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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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de la Morena-Barrio B, Palomo Á, Padilla J, Martín-Fernández L, Rojo-Carrillo JJ, Cifuentes R, Bravo-Pérez C, Garrido-Rodríguez P, Miñano A, Rubio AM, Pagán J, Llamas M, Vicente V, Vidal F, Lozano ML, Corral J, de la Morena-Barrio ME. Impact of genetic structural variants in factor XI deficiency: identification, accurate characterization, and inferred mechanism by long-read sequencing. J Thromb Haemost 2023; 21:1779-1788. [PMID: 36940803 DOI: 10.1016/j.jtha.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND Congenital factor XI (FXI) deficiency is a probably underestimated coagulopathy that confers antithrombotic protection. Characterization of genetic defects in F11 is mainly focused on the identification of single-nucleotide variants and small insertion/deletions because they represent up to 99% of the alterations accounting for factor deficiency, with only 3 gross gene defects of structural variants (SVs) having been described. OBJECTIVES To identify and characterize the SVs affecting F11. METHODS The study was performed in 93 unrelated subjects with FXI deficiency recruited in Spanish hospitals over a period of 25 years (1997-2022). F11 was analyzed by next-generation sequencing, multiplex ligand probe amplification, and long-read sequencing. RESULTS Our study identified 30 different genetic variants. Interestingly, we found 3 SVs, all heterozygous: a complex duplication affecting exons 8 and 9, a tandem duplication of exon 14, and a large deletion affecting the whole gene. Nucleotide resolution obtained by long-read sequencing revealed Alu repetitive elements involved in all breakpoints. The large deletion was probably generated de novo in the paternal allele during gametogenesis, and despite affecting 30 additional genes, no syndromic features were described. CONCLUSION SVs may account for a high proportion of F11 genetic defects implicated in the molecular pathology of congenital FXI deficiency. These SVs, likely caused by a nonallelic homologous recombination involving repetitive elements, are heterogeneous in both type and length and may be de novo. These data support the inclusion of methods to detect SVs in this disorder, with long-read-based methods being the most appropriate because they detect all SVs and achieve adequate nucleotide resolution.
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Affiliation(s)
- Belén de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ángeles Palomo
- Servicio de Hematología y Hemoterapia del centro Materno-Infantil del Hospital Regional Universitario Carlos de Haya, Málaga, Spain
| | - José Padilla
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Laura Martín-Fernández
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José Rojo-Carrillo
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Rosa Cifuentes
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Carlos Bravo-Pérez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Pedro Garrido-Rodríguez
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Antonia Miñano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Ana María Rubio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Pagán
- Servicio de Medicina Interna, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - María Llamas
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Vicente Vicente
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Francisco Vidal
- Laboratori de Coagulopaties Congènites, Banc de Sang i Teixits, Barcelona, Spain; Medicina Transfusional. Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - María Luisa Lozano
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
| | - María Eugenia de la Morena-Barrio
- Servicio de Hematología, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria-Pascual Parrilla, Centro de Investigación Biomédica en Red de Enfermedades Raras-Instituto de Salud Carlos III, Murcia, Spain.
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The role of chromosomal microarray and exome sequencing in prenatal diagnosis. Curr Opin Obstet Gynecol 2021; 33:148-155. [PMID: 33620893 DOI: 10.1097/gco.0000000000000692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in technologies have revolutionized prenatal diagnosis. Chromosomal microarray analysis (CMA) became a proven method and was implemented to detect gains and losses of DNA and absence of heterozygosity across the genome. Next-generation sequencing technologies have brought opportunities and challenges to genetic testing. Exome sequencing detects single-nucleotide variants (SNVs) across the exome and its prenatal application is an emerging field. We reviewed the literature to define the role of CMA and exome sequencing in prenatal diagnosis. RECENT FINDING The application of exome sequencing in genetic diagnosis shows increased diagnostic yield and could be potentially implemented for prenatal diagnosis of fetuses with one or more ultrasound structural abnormalities or suspected monogenetic conditions. Although CMA is a gold standard for copy number variant (CNV) detection, large clinical cohort studies emphasized integrated CNV and SNV analyses for precise molecular diagnosis. Recent studies also suggest low-pass genome sequencing-based CNV detection can identify genome-wide imbalances at higher resolutions. SUMMARY Data suggest exome sequencing for SNVs and CMA for CNV detection are the most effective approach for prenatal genetic diagnosis. Emerging evidences show genome sequencing has the potential to replace CMA and even exome sequencing to become a comprehensive genetic test in the clinical diagnostic laboratory.
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Hilger AC, Dworschak GC, Reutter HM. Lessons Learned from CNV Analysis of Major Birth Defects. Int J Mol Sci 2020; 21:ijms21218247. [PMID: 33153233 PMCID: PMC7663563 DOI: 10.3390/ijms21218247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022] Open
Abstract
The treatment of major birth defects are key concerns for child health. Hitherto, for the majority of birth defects, the underlying cause remains unknown, likely to be heterogeneous. The implicated mortality and/or reduced fecundity in major birth defects suggest a significant fraction of mutational de novo events among the affected individuals. With the advent of systematic array-based molecular karyotyping, larger cohorts of affected individuals have been screened over the past decade. This review discusses the identification of disease-causing copy-number variations (CNVs) among individuals with different congenital malformations. It highlights the differences in findings depending on the respective congenital malformation. It looks at the differences in findings of CNV analysis in non-isolated complex congenital malformations, associated with central nervous system malformations or intellectual disabilities, compared to isolated single organ-system malformations. We propose that the more complex an organ system is, and the more genes involved during embryonic development, the more likely it is that mutational de novo events, comprising CNVs, will confer to the expression of birth defects of this organ system.
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Affiliation(s)
- Alina Christine Hilger
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Gabriel Clemens Dworschak
- Department of Pediatrics, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Institute for Anatomy and Cell Biology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
| | - Heiko Martin Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, Children’s Hospital Medical Center, University Hospital Bonn, 53127 Bonn, Germany
- Correspondence: (A.C.H.); (G.C.D.); (H.M.R.); Tel.: +49-228-6885-419 (A.C.H. & G.C.D. & H.M.R.)
