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Victor Oluwaloseyi A, Aduragbemi Noah O, Lydia Oluwatoyin A, Gaffar Y, Moses O, Oyedayo Phillips A, Comfort Onaolapo M, Sylvester Olateju B, Ademola Ayodele A, Mega Obukohwo O, Ayodeji Folorunsho A. Metabolomics of male infertility. Clin Chim Acta 2024; 556:117850. [PMID: 38431200 DOI: 10.1016/j.cca.2024.117850] [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: 12/16/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
This review explores the use of metabolomics in male infertility. Metabolomics, an evolving omics technology that targets the products of cellular metabolism, is valuable for elucidating underlying pathophysiology of many disorders including male infertility. The identification of reliable biomarkers is essential for accurate diagnosis and for developing precision therapeutics for those afflicted by reproductive dysfunction. Unfortunately, despite significant progress to date, the intricate relationships between these metabolic pathways and male infertility remain elusive. It is clear, however, that additional research is required to more fully characterize the role of metabolomics in this disorder and in the potential development of targeted therapies for precision medicine.
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Affiliation(s)
- Amos Victor Oluwaloseyi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | - Odeyemi Aduragbemi Noah
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Ajayi Lydia Oluwatoyin
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Yusuff Gaffar
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olotu Moses
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Moyinoluwa Comfort Onaolapo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adelakun Ademola Ayodele
- Department of Medical Laboratory Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Ajayi Ayodeji Folorunsho
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Adeleke University, Ede, Osun State, Nigeria.
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Chadarevian JP, Davtyan H, Lombroso SI, Bennett FC, Blurton-Jones M. CRISPR generation of CSF1R-G795A human microglia for robust microglia replacement in a chimeric mouse model. STAR Protoc 2023; 4:102490. [PMID: 37516973 PMCID: PMC10407259 DOI: 10.1016/j.xpro.2023.102490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Chimeric mouse models have recently been developed to study human microglia in vivo. However, widespread engraftment of donor microglia within the adult brain has been challenging. Here, we present a protocol to introduce the G795A point mutation using CRISPR-Cas9 into the CSF1R locus of human pluripotent stem cells. We also describe an optimized microglial differentiation technique for transplantation into newborn or adult recipients. We then detail pharmacological paradigms to achieve widespread and near-complete engraftment of human microglia. For complete details on the use and execution of this protocol, please refer to Chadarevian et al. (2023).1.
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Affiliation(s)
- Jean Paul Chadarevian
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
| | - Hayk Davtyan
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA
| | - Sonia I Lombroso
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - F Chris Bennett
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mathew Blurton-Jones
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA.
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Ravel JM, Renaud M, Muller J, Becker A, Renard É, Remen T, Lefort G, Dexheimer M, Jonveaux P, Leheup B, Bonnet C, Lambert L. Clinical utility of periodic reinterpretation of CNVs of uncertain significance: an 8-year retrospective study. Genome Med 2023; 15:39. [PMID: 37221613 DOI: 10.1186/s13073-023-01191-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Array-CGH is the first-tier genetic test both in pre- and postnatal developmental disorders worldwide. Variants of uncertain significance (VUS) represent around 10~15% of reported copy number variants (CNVs). Even though VUS reanalysis has become usual in practice, no long-term study regarding CNV reinterpretation has been reported. METHODS This retrospective study examined 1641 CGH arrays performed over 8 years (2010-2017) to demonstrate the contribution of periodically re-analyzing CNVs of uncertain significance. CNVs were classified using AnnotSV on the one hand and manually curated on the other hand. The classification was based on the 2020 American College of Medical Genetics (ACMG) criteria. RESULTS Of the 1641 array-CGH analyzed, 259 (15.7%) showed at least one CNV initially reported as of uncertain significance. After reinterpretation, 106 of the 259 patients (40.9%) changed categories, and 12 of 259 (4.6%) had a VUS reclassified to likely pathogenic or pathogenic. Six were predisposing factors for neurodevelopmental disorder/autism spectrum disorder (ASD). CNV type (gain or loss) does not seem to impact the reclassification rate, unlike the length of the CNV: 75% of CNVs downgraded to benign or likely benign are less than 500 kb in size. CONCLUSIONS This study's high rate of reinterpretation suggests that CNV interpretation has rapidly evolved since 2010, thanks to the continuous enrichment of available databases. The reinterpreted CNV explained the phenotype for ten patients, leading to optimal genetic counseling. These findings suggest that CNVs should be reinterpreted at least every 2 years.
