: 10.1016/j.ajhg.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Nils Schärer
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Daniela Hauenstein
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Bence György
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Vincent Hahaut
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Ana Cristina Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | | | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Almudena Avila Fernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Cristina Rodilla Hernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Cristina Santos
- NOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal; Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon, Portugal
| | | | - Viet H Tran
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Veronika Vaclavik
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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Eid MM, Eid OM, Abdelrahman AH, Abdelrahman IFS, Aboelkomsan EAF, AbdelKader RMA, Hassan M, Farid M, Ibrahim AA, Abd El-Fattah SN, Mahrous R. Detection of AZFc gene deletion in a cohort of Egyptian patients with idiopathic male infertility. J Genet Eng Biotechnol 2023; 21:111. [PMID: 37947911 PMCID: PMC10638347 DOI: 10.1186/s43141-023-00584-9] [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: 03/27/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND The deletions of azoospermic factor regions (AZF) are considered risk factor of spermatogenic failure. AZF duplications or complex copy number variants (CNVs) were rarely studied because STS-PCR could not always detect these changes. The application of multiplex ligation-dependent probe amplification (MLPA) as a valuable test for detection of the deletion and or duplication was introduced to investigate the AZF sub-region CNVs. The MLPA technique is still not applied on a large scale, and the publications in this area of research are limited. The aim of this work was to evaluate the efficacy of MLPA assay to detect AZF-linked CNVs in idiopathic spermatogenic failure patients and to evaluate its importance as a prognostic marker in the reproduction outcome. RESULTS Forty infertile men (37 with azoospermia and 3 with severe oligozoospermia) and 20 normal fertile men were subjected to thorough clinical, pathological, and laboratory assessment, chromosomal study, MLPA, STS-PCR assays, histopathology study, and testicular sperm retrieval (TESE). Out of the 40 patients, 7 patients have shown CNV in the AZFc region, 6 patients have partial deletion, and one patient has partial duplication. Only one of the normal control has AZFc duplication. STS-PCR was able to detect the deletion in only 4 out of the 7 positive patients and none of the control. CONCLUSION We concluded that MLPA should be applied on a larger scale for the detection of Y chromosome microdeletion as a rapid, efficient, and cheap test.
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Affiliation(s)
- Maha M Eid
- Human Cytogenetic Department, Human Genetics and Genome Research Institute, National Research Center, Bohouth Street, 12311 Dokki, Cairo, Egypt
| | - Ola M Eid
- Human Cytogenetic Department, Human Genetics and Genome Research Institute, National Research Center, Bohouth Street, 12311 Dokki, Cairo, Egypt.
| | - Amany H Abdelrahman
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute, National Research Center, Cairo, Egypt
| | | | | | - Rania M A AbdelKader
- Human Cytogenetic Department, Human Genetics and Genome Research Institute, National Research Center, Bohouth Street, 12311 Dokki, Cairo, Egypt
| | - Mirhane Hassan
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute, National Research Center, Cairo, Egypt
| | - Marwa Farid
- Human Cytogenetic Department, Human Genetics and Genome Research Institute, National Research Center, Bohouth Street, 12311 Dokki, Cairo, Egypt
| | - Alshaymaa A Ibrahim
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute, National Research Center, Cairo, Egypt
| | - Safa N Abd El-Fattah
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute, National Research Center, Cairo, Egypt
| | - Rana Mahrous
- Human Cytogenetic Department, Human Genetics and Genome Research Institute, National Research Center, Bohouth Street, 12311 Dokki, Cairo, Egypt
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Thomas CP, Daloul R, Lentine KL, Gohh R, Anand PM, Rasouly HM, Sharfuddin AA, Schlondorff JS, Rodig NM, Freese ME, Garg N, Lee BK, Caliskan Y. Genetic evaluation of living kidney donor candidates: A review and recommendations for best practices. Am J Transplant 2023; 23:597-607. [PMID: 36868514 DOI: 10.1016/j.ajt.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023]
Abstract
The growing accessibility and falling costs of genetic sequencing techniques has expanded the utilization of genetic testing in clinical practice. For living kidney donation, genetic evaluation has been increasingly used to identify genetic kidney disease in potential candidates, especially in those of younger ages. However, genetic testing on asymptomatic living kidney donors remains fraught with many challenges and uncertainties. Not all transplant practitioners are aware of the limitations of genetic testing, are comfortable with selecting testing methods, comprehending test results, or providing counsel, and many do not have access to a renal genetic counselor or a clinical geneticist. Although genetic testing can be a valuable tool in living kidney donor evaluation, its overall benefit in donor evaluation has not been demonstrated and it can also lead to confusion, inappropriate donor exclusion, or misleading reassurance. Until more published data become available, this practice resource should provide guidance for centers and transplant practitioners on the responsible use of genetic testing in the evaluation of living kidney donor candidates.