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Farra C, Nassar AH, Mirza F, Abdouni L, Souaid M, Awwad J. BACs-on-Beads™ assay, a rapid aneuploidy test, improves the diagnostic yield of conventional karyotyping. Mol Biol Rep 2019; 47:169-177. [PMID: 31595440 DOI: 10.1007/s11033-019-05117-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/01/2019] [Indexed: 01/28/2023]
Abstract
BACs-on-Beads (BoBs™) assay is a rapid aneuploidy test (RAT) that detects numerical chromosomal aneuploidies and multiple microdeletion/microduplication syndromes. This study was conducted to appraise the usefulness of the BoB™ assay as a complementary diagnostic tool to conventional karyotyping for the rapid detection of chromosomal aneuploidies. A total of 485 prenatal (amniotic fluid and chorionic villi) and blood/products of conception samples were collected between July 2013 and August 2018, and analyzed by the BoBs™ assay and cytogenetic karyotyping and further validated by fluorescence in situ hybridization (FISH). Forty-three of 484 qualifying samples (8.9%) were identified as abnormal by the BoBs™ assay. The assay was comparable to karyotyping in the detection of common structural abnormalities (trisomy 21, trisomy 18, X, and Y), with a sensitivity of 96.0% and a specificity of 100%. BoBs™ assay detected 20 microdeletion and microduplication syndromes that were missed by karyotyping. BoBs™, however, missed 10 cases of polyploidies and chromosomal rearrangements which were identified by conventional karyotyping. Our findings suggest that BoBs™ is a reliable RAT which is suitable in combination with conventional karyotyping for the detection of common aneuploidies. The assay also improves the diagnostic yield by recognizing clinically relevant submicroscopic copy number gains and losses.
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Affiliation(s)
- Chantal Farra
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Anwar H Nassar
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fadi Mirza
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lina Abdouni
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mirna Souaid
- Medical Genetics, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Johnny Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon. .,Department of Obstetrics and Gynecology, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
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Rose R, Venkatesh A, Pietilä S, Jabeen G, Jagadeesh SM, Seshadri S. Utility and performance of bacterial artificial chromosomes-on-beads assays in chromosome analysis of clinical prenatal samples, products of conception and blood samples. J Obstet Gynaecol Res 2019; 45:830-840. [PMID: 30632238 DOI: 10.1111/jog.13920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/16/2018] [Indexed: 11/30/2022]
Abstract
AIM Chromosome analysis of prenatal samples and products of conception (POC) has conventionally been done by karyotyping (KT). Shortcomings of KT like high turnaround time and culture failure led to technology innovations, such as the bacterial artificial chromosomes (BAC)s-on-Beads (BoBs)-based tests, Prenatal BoBs (prenatal samples) and KaryoLite BoBs (POC samples). In the present study, we validated and evaluated the utility of each test on prenatal, POC and blood samples. METHODS Study A (n = 305; 259 prenatal + 46 blood/POC) and Study B (n = 176; 146 POC/chorionic vill + 30 blood/amniotic fluid) samples were analyzed using Prenatal and KaryoLite BoBs kits, respectively. KT, array-based Comparative Genomic Hybridization (arrayCGH) and fluorescence in situ hybridization (FISH) were used for comparison of results. Ability of KaryoLite BoBs to identify ring chromosomes was tested. RESULTS Prenatal BoBs had zero test failure rate and results of all samples were concordant with KT results. Totally four microdeletions were identified by Prenatal BoBs but not by KT. In Study B, all but two POC samples (one triploid and one tetraploid) were concordant with KT and arrayCGH. Partial chromosomal imbalance detection rate was ~64% and KaryoLite BoBs indicated the presence of a ring chromosome in all four cases. The failure rate of KaryoLite BoBs was 3%. CONCLUSION We conclude that Prenatal BoBs (common aneuploidies and nine microdeletions) together with KT constitutes more comprehensive prenatal testing compared to FISH and KT. KaryoLite BoBs for aneuploidies of all chromosomes is highly successful in POC analysis and the ability to indicate presence of ring chromosomes improves its clinical sensitivity. Both tests are robust and could also be used for different specimens.
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Affiliation(s)
- Rajiv Rose
- Molecular Laboratory, PerkinElmer Health Sciences, Ticel BioPark- Phase II, Chennai, India
| | - Aishwarya Venkatesh
- Molecular Laboratory, PerkinElmer Health Sciences, Ticel BioPark- Phase II, Chennai, India
| | - Sanna Pietilä
- Research & Development Laboratory, PerkinElmer, Singapore, Singapore
| | - Gazala Jabeen
- Cytogenetics Laboratory, PerkinElmer Health Sciences, Ticel BioPark-Phase II, Chennai, India
| | - Sujatha M Jagadeesh
- Molecular Laboratory, PerkinElmer Health Sciences, Ticel BioPark- Phase II, Chennai, India.,Cytogenetics Laboratory, PerkinElmer Health Sciences, Ticel BioPark-Phase II, Chennai, India.,Genetics Department, MediScan Systems, Chennai, India
| | - Suresh Seshadri
- Molecular Laboratory, PerkinElmer Health Sciences, Ticel BioPark- Phase II, Chennai, India.,Cytogenetics Laboratory, PerkinElmer Health Sciences, Ticel BioPark-Phase II, Chennai, India.,Prenatal Diagnosis and Therapy Center, MediScan Systems, Chennai, India
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Dong Z, Xie W, Chen H, Xu J, Wang H, Li Y, Wang J, Chen F, Choy KW, Jiang H. Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing. ACTA ACUST UNITED AC 2017; 94:8.17.1-8.17.16. [PMID: 28696555 DOI: 10.1002/cphg.43] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage and the lengthy turn-around time is not ideal for clinical implementation. In addition, the demand for computational resources also reduces the probability of clinical integration into each laboratory. Herein, a protocol providing CNV detection from low-pass, whole-genome sequencing (0.25×) in a clinical laboratory setting is described. The cost is reduced to less than $200 USD per sample and the turn-around time is within an acceptable clinically workable time-frame (7 days). © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Weiwei Xie
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huilin Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Bao'an Maternal and Child Health Hospital, Shenzhen, China
| | - Yun Li
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
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Ghaffari K, Hashemi M, Ebrahimi E, Shirkoohi R. BIRC5 Genomic Copy Number Variation in Early-Onset Breast Cancer. IRANIAN BIOMEDICAL JOURNAL 2017; 20:241-5. [PMID: 27372966 PMCID: PMC4983680 DOI: 10.7508/ibj.2016.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: Baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) gene is an inhibitor of apoptosis that expresses in human embryonic tissues but it is absent in most healthy adult tissues. The copy number of BIRC5 has been indicated to be highly increased in tumor tissues; however, its association with the age of onset in breast cancer is not well understood. Methods: Forty tumor tissues of breast cancer were obtained from Tumor Bank of Cancer Institute, Imam Khomeini Hospital, Tehran, Iran. BIRC5 gene copy number variation (CNV) was evaluated using Multiplex Ligation-dependent Probe Amplification (MLPA) and then compared with the age of onset for each patient. Results: BIRC5 amplification was seen in 17.5% of cases. Also, a significant association was observed between BIRC5 gene amplification and individuals under 40 years of age (P=0.04). Conclusion: BIRC5 gene has the potential to be a marker for the detection and prognosis of cancer at an early age.