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Affiliation(s)
- Jean-Marie Ravel
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Mathilde Renaud
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Jean Muller
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale, INSERM, UMRS_1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg Faculté de Médecine de Strasbourg, 67000, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, 67000, Strasbourg, France
| | - Aurélie Becker
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
| | - Émeline Renard
- Department of pediatrics, Regional University Hospital of Nancy, Allée du Morvan, 54511, Vandoeuvre-Lès-Nancy, France
| | | | | | | | | | - Bruno Leheup
- Service de génétique médicale, CHRU de Nancy, Nancy, France
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France.
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France.
| | - Laëtitia Lambert
- Service de génétique médicale, CHRU de Nancy, Nancy, France.
- Université de Lorraine, NGERE, F-54000Nancy, Inserm, France.
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Hu H, Huang Y, Hou R, Xu H, Liu Y, Liao X, Xu J, Jiang L, Wang D. Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up. BMC Med Genomics 2023; 16:69. [PMID: 37013593 PMCID: PMC10069036 DOI: 10.1186/s12920-023-01493-z] [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: 08/17/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.
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Affiliation(s)
- Huamei Hu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huanhuan Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Dan Wang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
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He W, Meng G, Hu X, Dai J, Liu J, Li X, Hu H, Tan Y, Zhang Q, Lu G, Lin G, Du J. Reclassification of DMD Duplications as Benign: Recommendations for Cautious Interpretation of Variants Identified in Prenatal Screening. Genes (Basel) 2022; 13:1972. [PMID: 36360209 PMCID: PMC9690433 DOI: 10.3390/genes13111972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 09/09/2023] Open
Abstract
Duplications are the main type of dystrophin gene (DMD) variants, which typically cause dystrophinopathies such as Duchenne muscular dystrophy and Becker muscular dystrophy. Maternally inherited exon duplication in DMD in fetuses is a relatively common finding of genetic screening in clinical practice. However, there is no standard strategy for interpretation of the pathogenicity of DMD duplications during prenatal screening, especially for male fetuses, in which maternally inherited pathogenic DMD variants more frequently cause dystrophinopathies. Here, we report three non-contiguous DMD duplications identified in a woman and her male fetus during prenatal screening. Multiplex ligation probe amplification and long-read sequencing were performed on the woman and her family members to verify the presence of DMD duplications. Structural rearrangements in the DMD gene were mapped by long-read sequencing, and the breakpoint junction sequences were validated using Sanger sequencing. The woman and her father carried three non-contiguous DMD duplications. Long-read and Sanger sequencing revealed that the woman's father carried an intact DMD copy and a complex structural rearrangement of the DMD gene. Therefore, we reclassified these three non-contiguous DMD duplications, one of which is listed as pathogenic, as benign. We postulate that breakpoint analysis should be performed on identified DMD duplication variants, and the pathogenicity of the duplications found during prenatal screening should be interpreted cautiously for clinical prediction and genetic/reproductive counseling.
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Affiliation(s)
- Wenbin He
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Guiquan Meng
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
| | - Xiao Hu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Jing Dai
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Jiyang Liu
- Changsha Health Committee, Changsha 410006, China
| | - Xiurong Li
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Hao Hu
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha 410008, China
- National Engineering and Research Center of Human Stem Cells, Changsha 410006, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
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Cokyaman T, Silan F. Diagnostic Utility of Array Comparative Genomic Hybridization in Children with Neurological Diseases. Fetal Pediatr Pathol 2022; 41:68-76. [PMID: 32401632 DOI: 10.1080/15513815.2020.1764683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. MATERIALS AND METHODS Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. RESULTS Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). CONCLUSION With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.