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Affiliation(s)
- Christie P Thomas
- Department of of Internal Medicine and Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA; VA Medical Center, Iowa City, Iowa, USA.
| | - Reem Daloul
- Division of Nephrology, Department of Internal Medicine, Allegheny General Hospital, Pittsburgh, Pennsylvania, USA
| | - Krista L Lentine
- Saint Louis University Transplant Center, SSM Health Saint Louis University Hospital, St. Louis, Missouri, USA
| | - Reginald Gohh
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Prince M Anand
- Mid-Carolinas Transplant Center, Medical University of South Carolina, Lancaster, South Carolina, USA
| | - Hila Milo Rasouly
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York City, New York, USA
| | - Asif A Sharfuddin
- Division of Nephrology and Transplant, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Johannes S Schlondorff
- Department of Internal Medicine, Ohio State University Medical Center, Columbus, Ohio, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Margaret E Freese
- Department of of Internal Medicine and Iowa Institute of Human Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Neetika Garg
- Division of Nephrology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Brian K Lee
- Kidney/Pancreas Transplant Center, Dell Seton Medical Center, University of Texas at Austin, Austin, Texas, USA
| | - Yasar Caliskan
- Saint Louis University Transplant Center, SSM Health Saint Louis University Hospital, St. Louis, Missouri, USA
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Salas-Huetos A, Aston KI. Defining new genetic etiologies of male infertility: progress and future prospects. Transl Androl Urol 2021; 10:1486-1498. [PMID: 33850783 PMCID: PMC8039605 DOI: 10.21037/tau.2020.03.43] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Male infertility is a common and complex disease, manifesting as a wide range of phenotypes, ranging from apparently normal semen parameters with an inexplicable inability to conceive, to the complete absence of sperm production. The diversity of male infertility phenotypes, coupled with the extreme complexity of spermatogenesis has significantly confounded the identification of the underlying genetic causes for these conditions, though incremental progress has been made, particularly in the past decade. In this review, we discuss the progress that has been made to date, tools and resources that have proven effective in accelerating discovery of novel genetic markers for male infertility, and areas in which we see the greatest potential for advancing the field in the coming years. These include the development and use of robust phenotyping tools, the continued development of in vitro and animal models for variant validation, increased utilization and refinement of whole genome approaches for discovery, and further expansion of consortia that assemble groups of clinicians and basic researchers with the unified goal of disentangling the complex genetic architecture of male infertility. As these resources mature, and funding agencies increasingly recognize the importance of these efforts for improving human health, the discovery of novel genetic markers for male infertility will certainly continue to accelerate.
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Affiliation(s)
- Albert Salas-Huetos
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
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Lee CL, Lee CH, Chuang CK, Chiu HC, Chen YJ, Chou CL, Wu PS, Chen CP, Lin HY, Lin SP. Array-CGH increased the diagnostic rate of developmental delay or intellectual disability in Taiwan. Pediatr Neonatol 2019; 60:453-460. [PMID: 30581099 DOI: 10.1016/j.pedneo.2018.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/03/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Unexplained developmental delay or intellectual disability (DD/ID) has an estimated prevalence of about 3%-5% in the general population of Taiwan. Array comparative genomic hybridization (array-CGH) is a high-resolution tool that can detect about 50 Kb chromosome aberrations. A previous study has reported a detection rate of 10%-20% for this array.1 This study aimed to investigate and compare the diagnosis rate for DD/ID using array-CGH and conventional chromosome study in DD/ID patients in Taiwan. METHODS We enrolled 177 patients with DD/ID who underwent array-CGH examination at the MacKay Memory Hospital between June 2010 and September 2017. The copy number variants (CNV) were classified into the following three groups: pathogenic (potential pathologic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance, VOUS), according to the ACMG guideline.2 RESULTS: Of the 177 enrolled patients, 100 (56.5%) were men and 77 (43.5%) were women. Ages ranged from 3 months to 50 years, with a median age of 5.2 years. Total 32.0% (32/100) male patients had pathogenic CNV, and 32.5% (25/77) female patients had pathogenic CNV. The ratio of pathogenic CNV in male and female patients was not significantly different (p = 0.379). The proportions of pathogenic CNV at <3 years, 3-6 years, 6-12 years, 12-18 years, and >18 years of age were 32.3% (31/96), 19.4% (6/31), 34.8% (8/23), 16.7% (2/12), and 66.7% (10/15), respectively. The overall diagnosed rate of DD/ID with pathogenic CNV was 27.7% (49/177) using array-CGH in this study. There were 105 patients with conventional karyotyping and array-CGH data at the same time. Nineteen (18.1%) patients had visible chromosomal abnormality. Total 32/105 (30.5%) patients could find at least one pathogenic CNVs. The array-CGH had a higher diagnosed rate than the conventional karyotyping in clinical application. CONCLUSIONS Although array-CGH could not detect point mutation, balanced translocations, inversions, or low-level mosaicism, the diagnosis rate in clinical application was up to 46.3% and 2.5 times that of conventional karyotyping analysis (18.1%). This study demonstrated that array-CGH is a powerful diagnostic tool and should be the first genetic test instead of conventional karyotyping analysis for patients with unexplained DD/ID.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
| | | | - Huei-Ching Chiu
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yen-Jiun Chen
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chao-Ling Chou
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Chih-Ping Chen
- Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Departments of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan; Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan.
| | - Shuan-Pei Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan.
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The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. BMC Med Genomics 2019; 12:111. [PMID: 31337399 PMCID: PMC6651926 DOI: 10.1186/s12920-019-0559-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 07/16/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). METHODS In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). RESULTS In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. In our cohort pathogenic/likely pathogenic microdeletions were more frequent than microduplications (69%; 51/74 vs. 31%; 23/74) ranging in size from 0.395 Mb to 10.676 Mb (microdeletions) and 0.544 Mb to 8.156 Mb (microduplications), but their sizes were not significantly different (P = 0.83). The pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger than benign CNVs (median 0.394 Mb) (P < 0.00001) and likewise the pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger in size than VOUS (median 0.469 Mb) (P < 0.00001). CONCLUSIONS Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.