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Affiliation(s)
- Kimia Ghaffari
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Elmira Ebrahimi
- Group of Genetics, Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shirkoohi
- Group of Genetics, Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
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Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet 2015; 16:172-83. [DOI: 10.1038/nrg3871] [Citation(s) in RCA: 565] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Choy RKW, Chen Y, Sun XF, Kwok YKY, Leung TY. BACs-on-beads: a new robust and rapid detection method for prenatal diagnosis. Expert Rev Mol Diagn 2014; 14:273-80. [PMID: 24649816 DOI: 10.1586/14737159.2014.899468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Karyotyping, the gold standard used for diagnosis of chromosomal abnormalities, is being progressively replaced by rapid aneuploidy testing (RAT) techniques such as quantitative fluorescence-PCR, FISH and multiplex ligation-dependent probe amplification for diagnosing the common aneuploidies or chromosomal microarray analysis for comprehensive genome-wide testing. However, due to technical limitations, current RATs are confined to the detection of common aneuploidies 13, 18, 21 and sex chromosomes. To overcome the limitations of RATs, a bacterial artificial chromosomes-on-beads (BoBs™) assay technology has been introduced for the detection of the common aneuploidies as well as specific microdeletion syndromes. The BoBs assay is a bead-based multiplex assay using polystyrene beads impregnated with two spectrally distinct infrared fluorochromes to create a liquid array of up to 100 unique spectral signatures that supports the analysis of that scale of simultaneous hybridization assays on a minute DNA sample. This review gives an overview on the collective experiences of BoBs applications in prenatal diagnosis.
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Affiliation(s)
- Richard Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
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Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ. Characterization of structural variants with single molecule and hybrid sequencing approaches. ACTA ACUST UNITED AC 2014; 30:3458-66. [PMID: 25355789 DOI: 10.1093/bioinformatics/btu714] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MOTIVATION Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.
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Affiliation(s)
- Anna Ritz
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
| | - Ali Bashir
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
| | - Suzanne Sindi
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
| | - David Hsu
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
| | - Iman Hajirasouliha
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
| | - Benjamin J Raphael
- Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI
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12
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Jiang YH, Wang Y, Xiu X, Choy KW, Pursley AN, Cheung SW. Genetic diagnosis of autism spectrum disorders: the opportunity and challenge in the genomics era. Crit Rev Clin Lab Sci 2014; 51:249-62. [PMID: 24878448 PMCID: PMC5937018 DOI: 10.3109/10408363.2014.910747] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genetic etiology for autism spectrum disorders (ASDs) was first suggested from twin studies reported in the 1970s. The identification of gene mutations in syndromic ASDs provided evidence to support a genetic cause of ASDs. More recently, genome-wide copy number variant and sequence analyses have uncovered a list of rare and highly penetrant copy number variants (CNVs) or single nucleotide variants (SNVs) associated with ASDs, which has strengthened the claim of a genetic etiology for ASDs. Findings from research studies in the genetics of ASD now support an important role for molecular diagnostics in the clinical genetics evaluation of ASDs. Various molecular diagnostic assays including single gene tests, targeted multiple gene panels and copy number analysis should all be considered in the clinical genetics evaluation of ASDs. Whole exome sequencing could also be considered in selected clinical cases. However, the challenge that remains is to determine the causal role of genetic variants identified through molecular testing. Variable expressivity, pleiotropic effects and incomplete penetrance associated with CNVs and SNVs also present significant challenges for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Yi Wang
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Xu Xiu
- Division of Child Development and Health, The Children’s Hospital of Fudan University Shanghai, People’s Republic of China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, and Joint Centre with Utrecht University Genetic core, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China
| | - Amber Nolen Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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13
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Krepischi ACV, Capelli LP, Silva AG, de Araújo ÉSS, Pearson PL, Heck B, da Costa CML, de Camargo B, Rosenberg C. Large germline copy number variations as predisposing factor in childhood neoplasms. Future Oncol 2014; 10:1627-33. [DOI: 10.2217/fon.14.41] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
ABSTRACT: Aims: Constitutive genetic factors are believed to predispose to cancer in children. This study investigated the role of rare germline copy number variations (CNVs) in pediatric cancer predisposition. Patients & methods: A total of 54 patients who developed cancer in infancy were screened by array-CGH for germline CNVs. Results: In total, 12 rare CNVs were detected, including a Xq27.2 triplication, and two >1.8 Mb deletions: one of them at 13q31, containing only RNA genes, and another at 3q26.33–q27.1, in a patient with congenital malformations. Detected rare CNVs are significantly larger than those identified in controls, and encompass genes never implicated in cancer predisposition. Conclusion: Our results suggest that constitutive CNVs contribute to the etiology of pediatric neoplasms, revealing new candidate genes for tumorigenesis.