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Affiliation(s)
- Turgay Cokyaman
- Pediatric Neurology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Fatma Silan
- Medical Genetics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Canakkale, Turkey
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Zhang Q, Qin Z, Yi S, Wei H, Zhou XZ, Su J. Clinical application of whole-exome sequencing: A retrospective, single-center study. Exp Ther Med 2021; 22:753. [PMID: 34035850 PMCID: PMC8135134 DOI: 10.3892/etm.2021.10185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to assess the practical diagnostic value of whole-exome sequencing (WES) in patients with different phenotypes and to explore possible strategies to increase the capability of WES in identifying disease-causing genes. A total of 1,360 patients (aged from 1 day to 42 years old) with manifestations of genetic diseases were genotyped using WES and statistical analysis was performed on the results obtained. Within this cohort, the overall positive rate of identification of a disease-causing gene alteration was 44.41%. The positive identification rate where trio-samples were used (from the proband and both parents) was higher than that where a single proband sample was used (50.00 vs. 43.71%), and 604 positive cases with 150 genetic syndromes, 510 genes and 718 mutations were detected. Missense mutations were the most common variations (n=335, 45.27%) and visual or auditory abnormalities (58.51%) had the highest rate of association with a genetic abnormality. The positive detection rate of WES was elevated with the increase in the number of clinical symptoms from 1 to 8. The present study indicated that WES may be used as a valuable tool in the clinic and the positive rate depends more on the professional experience of clinicians rather than on the analytical capabilities of the data analyst. At the same time, particular attention must be paid to certain possible factors (such as the age of the patients as well as possible exon deletions), which may affect the diagnostic rate while applying this process.
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Affiliation(s)
- Qiang Zhang
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
| | - Zailong Qin
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
| | - Shang Yi
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
| | - Hao Wei
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
| | - Xun Zhao Zhou
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
| | - Jiasun Su
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi, Nanning, Guangxi 530000, P.R. China
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Diniz BL, Santos AS, Glaeser AB, Guaraná BB, Lorea CF, Josahkian JA, Huber J, Rosa RFM, Zen PRG. Congenital Heart Defects and Dysmorphic Facial Features in Patients Suspicious of 22q11.2 Deletion Syndrome in Southern Brazil. J Pediatr Genet 2020; 9:227-234. [PMID: 32733742 PMCID: PMC7384886 DOI: 10.1055/s-0040-1713155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/05/2020] [Indexed: 10/24/2022]
Abstract
22q11.2 deletion syndrome (22q11.2DS) is considered one of the most frequently observed chromosomal abnormalities in association with congenital heart disease (CHD), which can also include some combination of other features. Thus, the aim of this work was to verify the profile of dysmorphic features and heart defects found in patients referred to a reference center in Southern Brazil with clinical findings suggestive of 22q11.2DS. In the overall sample group, only patients with dysmorphic facial features (skull, eyes, ear, and nose) associated with CHD (obstructive pulmonary valve ring, truncus arteriosus, and bicuspid aortic valve associated with atrial septal defect and/or right aortic arch) had a 22q11.2 deletion. These findings proved to be reliable clinical criteria for referral to perform fluorescent in situ hybridization investigation for 22q11.2 deletion.