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Baldan F, Passon N, Burra S, Demori E, Russo PD, Damante G. Quantitative PCR evaluation of deletions/duplications identified by array CGH. Mol Cell Probes 2019; 46:101421. [PMID: 31302230 DOI: 10.1016/j.mcp.2019.101421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 12/01/2022]
Abstract
Genomic deletions/duplications detected by array comparative genomic hybridization (aCGH) should be confirmed by an independent technology. This approach allows also to test, at low cost, inheritance of the imbalance. In the present study we explored the use of quantitative PCR (qPCR) to confirm aCGH-detected potentially clinically relevant imbalances. Only samples with DLRS <0.2 were tested for confirmation. aCGH results were confirmed in 102/118 cases (86.5%). A major element for non-confirmation was the dimension (and the probe coverage) of the putative aberration. Imbalances detected by 10 or less probes in aCGH assay were not confirmed in 11 out of 41 cases (26.8%), while those ones detected by 20 or more probes were always confirmed (46 cases). Among not confirmed imbalances, no statistical difference was found between deletions and duplication. Our data indicate that validation should be required for imbalances detected by less than 10 probes in aCGH assays.
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Affiliation(s)
| | - Nadia Passon
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Silvia Burra
- Department of Medicine, University of Udine, Udine, Italy
| | - Eliana Demori
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Patrizia Dello Russo
- Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
| | - Giuseppe Damante
- Department of Medicine, University of Udine, Udine, Italy; Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
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Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S. Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet 2019; 27:525-534. [PMID: 30622331 PMCID: PMC6460637 DOI: 10.1038/s41431-018-0326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/25/2017] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Split-hand-split-foot malformation (SHFM) is a rare condition that occurs in 1 in 8500-25,000 newborns and accounts for 15% of all limb reduction defects. SHFM is heterogeneous and can be isolated, associated with other malformations, or syndromic. The mode of inheritance is mostly autosomal dominant with incomplete penetrance, but can be X-linked or autosomal recessive. Seven loci are currently known: SHFM1 at 7q21.2q22.1 (DLX5 gene), SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27 (TP63 gene), SHFM5 at 2q31 and SHFM6 as a result of variants in WNT10B (chromosome 12q13). Duplications at 17p13.3 are seen in SHFM when isolated or associated with long bone deficiency. Tandem genomic duplications at chromosome 10q24 involving at least the DACTYLIN gene are associated with SHFM3. No point variant in any of the genes residing within the region has been identified so far, but duplication of exon 1 of the BTRC gene may explain the phenotype, with likely complex alterations of gene regulation mechanisms that would impair limb morphogenesis. We report on 32 new index cases identified by array-CGH and/or by qPCR, including some prenatal ones, leading to termination for the most severe. Twenty-two cases were presenting with SHFM and 7 with monodactyly only. Three had an overlapping phenotype. Additional findings were identified in 5 (renal dysplasia, cutis aplasia, hypogonadism and agenesis of corpus callosum with hydrocephalus). We present their clinical and radiological findings and review the literature on this rearrangement that seems to be one of the most frequent cause of SHFM.
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MESH Headings
- Adult
- Child, Preschool
- Chromosomes, Human, Pair 10/genetics
- Comparative Genomic Hybridization/methods
- F-Box Proteins/genetics
- Female
- Gene Rearrangement/genetics
- Genetic Predisposition to Disease
- Hand Deformities, Congenital/diagnostic imaging
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/physiopathology
- Humans
- Infant
- Limb Deformities, Congenital/diagnostic imaging
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/physiopathology
- Male
- Pedigree
- Phenotype
- Proteasome Endopeptidase Complex/genetics
- Proto-Oncogene Proteins/genetics
- Radiography
- Segmental Duplications, Genomic/genetics
- Wnt Proteins/genetics
- Young Adult
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Affiliation(s)
| | - Aleksander Jamsheer
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Fabienne Escande
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
- RADEME, EA 7364, Lille University, Lille, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
| | - Florence Petit
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | | | - Magdalena Socha
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Anna Jakubiuk-Tomaszuk
- Department of Pediatric Neurology and Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | | | | | | | - Alain Verloes
- Service de Génétique, Hôpital Robert Debré, Paris, France
| | | | | | | | | | - Albert David
- Service de Génétique, CHU Nantes, Nantes, France
| | - Chantal Farra
- American University of Beirut Medical Centre, Beirut, Lebanon
| | | | - Sébastien Jacquemont
- Department of Paediatrics, Faculty of Medicine, University of Montréal, Montreal, Canada
| | - Annick Rossi
- Laboratoire de Cytogénétique, EFS Normandie, Bois Guillaume, France
| | | | - Neeti Ghali
- North West Thames Regional Genetics Service, Harrow, UK
| | - Anne Moncla
- Laboratoire de Génétique Chromosomique, CHU Marseille, Marseille, France
| | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Elena Pollina
- Pathology Department, Queen Elizabeth Hospital, Woolwich, UK
| | | | - Joo Wook Ahn
- Genetics Laboratories, Guy's Hospital, London, UK
| | - Anne-Sylvie Valat
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - Aurélie Mezel
- Service de Chirurgie Orthopédique, CHRU Lille, Lille, France
| | - Philippe Bourgeot
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - David Zhang
- Institute of Neurology, University College London, London, UK
| | - Sylvie Manouvrier-Hanu
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
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9