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Affiliation(s)
- Ana Cristina Victorino Krepischi
- International Research Center, A C Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Amanda Gonçalves Silva
- International Research Center, A C Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Peter Lees Pearson
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Benjamin Heck
- Department of Pediatrics, A C Camargo Cancer Center, São Paulo, Brazil
- EmbrioConsult, São Paulo, Brazil
| | | | - Beatriz de Camargo
- Department of Pediatrics, A C Camargo Cancer Center, São Paulo, Brazil
- Pediatric Oncology Department, National Institute of Cancer, Rio de Janeiro, Brazil
| | - Carla Rosenberg
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
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14
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Choy KW, Kwok YK, Cheng YKY, Wong KM, Wong HK, Leung KO, Suen KW, Adler K, Wang CC, Lau TK, Schermer MJ, Lao TT, Leung TY. Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series. BJOG 2014; 121:1245-52. [PMID: 24893808 DOI: 10.1111/1471-0528.12873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2014] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To evaluate the diagnostic performance of the BACs-on-Beads(™) (BoBs(™)) assay for prenatal detection of chromosomal abnormalities. DESIGN Retrospective study. SETTING Tertiary prenatal diagnosis centre. POPULATION Women referred for prenatal diagnosis. METHODS We retrieved 2153 archived DNA samples collected between January 2010 and August 2011 for the BoBs(™) assay. These samples had previously been tested by quantitative fluorescence polymerase chain reaction (QF-PCR) and karyotyping. In the BoBs(™) assay a sample was defined as normal disomic when the ratio of the fluorescence intensities in a chromosome locus lay within the threshold (mean ratio ± 2SD), and as deleted or duplicated when the ratio was below the lower threshold (0.6-0.8) or above the upper threshold (1.3-1.4), respectively. The BoBs(™) results were further validated by microarray and compared in a blinded manner with the original QF-PCR and karyotyping results. MAIN OUTCOME MEASURES Concordance of any numerical, structural, and submicroscopic chromosomal abnormalities between the methods. RESULTS BACs-on-Beads(™) was similar to karyotyping and QF-PCR in detecting trisomy 13, trisomy 18, trisomy 21, and sex chromosomal aneuploidies, and superior to QF-PCR in detecting major structural abnormalities (53.3 versus 13.3%) and mosaicism (28.6 versus 0%) involving chromosomal abnormalities other than the common aneuploidies. BoBs(™) detected six microdeletion syndromes missed by karyotyping and QF-PCR; however, BoBs(™) missed two cases of triploidy identified by QF-PCR. Therefore, the sensitivity of BoBs(™) is 96.7% (95% CI 92.6-98.7%), and its specificity is 100% (95% CI 99.8-100%). CONCLUSIONS BACs-on-Beads(™) can replace QF-PCR for triaging in prenatal diagnosis, and gives a better diagnostic yield than current rapid aneuploidy tests.
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Affiliation(s)
- K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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15
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Microarrays as a diagnostic tool in prenatal screening strategies: ethical reflection. Hum Genet 2014; 133:163-72. [PMID: 24077959 DOI: 10.1007/s00439-013-1365-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/18/2013] [Indexed: 01/09/2023]
Abstract
Genomic microarray analysis is increasingly being applied as a prenatal diagnostic tool. Microarrays enable searching the genome at a higher resolution and with higher sensitivity than conventional karyotyping for identifying clinically significant chromosomal abnormalities. As yet, no clear guidelines exist on whether microarrays should be applied prenatally for all indications or only in selected cases such as ultrasound abnormalities, whether a targeted or genome-wide array should be used, and what these should include exactly. In this paper, we present some ethical considerations on the prenatal use of microarrays. There is a strong consensus, at least in Western countries, that the aim of prenatal screening for foetal abnormalities should be understood as facilitating autonomous reproductive choice for prospective parents. The tests offered should be valid and useful to reach that purpose. Against this background, we address several ethical issues raised by the prenatal application of microarrays. First, we argue that the general distinction between a targeted and a genome-wide microarray needs to be scrutinised. Then we examine whether microarrays are 'suitable tests' to serve either a screening or a diagnostic purpose. Given the wide range of findings possibly generated by microarrays, the question arises whether microarrays actually promote or interfere with autonomous reproductive decision-making. Moreover, if variants of unknown clinical significance are identified, this adds to the burden and complexity of reproductive decision-making. We suggest a qualified use of microarrays in the prenatal context.
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16
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Abstract
The glyoxalase I gene GLO1 is a hotspot for copy number variation in the human and mouse genomes. The additional copies are often functional, giving rise to 2–4-fold increased glyoxalase I expression and activity. The prevalence of GLO1 copy number increase in the human population appears to be approximately 2% and may be linked to a risk of obesity, diabetes and aging. Increased GLO1 copy number has been found in human tumour cell lines and primary human tumours. The minimum common copy number increase region was approximately 1 Mb and it contained GLO1 and seven other genes. The increased copy number was generally functional, being associated with increased glyoxalase I protein and multidrug resistance in cancer chemotherapy. Glo1 duplication in the mouse genome is found within approximately 0.5 Mb of duplicated DNA. It was claimed to be linked to anxiety phenotypes, but other related discordant findings have doubted the association with glyoxalase I and further investigation is required.
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17
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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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18
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Li M, Wen Y, Fu W. A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer. Cancer Inform 2014; 13:95-103. [PMID: 26279618 PMCID: PMC4519351 DOI: 10.4137/cin.s15203] [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: 04/09/2014] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/06/2022] Open
Abstract
Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (HMM)-based method, referred to as the PICR-CNV, for copy number inference. The proposed method first estimates copy number abundance for each single SNP on a single array based on the raw fluorescence values, and then standardizes the estimated copy number abundance to achieve equal footing among multiple arrays. This method requires no between-array normalization, and thus, maintains data integrity and independence of samples among individual subjects. In addition to our efforts to apply new statistical technology to raw fluorescence values, the HMM has been applied to the standardized copy number abundance in order to reduce experimental noise. Through simulations, we show our refined method is able to infer copy number variants accurately. Application of the proposed method to a breast cancer dataset helps to identify genomic regions significantly associated with the disease.