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Affiliation(s)
- Bruna Lixinski Diniz
- Department of Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Andressa Barreto Glaeser
- Department of Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Bruna Baierle Guaraná
- Department of Internal Medicine, Clinical Genetics, UFCSPA and Irmandade Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Cláudia Fernandes Lorea
- Child and Adolescent Health Care Unit, Hospital Escola da Universidade Federal de Pelotas (HE-UFPEL), Pelotas, RS, Brazil
| | - Juliana Alves Josahkian
- Department of Clinical Medicine, Hospital Universitário de Santa Maria (HU-SM), Santa Maria, RS, Brazil
| | - Janaína Huber
- Department of Congenital and Pediatric Heart Disease, Instituto de Cardiologia/Fundacão Universitária de Cardiologia, Porto Alegre, RS, Brazil
| | - Rafael Fabiano Machado Rosa
- Department of Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
- Department of Internal Medicine, Clinical Genetics, UFCSPA and Irmandade Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Paulo Ricardo Gazzola Zen
- Department of Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
- Department of Internal Medicine, Clinical Genetics, UFCSPA and Irmandade Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
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Roelandt MA, Devriendt K, de Llano-Pérula MC, Raes M, Willems G, Verdonck A. Dental and Craniofacial Characteristics in Patients With 14Q22.1-Q22.2 Deletion: A Case Series. Cleft Palate Craniofac J 2020; 58:505-513. [PMID: 33063524 DOI: 10.1177/1055665620954090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This case series is a follow-up report focusing on dental and facial characteristics in patients with a rare microdeletion in chromosome 14q22.1-q22.2. Usually, these patients have severe ocular, brain, and digital abnormalities. However, this case series shows that clinical presentation can be mild. Four relatives spanning 3 generations were diagnosed with a familial autosomal dominant 2.79 Mb microdeletion in chromosome 14q22.1-q22.2. Genetic screening was done by the Bacterial Artificial Chromosome array-comparative genome hybridization and was confirmed by the fluorescence in situ hybridization technique. Dental and craniofacial data were collected from medical files, clinical examinations, clinical photos, panoramic and cephalometric radiographs, and dental casts. Written informed consent for scientific use was obtained for all family members. No larger syndrome could be identified. All cases had similar facial red flag characteristics, consisting of a long face with retrognathia and open mouth relation, associated oral clefts in varying degrees, depressed nasal bridge, delayed tooth development, hypertelorism, and low-set angular ears. The dental casts showed a distal molar occlusion and a lack of space in the dental arches. Developmental delay was noted together with limb defects such as poly- and syndactyly. Microphthalmia and hearing loss were present in the most severe cases. This rare congenital disorder, associated with facial dysmorphia, oral clefts, and tooth agenesis, can remain undiagnosed until adulthood. A family history of short stature, developmental delay, poly- or syndactyly, and micropthalmia are suggestive features. Similar reports help to raise awareness among dental practitioners, leading to an early genetic diagnosis.
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Affiliation(s)
- Marie Anne Roelandt
- Department of Oral Health Sciences-Orthodontics, 60182KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | | | - Maria Cadenas de Llano-Pérula
- Department of Oral Health Sciences-Orthodontics, 60182KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - Margot Raes
- Department of Oral Health Sciences-Orthodontics, 60182KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - Guy Willems
- Department of Oral Health Sciences-Orthodontics, 60182KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium
| | - Anna Verdonck
- Department of Oral Health Sciences-Orthodontics, 60182KU Leuven and Dentistry, University Hospitals Leuven, Leuven, Belgium.,Multidisciplinary Cleft Lip and Palate Team, University Hospitals Leuven, Leuven, Belgium
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Gürkan H, Atli Eİ, Atli E, Bozatli L, Altay MA, Yalçintepe S, Özen Y, Eker D, Akurut Ç, Demır S, Görker I. Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders. Noro Psikiyatr Ars 2020; 57:177-191. [PMID: 32952419 PMCID: PMC7481981 DOI: 10.29399/npa.24890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/16/2020] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Aneuploids, copy number variations (CNVs), and single nucleotide variants in specific genes are the main genetic causes of developmental delay (DD) and intellectual disability disorder (IDD). These genetic changes can be detected using chromosome analysis, chromosomal microarray (CMA), and next-generation DNA sequencing techniques. Therefore; In this study, we aimed to investigate the importance of CMA in determining the genomic etiology of unexplained DD and IDD in 123 patients. METHOD For 123 patients, chromosome analysis, DNA fragment analysis and microarray were performed. Conventional G-band karyotype analysis from peripheral blood was performed as part of the initial screening tests. FMR1 gene CGG repeat number and methylation analysis were carried out to exclude fragile X syndrome. RESULTS CMA analysis was performed in 123 unexplained IDD/DD patients with normal karyotypes and fragile X screening, which were evaluated by conventional cytogenetics. Forty-four CNVs were detected in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients were reported. In 6 patients, one or more pathogenic CNVs were determined. Therefore, the diagnostic efficiency of CMA was found to be 31.7% (39/123). CONCLUSION Today, genetic analysis is still not part of the routine in the evaluation of IDD patients who present to psychiatry clinics. A genetic diagnosis from CMA can eliminate genetic question marks and thus alter the clinical management of patients. Approximately one-third of the positive CMA findings are clinically intervenable. However, the emergence of CNVs as important risk factors for multiple disorders increases the need for individuals with comorbid neurodevelopmental conditions to be the priority where the CMA test is recommended.