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Early Hereditary Diffuse Gastric Cancer (eHDGC) is Characterized by Subtle Genomic Instability and Active DNA Damage Response. Pathol Oncol Res 2018; 25:711-721. [PMID: 30547291 DOI: 10.1007/s12253-018-0547-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/16/2018] [Indexed: 12/26/2022]
Abstract
Diffuse gastric cancer (DGC) is one of the two primary types of stomach cancer. Carriers of germline mutations in the gene encoding E-cadherin are predisposed to DGC. The primary aim of the present study was to determine if genomic instability is an early event in DGC and how it may lead to disease progression. Chromosomal aberrations in early intramucosal hereditary diffuse gastric cancer (eHDGC) were assessed using array comparative genomic hybridization (array CGH). Notably, no aneuploidy or other large-scale chromosomal rearrangements were detected. Instead, all aberrations affected small regions (< 4.8 Mb) and were predominantly deletions. Analysis of DNA sequence patterns revealed that essentially all aberrations possessed the characteristics of common fragile sites. These results and the results of subsequent immunohistochemical examinations demonstrated that unlike advanced DGC, eHDGCs is characterized by low levels of genomic instability at fragile sites. Furthermore, they express an active DNA damage response, providing a molecular basis for the observed indolence of eHDGC. This finding is an important step to understanding the pathology underlying natural history of DGC and supports a revision of the current definition of eHDGC as a malignant disease.
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García-Acero M, Suárez-Obando F, Gómez-Gutiérrez A. CGH analysis in Colombian patients: findings of 1374 arrays in a seven-year study. Mol Cytogenet 2018; 11:46. [PMID: 30166995 PMCID: PMC6104019 DOI: 10.1186/s13039-018-0398-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background Array-based comparative genome hybridization (array CGH) is a first-line test used in the genetic evaluation of individuals with multiple anomalies, developmental delays, and cognitive deficits. In this study, we analyzed clinical indications and findings of array CGH tests of Colombian individuals forwarded to a reference laboratory over a period of seven years in order to evaluate the diagnostic performance of the test in our population. Results The results of 1374 array CGH analyses of Colombian individuals were referred to the Andean Reference Institute in Colombia (Instituto de Referencia Andino) during a 7-year period (2009–2015). Chromosomal imbalances were detected in 488 cases (35%), whereas 121 cases were classified as nonpathogenic variants, 65 cases (4.7%) were classified as variants of uncertain significance, and 302 cases (22%) were classified as abnormal or pathogenic. The most common findings in the abnormal and/or pathogenic set were deletions, followed by duplications and complex rearrangements. Variants in the carrier status of autosomal recessive diseases were identified as incidental findings in 29 subjects (2%). Conclusions Clinical indications preceding the referral of aCGH in Colombian patients are not standardized and result in unexpected pathogenic variants as well as secondary findings that need careful interpretation. Development of local infrastructure will probably improve the communication between all stakeholders, to ensure accurate clinical diagnoses.
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Affiliation(s)
- Mary García-Acero
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fernando Suárez-Obando
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia.,2Servicio de Genética, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alberto Gómez-Gutiérrez
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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11
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Tropeano M, Howley D, Gazzellone MJ, Wilson CE, Ahn JW, Stavropoulos DJ, Murphy CM, Eis PS, Hatchwell E, Dobson RJB, Robertson D, Holder M, Irving M, Josifova D, Nehammer A, Ryten M, Spain D, Pitts M, Bramham J, Asherson P, Curran S, Vassos E, Breen G, Flinter F, Ogilvie CM, Collier DA, Scherer SW, McAlonan GM, Murphy DG. Microduplications at the pseudoautosomal SHOX locus in autism spectrum disorders and related neurodevelopmental conditions. J Med Genet 2016; 53:536-47. [PMID: 27073233 DOI: 10.1136/jmedgenet-2015-103621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND The pseudoautosomal short stature homeobox-containing (SHOX) gene encodes a homeodomain transcription factor involved in cell-cycle and growth regulation. SHOX/SHOX enhancers deletions cause short stature and skeletal abnormalities in a female-dominant fashion; duplications appear to be rare. Neurodevelopmental disorders (NDDs), such as autism spectrum disorders (ASDs), are complex disorders with high heritability and skewed sex ratio; several rare (<1% frequency) CNVs have been implicated in risk. METHODS We analysed data from a discovery series of 90 adult ASD cases, who underwent clinical genetic testing by array-comparative genomic hybridisation (CGH). Twenty-seven individuals harboured CNV abnormalities, including two unrelated females with microduplications affecting SHOX. To determine the prevalence of SHOX duplications and delineate their associated phenotypic spectrum, we subsequently examined array-CGH data from a follow-up sample of 26 574 patients, including 18 857 with NDD (3541 with ASD). RESULTS We found a significant enrichment of SHOX microduplications in the NDD cases (p=0.00036; OR 2.21) and, particularly, in those with ASD (p=9.18×10(-7); OR 3.63) compared with 12 594 population-based controls. SHOX duplications affecting the upstream or downstream enhancers were enriched only in females with NDD (p=0.0043; OR 2.69/p=0.00020; OR 7.20), but not in males (p=0.404; OR 1.38/p=0.096; OR 2.21). CONCLUSIONS Microduplications at the SHOX locus are a low penetrance risk factor for ASD/NDD, with increased risk in both sexes. However, a concomitant duplication of SHOX enhancers may be required to trigger a NDD in females. Since specific SHOX isoforms are exclusively expressed in the developing foetal brain, this may reflect the pathogenic effect of altered SHOX protein dosage on neurodevelopment.