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Affiliation(s)
- Ming Li
- Division of Biostatistics, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yalu Wen
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing MI, USA
| | - Wenjiang Fu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing MI, USA. ; Department of Mathematics, University of Houston, Houston, TX, USA
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19
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Nossent JC, Becker-Merok A, Rischmueller M, Lester S. Susceptibility for Lupus Nephritis by Low Copy Number of the FCGR3B Gene Is Linked to Increased Levels of Pathogenic Autoantibodies. Autoimmune Dis 2013; 2013:750814. [PMID: 23864940 PMCID: PMC3705838 DOI: 10.1155/2013/750814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
Low copy number (CN) of the FCGR3B gene reduces FCGR3B membrane expression on neutrophils and results in clearance of a smaller amount of immune complex. We investigated FCGR3B CN in relation to the clinical phenotype in a Caucasian SLE cohort (n = 107). FCGR3B CN was determined by three different qPCR parameter estimations (Ct-, Cy0, and cpD1) and confirmed by the FCGR2C/FCGR2A paralog ratio test. Clinical and serological data were then analyzed for their association with FCGR3B CN. Low FCGR3B CN (<2) was more frequent in SLE patients than in healthy controls (n = 162) (20% versus 6%, OR 4.15, P = 0.003) and associated with higher disease activity scores (SLEDAI 10.4 versus 6.1, P = 0.03), lupus nephritis (LN) (25 versus 5%, P = 0.03), and increased levels of antibodies against dsDNA (81 versus 37 IU, P = 0.03), C1q (22 versus 6 IU, P = 0.003), and ribosomal P (10 versus 5 IU, P = 0.01). No such associations were seen with antibodies against extractable nuclear antigens or high FCGR3B CN (>2). In multivariate analyses, LN was independently associated with anti-C1q-Ab levels (P = 0.03) and low FCGR3B CN (P = 0.09). We conclude that the susceptibility for LN in patients with low FCGR3B CN is linked to increased levels of pathogenic autoantibodies.
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Affiliation(s)
- Johannes C. Nossent
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
| | - Andrea Becker-Merok
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
| | - Maureen Rischmueller
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
- Division of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Sue Lester
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
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20
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Boonpeng H, Yusoff K. The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges. Mol Cytogenet 2013; 6:8. [PMID: 23448375 PMCID: PMC3599593 DOI: 10.1186/1755-8166-6-8] [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: 09/21/2012] [Accepted: 01/03/2013] [Indexed: 01/08/2023] Open
Abstract
The ultimate goal of human genetics is to understand the role of genome variation in elucidating human traits and diseases. Besides single nucleotide polymorphism (SNP), copy number variation (CNV), defined as gains or losses of a DNA segment larger than 1 kb, has recently emerged as an important tool in understanding heritable source of human genomic differences. It has been shown to contribute to genetic susceptibility of various common and complex diseases. Despite a handful of publications, its role in cardiovascular diseases remains largely unknown. Here, we deliberate on the currently available technologies for CNV detection. The possible utility and the potential roles of CNV in exploring the mechanisms of cardiac remodeling in hypertension will also be addressed. Finally, we discuss the challenges for investigations of CNV in cardiovascular diseases and its possible implications in diagnosis of hypertension-related left ventricular hypertrophy (LVH).
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Affiliation(s)
- Hoh Boonpeng
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Sungai, Buloh, 47000, Malaysia.
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21
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Testa CM. Key issues in essential tremor genetics research: Where are we now and how can we move forward? TREMOR AND OTHER HYPERKINETIC MOVEMENTS (NEW YORK, N.Y.) 2013; 3. [PMID: 23450143 PMCID: PMC3582856 DOI: 10.7916/d8q23z0z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 12/04/2012] [Indexed: 01/06/2023]
Abstract
Background Genetics research is an avenue towards understanding essential tremor (ET). Advances have been made in genetic linkage and association: there are three reported ET susceptibility loci, and mixed but growing data on risk associations. However, causal mutations have not been forthcoming. This disappointing lack of progress has opened productive discussions on challenges in ET and specifically ET genetics research, including fundamental assumptions in the field. Methods This article reviews the ET genetics literature, results to date, the open questions in ET genetics and the current challenges in addressing them. Results Several inherent ET features complicate genetic linkage and association studies: high potential phenocopy rates, inaccurate tremor self-reporting, and ET misdiagnoses are examples. Increasing use of direct examination data for subjects, family members, and controls is one current response. Smaller moves towards expanding ET phenotype research concepts into non-tremor features, clinically disputed ET subsets, and testing phenotype features instead of clinical diagnosis against genetic data are gradually occurring. The field has already moved to considering complex trait mechanisms requiring detection of combinations of rare genetic variants. Hypotheses may move further to consider novel mechanisms of inheritance, such as epigenetics. Discussion It is an exciting time in ET genetics as investigators start moving past assumptions underlying both phenotype and genetics experimental contributions, overcoming challenges to collaboration, and engaging the ET community. Multicenter collaborative efforts comprising rich longitudinal prospective phenotype data and neuropathologic analysis combined with the latest in genetics experimental design and technology will be the next wave in the field.
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Affiliation(s)
- Claudia M Testa
- Virginia Commonwealth University, Parkinson's and Movement Disorders Center, Richmond Virginia, USA
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22
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Abstract
Fetal imaging technology has been advancing remarkably and prenatal detection and diagnoses have been moved forward from the second and third trimesters to the first trimester. Structural abnormalities detected by fetal imaging often lead to prenatal diagnoses of genetic disorders. However, there are still dilemmas in fetal diagnoses in normal karyotype cases with strong suspicion of congenital genetic disorders from sonographic findings. When fetal sonography reveals multiple minor abnormalities originating from various organs, counseling dilemmas and parental anxieties become greater than before karyotyping. Array-comparative genomic hybridization (aCGH) was developed as a high-resolution analysis of DNA copy number variations (CNVs). In seven cases presenting with abnormal brain structures by fetal imaging, abnormal CNVs were confirmed by aCGH but conventional karyotyping yielded normal results. Although careful patient selection is required in order to deal with microarray results and parental counseling, 'sonogenetics' - incorporating the idea of 'fetuses first' - will play an important role in the era of molecular genetics. Recent advances in non-invasive prenatal testing by using fetal cell-free DNA in maternal plasma has the potential to generate misleading prenatal diagnoses without the observation of fetuses. However, no fetal diagnoses should be made without observing fetuses and we must not forget 'the fetus as a patient'.
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Affiliation(s)
- Ritsuko K Pooh
- CRIFM Clinical Research Institute of Fetal Medicine PMC, 7-3-7, Uehommachi, Tennoji, Osaka #543-0001, Japan.