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Affiliation(s)
- Hakan Gürkan
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Emine İkbal Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Engin Atli
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Leyla Bozatli
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
| | - Mengühan Araz Altay
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
| | - Sinem Yalçintepe
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Yasemin Özen
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Damla Eker
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Çisem Akurut
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Selma Demır
- Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey
| | - Işık Görker
- Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey
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11
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Zhuang J, Wang Y, Zeng S, Lv C, Lin Y, Jiang Y. A prenatal diagnosis and genetics study of five pedigrees in the Chinese population with Xp22.31 microduplication. Mol Cytogenet 2019; 12:50. [PMID: 31857824 PMCID: PMC6907354 DOI: 10.1186/s13039-019-0461-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022] Open
Abstract
Background Copy number variations (CNVs) can contribute to human phenotype, phenotypic diversity and disease susceptibility, while others may benign. In the current study, an attempt to investigate the pathogenicity of CNVs in chromosome Xp22.31 was explored. Methods G-banding and SNP-array techniques were used to analyze chromosome karyotypes and CNVs in fetuses. Parents associate with five different pedigrees possessing high risk factors in pregnancy were considered with such parameters as advanced age, high risk of serological screening and ultrasound abnormalities. Results The fetuses’ amniotic fluid karyotypes were 46, XX and those of their parents with the five pedigrees revealed no abnormalities. Here, we noticed a series of individuals with Xp22.31 duplications ranging from 534.6 kb to 1.6 Mb. It was detected through SNP array that the fetuses in Pedigree 1 and 2 had ~ 600 kb duplications in the Xp22.31 region of their X chromosomes which contained two OMIM genes, HDHD1 (OMIM: 306480) and part of STS (OMIM: 300747). The fetuses of Pedigrees 3, 4 and 5 had 1.6 Mb duplication in the same chromosome which contained four OMIM genes: HDHD1 (OMIM: 306480), STS (OMIM: 300747), PNPLA4 (OMIM: 300102) and VCX (OMIM: 300229). The duplications in the fetuses of Pedigrees 1 and 5 were inherited from the non-phenotypic parents. Pedigrees 3 and 4 refused to perform parental verification. Finally, four of the five pedigrees continue towards pregnancy with no abnormalities being observed during followed-ups. Conclusion Our study first showed duplications of Xp22.31 in Chinese population. Clinical and genetic investigation on five different pedigrees, we consider the duplication of these fragments as likely benign copy number variants (CNVs). We suggest that the duplications of Xp22.31 with recurrent duplication as a benign CNVs .