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Affiliation(s)
- Maria Tropeano
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, CS, Italy
| | - Deirdre Howley
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Matthew J Gazzellone
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C Ellie Wilson
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK Individual Differences, Language and Cognition Lab, Department of Developmental and Educational Psychology, University of Seville, Seville, Spain
| | - Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Peggy S Eis
- Population Diagnostics, Inc., Melville, New York, USA
| | - Eli Hatchwell
- Population Diagnostics, Inc., Melville, New York, USA
| | - Richard J B Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Dene Robertson
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Annelise Nehammer
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Mina Ryten
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Debbie Spain
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Mark Pitts
- Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK
| | - Jessica Bramham
- UCD School of Psychology, University College Dublin, Dublin, Ireland
| | - Philip Asherson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sarah Curran
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Evangelos Vassos
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Discovery Neuroscience Research, Eli Lilly and Company Ltd, Erl Wood Manor, Windlesham, Surrey, UK
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Grainne M McAlonan
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK Adult Autism Spectrum and ADHD Services, Behavioural and Developmental Psychiatry, Clinical Academic Group, King's Health Partners, London, UK National Institute for Health Research (NIHR) Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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Baltaci E, Karaman E, Dalay N, Buyru N. Analysıs of gene copy number changes ın head and neck cancer. Clin Otolaryngol 2016; 43:1004-1009. [PMID: 27259694 DOI: 10.1111/coa.12686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/01/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Chromosomal alterations and copy number changes are frequent events in tumors, leading to amplification of focal regions containing several oncogenes. Gains and losses of several regions have been reported in head and neck cancer (HNC) but the copy number changes of the individual genes located in these regions have not been analyzed so far. In this study we aimed to analyze the copy number variations in patients with HNC. DESIGN Prospective study SETTING: University hospital PARTICIPANTS: 50 patients with squamous cell carcinoma of the head and neck METHODS: Copy number changes and amplifications of 22 genes in tumors and matched tissue were analyzed by MLPA which allows simultaneous analysis of gene copy numbers in multiple genetic regions. RESULTS Amplifications were observed in 52% and losses were detected in 20% of the samples. Chromosome 8 was found to harbor the most frequent copy number alterations. The most frequently amplified genes were CCND1 and the MED1 genes followed by the MTDH and MYC genes on the long arm and ZNF703 on the short arm of chromosome 8. Amplification of the ZNF703, PRDM14 and MYC genes were highly correlated suggesting that the genes displaying high copy number changes on chromosome 8 collaborate during carcinogenesis. CONCLUSIONS The alterations found in our study supports the contribution of gene amplifications and indicate cooperation between certain oncogenes in the pathogenesis of HNSCC. Correlations between amplification of less familiar genes and known oncogenes warrant further investigation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- E Baltaci
- Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - E Karaman
- Department of Otorhinolaryngology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - N Dalay
- Oncology Institute, Istanbul University, Istanbul, Turkey
| | - N Buyru
- Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
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13
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Aypar U, Hoppman NL, Thorland EC, Dawson DB. Patients with mosaic methylation patterns of the Prader-Willi/Angelman Syndrome critical region exhibit AS-like phenotypes with some PWS features. Mol Cytogenet 2016; 9:26. [PMID: 27006693 PMCID: PMC4802915 DOI: 10.1186/s13039-016-0233-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/09/2016] [Indexed: 01/29/2023] Open
Abstract
Background Loss of expression of imprinted genes in the 15q11.2-q13 region is known to cause either Prader-Willi syndrome (PWS) or Angelman syndrome (AS), depending on the parent of origin. In some patients (1 % in PWS and 2–4 % in AS), the disease is due to aberrant imprinting or gene silencing, or both. Results We report here a 4-year-old boy on whom a chromosomal microarray (CMA) was performed due to mild hand tremors, mild developmental delays, and clumsiness. CMA revealed absence of heterozygosity (AOH) spanning the entire chromosome 15, suggesting uniparental isodisomy 15. The patient had no definitive phenotypic features of PWS or AS. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) was performed to determine the parent of origin of the uniparental disomy (UPD) by examining methylation status at maternally imprinted sites. Interestingly, our patient had a mosaic methylation pattern. We identified nine additional previously tested patients with a similar mosaic methylation pattern. CMA was performed on these individuals retrospectively to test whether patients with mosaic methylation are more likely to have UPD of chromosome 15. Of the nine patients, only one had regions of AOH on chromosome 15; however, this patient had numerous regions of AOH on multiple chromosomes suggestive of consanguinity. Conclusion The patients with mosaic methylation had milder or atypical features of AS, and the majority also had some features characteristic of PWS. We suggest that quantitative methylation analysis be performed for cases of atypical PWS or AS. It is also important to follow up with methylation testing when whole-chromosome isodisomy is detected.