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23
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de Jong A, Dondorp WJ, Krumeich A, Boonekamp J, van Lith JMM, de Wert GMWR. The scope of prenatal diagnosis for women at increased risk for aneuploidies: views and preferences of professionals and potential users. J Community Genet 2012; 4:125-35. [PMID: 23138342 DOI: 10.1007/s12687-012-0126-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/16/2012] [Indexed: 12/23/2022] Open
Abstract
The increasing number of prenatal diagnostic tests in prenatal screening strategies, raises the question what tests to offer and why. This qualitative study investigated the views and preferences of professionals and potential users regarding four diagnostic test options for women at increased risk for common aneuploidies. Seven focus group sessions were conducted in The Netherlands between October 2009 and June 2010, with various categories of participants (n = 55): professionals engaged in prenatal testing and potential users of this testing (meaning pregnant women and parents of young children). Participants were invited to mention all pros and cons and their preferences regarding four hypothetical diagnostic test options, presented on vignettes: a standard offer of rapid aneuploidy detection, karyotyping or array comparative genomic hybridization, representing a narrow, traditional and broad test, respectively, and the option of individualised choice. Then, a semi-structured group interview was conducted. The data were analysed by the constant comparative method. Participants identified similar test-specific pros and cons but showed different preferences. Users' opinion on what test to offer as a general policy differed from what they would choose themselves. All participants agreed that in theory, users should be enabled to make an informed choice about what test to apply, but they disagreed about the feasibility of this ideal. Standard narrow testing was favoured for its limiting effects on emotional and organisational burdens; individualised choice was preferred for assuring women's decisive influence. The varying opinions reflect different views on what autonomy in the prenatal screening context means, suggest that a single standard test offer is inadequate and that differentiation will be needed.
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Affiliation(s)
- Antina de Jong
- Department of Health, Ethics & Society, Maastricht University, PO Box 616, Maastricht, 6200, MD, The Netherlands,
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24
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Single nucleotide polymorphism microarray analysis in cortisol-secreting adrenocortical adenomas identifies new candidate genes and pathways. Neoplasia 2012; 14:206-18. [PMID: 22496620 DOI: 10.1593/neo.111758] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/13/2012] [Accepted: 02/13/2012] [Indexed: 02/04/2023] Open
Abstract
The genetic mechanisms underlying adrenocortical tumor development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays (Affymetrix SNP 6.0) to detect copy number alterations (CNAs) and copy-neutral losses of heterozygosity (cnLOH) in 15 cortisol-secreting adrenocortical adenomas with matched blood samples. We focused on microalterations aiming to discover new candidate genes involved in early tumorigenesis and/or autonomous cortisol secretion. We identified 962 CNAs with a median of 18 CNAs per sample. Half of them involved noncoding regions, 89% were less than 100 kb, and 28% were found in at least two samples. The most frequently gained regions were 5p15.33, 6q16.1, 7p22.3-22.2, 8q24.3, 9q34.2-34.3, 11p15.5, 11q11, 12q12, 16q24.3, 20p11.1-20q21.11, and Xq28 (≥20% of cases), most of them being identified in the same three adenomas. These regions contained among others genes like NOTCH1, CYP11B2, HRAS, and IGF2. Recurrent losses were less common and smaller than gains, being mostly localized at 1p, 6q, and 11q. Pathway analysis revealed that Notch signaling was the most frequently altered. We identified 46 recurrent CNAs that each affected a single gene (31 gains and 15 losses), including genes involved in steroidogenesis (CYP11B1) or tumorigenesis (CTNNB1, EPHA7, SGK1, STIL, FHIT). Finally, 20 small cnLOH in four cases affecting 15 known genes were found. Our findings provide the first high-resolution genome-wide view of chromosomal changes in cortisol-secreting adenomas and identify novel candidate genes, such as HRAS, EPHA7, and SGK1. Furthermore, they implicate that the Notch1 signaling pathway might be involved in the molecular pathogenesis of adrenocortical tumors.
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25
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Corrales NLL, Mrasek K, Voigt M, Liehr T, Kosyakova N. Copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitors. Gene 2012; 506:377-9. [PMID: 22820389 DOI: 10.1016/j.gene.2012.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 01/22/2023]
Abstract
Results from the analysis of copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitor cell lines (hiPSC and hESC-derived NPC) are presented. Two different types of CNVs were detected: a) CNVs inherited from the original source of pluripotent cells (hESC and hiPSC) and b) CNVs detected either in the original source of pluripotent cells or in the derived NPC cell lines but not in both at the same time. Our data suggest that submicroscopic chromosomal changes happened during culture and manipulation of cells and those differentiation procedures could result in gains and losses of genomic regions in pluripotent cell-derived neuroprogenitors. Overall, the results indicate that even chromosomally stable stem cell lines would need to be analyzed in detail by high resolution methodologies before their clinical use.
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26
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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Li X, Zhou J, Nahas SA, Wan H, Hu H, Gatti RA. Common copy number variations in fifty radiosensitive cell lines. Genomics 2012; 99:96-100. [DOI: 10.1016/j.ygeno.2011.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 01/15/2023]
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Buizer-Voskamp JE, Muntjewerff JW, Strengman E, Sabatti C, Stefansson H, Vorstman JAS, Ophoff RA. Genome-wide analysis shows increased frequency of copy number variation deletions in Dutch schizophrenia patients. Biol Psychiatry 2011; 70:655-62. [PMID: 21489405 PMCID: PMC3137747 DOI: 10.1016/j.biopsych.2011.02.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 01/30/2023]
Abstract
BACKGROUND Since 2008, multiple studies have reported on copy number variations (CNVs) in schizophrenia. However, many regions are unique events with minimal overlap between studies. This makes it difficult to gain a comprehensive overview of all CNVs involved in the etiology of schizophrenia. We performed a systematic CNV study on the basis of a homogeneous genome-wide dataset aiming at all CNVs ≥ 50 kilobase pair. We complemented this analysis with a review of cytogenetic and chromosomal abnormalities for schizophrenia reported in the literature with the purpose of combining classical genetic findings and our current understanding of genomic variation. METHODS We investigated 834 Dutch schizophrenia patients and 672 Dutch control subjects. The CNVs were included if they were detected by QuantiSNP (http://www.well.ox.ac.uk/QuantiSNP/) as well as PennCNV (http://www.neurogenome.org/cnv/penncnv/) and contain known protein coding genes. The integrated identification of CNV regions and cytogenetic loci indicates regions of interest (cytogenetic regions of interest [CROIs]). RESULTS In total, 2437 CNVs were identified with an average number of 2.1 CNVs/subject for both cases and control subjects. We observed significantly more deletions but not duplications in schizophrenia cases versus control subjects. The CNVs identified coincide with loci previously reported in the literature, confirming well-established schizophrenia CROIs 1q42 and 22q11.2 as well as indicating a potentially novel CROI on chromosome 5q35.1. CONCLUSIONS Chromosomal deletions are more prevalent in schizophrenia patients than in healthy subjects and therefore confer a risk factor for pathogenicity. The combination of our CNV data with previously reported cytogenetic abnormalities in schizophrenia provides an overview of potentially interesting regions for positional candidate genes.