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Affiliation(s)
- Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - Erik C Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
| | - D Brian Dawson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905 USA
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Garcia S, de Haro T, Zafra-Ceres M, Poyatos A, Gomez-Capilla JA, Gomez-Llorente C. Identification of de novo mutations of Duchénnè/Becker muscular dystrophies in southern Spain. Int J Med Sci 2014; 11:988-93. [PMID: 25076844 PMCID: PMC4115237 DOI: 10.7150/ijms.8391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/12/2014] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Duchénnè/Becker muscular dystrophies (DMD/BMD) are X-linked diseases, which are caused by a de novo gene mutation in one-third of affected males. The study objectives were to determine the incidence of DMD/BMD in Andalusia (Spain) and to establish the percentage of affected males in whom a de novo gene mutation was responsible. METHODS Multiplex ligation-dependent probe amplification (MLPA) technology was applied to determine the incidence of DMD/BMD in 84 males with suspicion of the disease and 106 female relatives. RESULTS Dystrophin gene exon deletion (89.5%) or duplication (10.5%) was detected in 38 of the 84 males by MLPA technology; de novo mutations account for 4 (16.7%) of the 24 mother-son pairs studied. CONCLUSIONS MLPA technology is adequate for the molecular diagnosis of DMD/BMD and establishes whether the mother carries the molecular alteration responsible for the disease, a highly relevant issue for genetic counseling.
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Affiliation(s)
- Susana Garcia
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Tomás de Haro
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
- 2. Instituto de Investigación Biosanitaria ibs. Granada, Spain
| | - Mercedes Zafra-Ceres
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Antonio Poyatos
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Jose A. Gomez-Capilla
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
- 2. Instituto de Investigación Biosanitaria ibs. Granada, Spain
- 3. Departamento de Bioquímica y Biología Molecular III e Inmunología. Facultad de Medicina. Universidad de Granada. Avd/ Madrid s/n 18071, Granada, Spain
| | - Carolina Gomez-Llorente
- 4. Departamento de Bioquímica y Biología Molecular II. Instituto de Nutrición y Tecnología de los Alimentos “José Mataix”. Centro de Investigaciones Biomédicas. Universidad de Granada. Avd/ Conocimiento s/n 18100 Armilla, Granada, Spain
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15
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Le Tanno P, Poreau B, Devillard F, Vieville G, Amblard F, Jouk PS, Satre V, Coutton C. Maternal complex chromosomal rearrangement leads to TCF12 microdeletion in a patient presenting with coronal craniosynostosis and intellectual disability. Am J Med Genet A 2014; 164A:1530-6. [PMID: 24648389 DOI: 10.1002/ajmg.a.36467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/29/2013] [Indexed: 01/21/2023]
Abstract
We report on a young child with intellectual disability and unilateral coronal craniosynostosis leading to craniofacial malformations. Standard karyotype showed an apparently balanced translocation between chromosomes 2 and 15 [t(2;15)(q21;q21.3)], inherited from his mother. Interestingly, array-CGH 180K showed a 3.64 Mb de novo deletion on chromosome 15 in the region 15q21.3q22.2, close to the chromosome 15 translocation breakpoints. This deletion leads to haploinsufficiency of TCF12 gene that can explain the coronal craniosynostosis described in the patient. Additional FISH analyses showed a complex balanced maternal chromosomal rearrangement combining the reciprocal translocation t(2;15)(q21;q21.3), and an insertion of the 15q22.1 segment into the telomeric region of the translocated 15q fragment. The genomic imbalance in the patient is likely caused by a crossing-over that occurs in the recombination loop formed during the maternal meiosis resulting in the deletion of the inserted fragment. This original case of a genomic microdeletion of TCF12 exemplifies the importance of array-CGH in the clinical investigation of apparently balanced rearrangements but also the importance of FISH analysis to identify the chromosomal mechanism causing the genomic imbalance.
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Affiliation(s)
- Pauline Le Tanno
- Laboratoire de Génétique Chromosomique, Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
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16
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Strassberg M, Fruhman G, Van den Veyver IB. Copy-number changes in prenatal diagnosis. Expert Rev Mol Diagn 2014; 11:579-92. [DOI: 10.1586/erm.11.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ahn JW, Dixit A, Johnston C, Ogilvie CM, Collier DA, Curran S, Dobson RJB. BBGRE: brain and body genetic resource exchange. Database (Oxford) 2013; 2013:bat067. [PMID: 24077841 PMCID: PMC3785255 DOI: 10.1093/database/bat067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 07/10/2013] [Accepted: 09/06/2013] [Indexed: 11/22/2022]
Abstract
Studies of copy number variation (genomic imbalance) are providing insight into both complex and Mendelian genetic disorders. Array comparative genomic hybridization (array CGH), a tool for detecting copy number variants at a resolution previously unattainable in clinical diagnostics, is increasingly used as a first-line test at clinical genetics laboratories. Many copy number variants are of unknown significance; correlation and comparison with other patients will therefore be essential for interpretation. We present a resource for clinicians and researchers to identify specific copy number variants and associated phenotypes in patients from a single catchment area, tested using array CGH at the SE Thames Regional Genetics Centre, London. User-friendly searching is available, with links to external resources, providing a powerful tool for the elucidation of gene function. We hope to promote research by facilitating interactions between researchers and patients. The BBGRE (Brain and Body Genetic Resource Exchange) resource can be accessed at the following website: http://bbgre.org DATABASE URL: http://bbgre.org.