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Affiliation(s)
- Jacobine E Buizer-Voskamp
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands, Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Jan-Willem Muntjewerff
- Department of Psychiatry, University Medical Centre St Radboud, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | | | - Eric Strengman
- Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Chiara Sabatti
- Department of Health Research and Policy, Stanford University School of Medicine, HRP Redwood Building, Stanford, CA 94305-5405, USA
| | - Hreinn Stefansson
- CNS Division, deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Jacob AS Vorstman
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Roel A Ophoff
- Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands, Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands, Center for Neurobehavioral Genetics, University of California, 695 Charles E Young Drive South, Los Angeles, CA 90095, USA
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29
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Leung TY, Vogel I, Lau TK, Chong W, Hyett JA, Petersen OB, Choy KW. Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency and apparently normal karyotype. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2011; 38:314-319. [PMID: 21400624 DOI: 10.1002/uog.8988] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/28/2011] [Indexed: 05/30/2023]
Abstract
OBJECTIVE Fetal nuchal translucency (NT) is assessed by ultrasonography as a screening tool for aneuploidy at 11 to 13 + 6 weeks' gestation. Fetuses with increased NT but apparently normal karyotype are still at higher risk of structural abnormality and a range of genetic syndromes, which may be related to major and submicroscopic chromosomal abnormalities. The aim of this study was to report the prevalence of submicroscopic chromosomal abnormalities in a cohort of apparently euploid fetuses that presented with increased NT. METHODS DNA was extracted from stored chorionic villus samples from fetuses found to have increased NT (> 3.5 mm) during first-trimester screening. These samples were examined by microarray-based comparative genomic hybridization (aCGH) using a 44K oligonucleotide array specifically constructed for prenatal screening. Variations in copy number (CNVs) were reported after excluding known non-pathogenic variants and after validation with multiplex ligation-dependent probe amplification (MLPA) or real-time quantitative polymerase chain reaction (qPCR). The prevalence of pathogenic CNVs is reported and the association with NT and other ultrasound findings described. RESULTS CNVs were reported in 6/48 (12.5%) cases by aCGH and the microdeletions or microduplications ranged from 1.1 to 7.9 Mb. Five of these were validated by MLPA/real-time qPCR and four (8.3%) were considered to be pathogenic and clinically significant. The incidence of pathogenic CNVs was 20.0% (2/10) among those cases with other sonographic anomalies and 5.3% (2/38) among those without. CONCLUSION aCGH allows detection of submicroscopic chromosomal abnormalities, the prevalence of which may be increased in fetuses with NT > 3.5 mm and an apparently normal karyotype.
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Affiliation(s)
- T Y Leung
- Fetal Medicine Unit, Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
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Jack MM, Ryals JM, Wright DE. Characterisation of glyoxalase I in a streptozocin-induced mouse model of diabetes with painful and insensate neuropathy. Diabetologia 2011; 54:2174-82. [PMID: 21633909 PMCID: PMC3762253 DOI: 10.1007/s00125-011-2196-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/27/2011] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS Diabetic peripheral neuropathy (DN) is a common complication of diabetes; however, the mechanisms producing positive or negative symptoms are not well understood. The enzyme glyoxalase I (GLO1) detoxifies reactive dicarbonyls that form AGEs and may affect the way sensory neurons respond to heightened AGE levels in DN. We hypothesised that differential GLO1 levels in sensory neurons may lead to differences in AGE formation and modulate the phenotype of DN. METHODS Inbred strains of mice were used to assess the variability of Glo1 expression by quantitative RT-PCR. Non-diabetic C57BL/6 mice were used to characterise the distribution of GLO1 in neural tissues by immunofluorescence. Behavioural assessments were conducted in diabetic A/J and C57BL/6 mice to determine mechanical sensitivity, and GLO1 abundance was determined by western blot. RESULTS GLO1 immunoreactivity was found throughout the nervous system, but selectively in small, unmyelinated peptidergic dorsal root ganglia (DRG) neurons that are involved in pain transmission. GLO1 protein was present at various levels in DRG from different inbred mice strains. Diabetic A/J and C57BL/6 mice, two mouse strains with different levels of GLO1, displayed dramatically different behavioural responses to mechanical stimuli. Diabetic C57BL/6 mice also had a reduced abundance of GLO1 following diabetes induction. CONCLUSIONS/INTERPRETATION These findings reveal that the abundance of GLO1 varies between different murine strains and within different sensory neuron populations. These differences could lead to different responses of sensory neurons to the toxic effects of hyperglycaemia and reactive dicarbonyls associated with diabetes.
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Affiliation(s)
- M M Jack
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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31
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Abstract
PURPOSE OF REVIEW Evaluation of copy number variation by microarray analysis has significant advantages over standard metaphase karyotyping and is quickly becoming the primary means of postnatal genetic evaluation for neonates and infants with dysmorphic features or cognitive difficulties. Before this technology is routinely used for prenatal diagnosis, further evaluation of its value and the clinical dilemmas it may introduce requires further study. This article reviews the recent literature on array technology use in prenatal diagnosis. RECENT FINDINGS The use of microarray analysis for routine prenatal diagnosis is still being investigated. Use in certain prenatal situations such as the fetus with structural anomalies or those who are stillborn appears to add important, clinically relevant information. There are a broad range of array designs available and recent research has focused on the appropriate design for prenatal testing. Patient counseling may occasionally be difficult because of the uncertain phenotype associated with some array findings. SUMMARY We present a brief overview of microarray technology including benefits and limitations. Previous research regarding use of microarray in prenatal diagnosis including specific scenarios of anomalous fetuses and abnormal karyotype is reviewed. Current guidelines and the authors' recommendations are presented.