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Affiliation(s)
- Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - Abhishek Dixit
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - Caroline Johnston
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - Caroline M. Ogilvie
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - David A. Collier
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - Sarah Curran
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
| | - Richard J. B. Dobson
- Department of Cytogenetics, Guy's and St Thomas NHS Foundation Trust, London, SE1 9RT, UK, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, London, SE5 8AF and NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation, London, SE5 8AF
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John N, Rajasekhar M, Girisha KM, Sharma PSVN, Gopinath PM. Multiplex ligation-dependant probe amplification study of children with idiopathic mental retardation in South India. INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:165-70. [PMID: 24019617 PMCID: PMC3758722 DOI: 10.4103/0971-6866.116115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND: Mental retardation (MR) is a heterogeneous dysfunction of the central nervous system exhibiting complex phenotypes and has an estimated prevalence of 1-3% in the general population. However, in about 50% of the children diagnosed with any form of intellectual disability or developmental delay the cause goes undetected contributing to idiopathic intellectual disability. MATERIALS AND METHODS: A total of 122 children with developmental delay/MR were studied to identify the microscopic and submicroscopic chromosome rearrangements by using the conventional cytogenetics and multiplex ligation dependent probe amplification (MLPA) analysis using SALSA MLPA kits from Microbiology Research Centre Holland [MRC] Holland. RESULTS: All the recruited children were selected for this study, after thorough clinical assessment and metaphases prepared were analyzed by using automated karyotyping system. None was found to have chromosomal abnormality; MLPA analysis was carried out in all subjects and identified in 11 (9%) patients. CONCLUSION: Karyotype analysis in combination with MLPA assays for submicroscopic micro-deletions may be recommended for children with idiopathic MR.
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Affiliation(s)
- Neetha John
- Division of Biotechnology, Manipal Life Sciences Centre, Manipal University, Manipal, Karnataka, India
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Abstract
Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.
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Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics. ACTA ACUST UNITED AC 2013; 21:189-206. [PMID: 23111197 DOI: 10.1097/pdm.0b013e3182595516] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The increasing knowledge about genetic alterations and molecular biomarkers in cancer initiation and progression opens new possibilities for the treatment of various types of cancer. This requires the inclusion of sensitive, and preferably multiplex, methods for the detection of molecular genetic alterations in the toolbox of classic pathology. Multiplex ligation-dependent probe amplification (MLPA) is a multiplex polymerase chain reaction-based method that can detect changes in the gene copy number status, DNA methylation, and point mutations simultaneously. MLPA probes recognize target sequences of only 50 to 100 nucleotides in length. This makes it possible to use MLPA even on highly fragmented DNA, and allows the detection of small deletions encompassing only a single exon. MLPA is a reliable, cost-effective, and robust method that can be performed using a standard thermocycler and capillary electrophoresis equipment, generating results within 24 hours with a short hands-on working time. Up to 50 different genomic locations can be tested in a single reaction, which can be sufficient to detect those genetic alterations that are of diagnostic and prognostic significance in a certain tumor entity. In the last years, MLPA has been used successfully in tumor diagnostics and in cancer research. This review gives an overview on the collected experience of MLPA applications on tumor DNA, about the advantages but also potential pitfalls and limitations of this technique.
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Tropeano M, Ahn JW, Dobson RJB, Breen G, Rucker J, Dixit A, Pal DK, McGuffin P, Farmer A, White PS, Andrieux J, Vassos E, Ogilvie CM, Curran S, Collier DA. Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders. PLoS One 2013; 8:e61365. [PMID: 23637818 PMCID: PMC3630198 DOI: 10.1371/journal.pone.0061365] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 03/08/2013] [Indexed: 01/26/2023] Open
Abstract
Copy number variants (CNVs) at chromosome 16p13.11 have been associated with a range of neurodevelopmental disorders including autism, ADHD, intellectual disability and schizophrenia. Significant sex differences in prevalence, course and severity have been described for a number of these conditions but the biological and environmental factors underlying such sex-specific features remain unclear. We tested the burden and the possible sex-biased effect of CNVs at 16p13.11 in a sample of 10,397 individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH); cases were compared with 11,277 controls. In order to identify candidate phenotype-associated genes, we performed an interval-based analysis and investigated the presence of ohnologs at 16p13.11; finally, we searched the DECIPHER database for previously identified 16p13.11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13.11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13.11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2.59; p = 0.0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5.62; p = 0.0002), but not in females (OR = 1.19, p = 0.673). The same pattern of results was also observed in the DECIPHER sample. Interval-based analysis showed a significant enrichment of case CNVs containing interval II (OR = 2.59; p = 0.0005), located in the 0.83 Mb genomic region between 15.49-16.32 Mb, and encompassing the four ohnologs NDE1, MYH11, ABCC1 and ABCC6. Our data confirm that duplications and deletions at 16p13.11 represent incompletely penetrant pathogenic mutations that predispose to a range of neurodevelopmental disorders, and suggest a sex-limited effect on the penetrance of the pathological phenotypes at the 16p13.11 locus.
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Affiliation(s)
- Maria Tropeano
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Richard J. B. Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - James Rucker
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Abhishek Dixit
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Deb K. Pal
- Department of Clinical Neuroscience, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Peter McGuffin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Anne Farmer
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Peter S. White
- Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joris Andrieux
- Institut de Génétique Médicale, CHRU de Lille, Lille, France
| | - Evangelos Vassos
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Caroline Mackie Ogilvie
- Department of Cytogenetics, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Sarah Curran
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
- Discovery Neuroscience Research, Eli Lilly and Company Ltd, Lilly Research Laboratories, Erl Wood Manor, Windlesham, Surrey, United Kingdom
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Ahn JW, Bint S, Bergbaum A, Mann K, Hall RP, Ogilvie CM. Array CGH as a first line diagnostic test in place of karyotyping for postnatal referrals - results from four years' clinical application for over 8,700 patients. Mol Cytogenet 2013; 6:16. [PMID: 23560982 PMCID: PMC3632487 DOI: 10.1186/1755-8166-6-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/13/2013] [Indexed: 11/18/2022] Open
Abstract
Background Array CGH is widely used in cytogenetics centres for postnatal constitutional genome analysis, and is now recommended as a first line test in place of G-banded chromosome analysis. At our centre, first line testing by oligonucleotide array CGH for all constitutional referrals for genome imbalance has been in place since June 2008, using a patient vs patient hybridisation strategy to minimise costs. Findings Out of a total of 13,412 patients tested with array CGH, 8,794 (66%) had array CGH as the first line test. Referral indications for this first line group ranged from neonatal congenital anomalies through to adult neurodisabilities; 25% of these patients had CNVs either in known pathogenic regions or in other regions where imbalances have not been reported in the normal population. Of these CNVs, 46% were deletions or nullisomy, 53% were duplications or triplications, and mosaic imbalances made up the remainder; 87% were <5Mb and would likely not be detected by G-banded chromosome analysis. For cases with completed inheritance studies, 20% of imbalances were de novo. Conclusions Array CGH is a robust and cost-effective alternative to traditional cytogenetic methodology; it provides a higher diagnostic detection rate than G-banded chromosome analysis, and adds to the sum of information and understanding of the role of genomic imbalance in disease. Use of novel hybridisation strategies can reduce costs, allowing more widespread testing.
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Affiliation(s)
- Joo Wook Ahn
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, SE1 9RT, UK.
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Mutations in the γ-Secretase Genes NCSTN , PSENEN , and PSEN1 Underlie Rare Forms of Hidradenitis Suppurativa (Acne Inversa). J Invest Dermatol 2012; 132:2459-2461. [DOI: 10.1038/jid.2012.162] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Coutton C, Vieville G, Satre V, Devillard F, Amblard F. Multiplex Ligation-dependent Probe Amplification (MLPA) et sondes « à façon » entièrement synthétiques. Guide pratique, recommandations et expérience au CHU de Grenoble. Ing Rech Biomed 2012. [DOI: 10.1016/j.irbm.2012.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ferreira SI, Matoso E, Venâncio M, Saraiva J, Melo JB, Carreira IM. Critical region in 2q31.2q32.3 deletion syndrome: Report of two phenotypically distinct patients, one with an additional deletion in Alagille syndrome region. Mol Cytogenet 2012; 5:25. [PMID: 22550961 PMCID: PMC3460744 DOI: 10.1186/1755-8166-5-25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/17/2012] [Indexed: 12/04/2022] Open
Abstract
Background Standard cytogenetic analysis has revealed to date more than 30 reported cases presenting interstitial deletions involving region 2q31-q32, but with poorly defined breakpoints. After the postulation of 2q31.2q32.3 deletion as a clinically recognizable disorder, more patients were reported with a critical region proposed and candidate genes pointed out. Results We report two female patients with de novo chromosome 2 cytogenetically visible deletions, one of them with an additional de novo deletion in chromosome 20p12.2p12.3. Patient I presents a 16.8 Mb deletion in 2q31.2q32.3 while patient II presents a smaller deletion of 7 Mb in 2q32.1q32.3, entirely contained within patient I deleted region, and a second 4 Mb deletion in Alagille syndrome region. Patient I clearly manifests symptoms associated with the 2q31.2q32.3 deletion syndrome, like the muscular phenotype and behavioral problems, while patient II phenotype is compatible with the 20p12 deletion since she manifests problems at the cardiac level, without significant dysmorphisms and an apparently normal psychomotor development. Conclusions Whereas Alagille syndrome is a well characterized condition mainly caused by haploinsufficiency of JAG1 gene, with manifestations that can range from slight clinical findings to major symptoms in different domains, the 2q31.2q32.3 deletion syndrome is still being delineated. The occurrence of both imbalances in reported patient II would be expected to cause a more severe phenotype compared to the individual phenotype associated with each imbalance, which is not the case, since there are no manifestations due to the 2q32 deletion. This, together with the fact that patient I deleted region overlaps previously reported cases and patient II deletion is outside this common region, reinforces the existence of a critical region in 2q31.3q32.1, between 181 to 185 Mb, responsible for the clinical phenotype.
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Affiliation(s)
- Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
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