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Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort. Eur J Hum Genet 2011; 19:1167-72. [PMID: 21731056 DOI: 10.1038/ejhg.2011.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To date, hundreds of thousands of copy-number variation (CNV) data have been reported using various platforms. The proportion of Asians in these data is, however, relatively small as compared with that of other ethnic groups, such as Caucasians and Yorubas. Because of limitations in platform resolution and the high noise level in signal intensity, in most CNV studies (particularly those using single nucleotide polymorphism arrays), the average number of CNVs in an individual is less than the number of known CNVs. In this study, we ascertained reliable, common CNV regions (CNVRs) and identified actual frequency rates in the Korean population to provide more CNV information. We performed two-stage analyses for detecting structural variations with two platforms. We discovered 576 common CNVRs (88 CNV segments on average in an individual), and 87% (501 of 576) of these CNVRs overlapped by ≥1 bp with previously validated CNV events. Interestingly, from the frequency analysis of CNV profiles, 52 of 576 CNVRs had a frequency rate of <1% in the 8842 individuals. Compared with other common CNV studies, this study found six common CNVRs that were not reported in previous CNV studies. In conclusion, we propose the data-driven detection approach to discover common CNVRs including those of unreported in the previous Korean CNV study while minimizing false positives. Through our approach, we successfully discovered more common CNVRs than previous Korean CNV study and conducted frequency analysis. These results will be a valuable resource for the effective level of CNVs in the Korean population.
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Glyoxalase in ageing. Semin Cell Dev Biol 2011; 22:293-301. [DOI: 10.1016/j.semcdb.2011.02.013] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 11/15/2022]
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Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ. Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinformatics 2011; 12:114. [PMID: 21510904 PMCID: PMC3112242 DOI: 10.1186/1471-2105-12-114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 04/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs), including deletions, amplifications, and other rearrangements, are common in human and cancer genomes. Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants. Comparison of copy number data from multiple individuals reveals recurrent variants. Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant. RESULTS We introduce Neighborhood Breakpoint Conservation (NBC), an algorithm for identifying rearrangement breakpoints that are highly conserved at the same locus in multiple individuals. NBC detects recurrent breakpoints at varying levels of resolution, including breakpoints whose location is exactly conserved and breakpoints whose location varies within a gene. NBC also identifies pairs of recurrent breakpoints such as those that result from fusion genes. We apply NBC to aCGH data from 36 primary prostate tumors and identify 12 novel rearrangements, one of which is the well-known TMPRSS2-ERG fusion gene. We also apply NBC to 227 glioblastoma tumors and predict 93 novel rearrangements which we further classify as gene truncations, germline structural variants, and fusion genes. A number of these variants involve the protein phosphatase PTPN12 suggesting that deregulation of PTPN12, via a variety of rearrangements, is common in glioblastoma. CONCLUSIONS We demonstrate that NBC is useful for detection of recurrent breakpoints resulting from copy number variants or other structural variants, and in particular identifies recurrent breakpoints that result in gene truncations or fusion genes. Software is available at http://http.//cs.brown.edu/people/braphael/software.html.
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Affiliation(s)
- Anna Ritz
- Department of Computer Science, Brown University, Providence, RI, USA.
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Gross SJ, Bajaj K, Garry D, Klugman S, Karpel BM, Roe AM, Wagner BJ, Zhan J, Apfelroth SD, Schreiber-Agus N. Rapid and novel prenatal molecular assay for detecting aneuploidies and microdeletion syndromes. Prenat Diagn 2011; 31:259-66. [PMID: 21207408 DOI: 10.1002/pd.2674] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 10/22/2010] [Accepted: 10/24/2010] [Indexed: 11/12/2022]
Abstract
OBJECTIVES To develop a targeted aneuploidy and microdeletion detection platform for use in the prenatal setting, to assess the integrity of the platform with a robust validation system, and to prospectively determine the performance of the platform under routine clinical conditions. METHODS To generate proxies for the various disorders assessed by the assay for analytical validation purposes, cells from ten microdeletion syndromes as well as from common aneuploidies were spiked into cleared amniotic fluid. Genomic DNA was isolated, labeled, and hybridized to microbeads that have been coupled to DNA derived from Bacterial Artificial Chromosome (BAC) from the relevant regions targeted by the array. Beads were read using a flow cytometric multiplex bead array detection system. In the prospective part of the study, 104 amniotic fluid samples were collected and analyzed. RESULTS All microdeletion syndromes and aneuploidies were validated in a blinded fashion. In the prospective study, the total number of readable samples was 101 of 104 (97%). All sample results were confirmed independently. CONCLUSION The bead array approach is a rapid and reliable test for detecting aneuploidies and microdeletions. This assay has the potential to provide the benefit of expanded molecular cytogenetic testing to pregnant women undergoing invasive prenatal diagnosis. This approach may be especially useful in parts of the world where cytogenetic personnel and facilities may be limited.
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Affiliation(s)
- Susan J Gross
- Department of Obstetrics and Gynecology, North Bronx Healthcare Network, Albert Einstein College of Medicine, Bronx, NY, USA.
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Leung TY, Pooh RK, Wang CC, Lau TK, Choy KW. Classification of pathogenic or benign status of CNVs detected by microarray analysis. Expert Rev Mol Diagn 2010; 10:717-21. [PMID: 20843196 DOI: 10.1586/erm.10.68] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multiple lines of evidence indicated that microarray analysis has a better diagnostic yield of clinically significant genetic changes than do conventional methods in patients with constitutional abnormalities. However, interpretation of microarray data is complicated by the presence of both novel and recurrent copy number variants (CNVs) of unknown significance. To address this issue, Hehir-Kwa et al. described a new computational method for determining the pathogenicity between benign and mental retardation (MR)-associated CNVs among patients with MR. This study demonstrated the value of objectively prioritizing MR-associated CNVs using structural and functional genomic features in diagnostics. In this regard, we discuss an evidence-based summary of how to classify pathogenic or benign status of a CNV in clinical genetics and advocate that there is a need for algorithmic adjustment between constitutional cytogenetic and prenatal diagnosis settings.
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Affiliation(s)
- Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR
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Ramayo-Caldas Y, Castelló A, Pena RN, Alves E, Mercadé A, Souza CA, Fernández AI, Perez-Enciso M, Folch JM. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics 2010; 11:593. [PMID: 20969757 PMCID: PMC3091738 DOI: 10.1186/1471-2164-11-593] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 10/22/2010] [Indexed: 12/17/2022] Open
Abstract
Background Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips. Results We used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species. Conclusions Our results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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