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Chunling Lv
- Zhejiang Biosan technology Co., Ltd, Zhejiang, People's Republic of China
| | - Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
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12
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Candelo E, Ramirez-Montaño D, Pachajoa H. Microduplication of Xp22.31 and MECP2 Pathogenic Variant in a Girl with Rett Syndrome: A Case Report. IRANIAN JOURNAL OF MEDICAL SCIENCES 2019; 44:347-353. [PMID: 31439979 PMCID: PMC6661518 DOI: 10.30476/ijms.2019.44945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Rett syndrome (RS) is a neurodevelopmental infantile disease characterized by an early normal psychomotor development followed by a regression in the acquisition of normal developmental stages. In the majority of cases, it leads to a sporadic mutation in the MECP2 gene, which is located on the X chromosome. However, this syndrome has also been associated with microdeletions, gene translocations, and other gene mutations. A 12-year-old female Colombian patient was presented with refractory epilepsy and regression in skill acquisition (especially language with motor and verbal stereotypies, hyperactivity, and autistic spectrum disorder criteria). The patient was born to non-consanguineous parents and had an early normal development until the age of 36 months. Comparative genomic hybridization array-CGH (750K) was performed and Xp22.31 duplication was detected (6866889-8115153) with a size of 1.248 Mb associated with developmental delay, epilepsy, and autistic traits. Given the clinical criteria of RS, MECP2 sequencing was performed which showed a de novo pathogenic variant c.338C>G (p.Pro113Arg). The features of RS include intellectual disability, developmental delay, and autism. These features are associated with copy number variations (CNVs) on the X chromosome (Xp22.31 microduplication). Here we present the first reported case of simultaneous CNV and MECP2 pathogenic mutation in a patient with RS. We propose that both DNA alterations might have a synergistic effect and could lead to variable expressivity of the phenotype.
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Affiliation(s)
- Estephania Candelo
- Center for Research on Congenital Anomalies and Rare Diseases (CIACER), Health Sciences Faculty, L Building, Universidad Icesi, Cali, Colombia
| | - Diana Ramirez-Montaño
- Center for Research on Congenital Anomalies and Rare Diseases (CIACER), Health Sciences Faculty, L Building, Universidad Icesi, Cali, Colombia
| | - Harry Pachajoa
- Center for Research on Congenital Anomalies and Rare Diseases (CIACER), Health Sciences Faculty, L Building, Universidad Icesi, Cali, Colombia.,Department of Genetics, Fundación Valle del Lili, Cali, Colombia
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13
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [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: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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14
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Hu H, Wang L, Wu J, Zhou P, Fu J, Sun J, Cai W, Liu H, Yang Y. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies. Hum Genomics 2019; 13:14. [PMID: 30871627 PMCID: PMC6419401 DOI: 10.1186/s40246-019-0198-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the development of whole-genome sequencing technology, small subchromosomal deletions and duplications that could not be detected by conventional karyotyping are now able to be detected with NIPT technology. Methods In the present study, we examined 8141 single pregnancies with NIPT to calculate the positive predictive values of each of the chromosome aneuploidies and the subchromosomal microdeletions and microduplications. Results We confirmed that the positive predictive values (PPV) for trisomy 13, trisomy 18, trisomy 21, and sex chromosome aneuploidy were 14.28%, 60%, 80%, and 45.83%, respectively. At the same time, we also found 51 (0.63%) positive cases for chromosomal microdeletions or microduplications but only 13 (36.11%) true-positive cases. These results indicate that NIPT for trisomy 21 detection had the highest accuracy, while accuracy was low for chromosomal microdeletion and microduplications. Conclusions Therefore, it is very important to improve the specificity, accuracy, and sensitivity of NIPT technology for the detection of subchromosomal microdeletions and microduplications.
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Affiliation(s)
- Hua Hu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Li Wang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiayan Wu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Peng Zhou
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jingli Fu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiuchen Sun
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Weiyi Cai
- CapitalBio Technology Inc., Beijing, 101111, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China.
| | - Ying Yang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China.
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15
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Roumelioti FM, Louizou E, Karras S, Neroutsou R, Velissariou V, Gagos S. Unbalanced X;9 translocation in an infertile male with de novo duplication Xp22.31p22.33. J Assist Reprod Genet 2019; 36:769-775. [PMID: 30675680 DOI: 10.1007/s10815-019-01405-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Male carriers of an X-autosome translocation are generally infertile, regardless of the position of the breakpoint on the X chromosome while the pathogenicity of Xp22.3 subtelomeric duplications is under debate. To shed light into this controversy, we present a rare case, of an azoospermic male with no other significant clinical findings, in whom classical cytogenetics revealed additional unbalanced chromosomal material, at the telomere of the long arm of one homolog of chromosome 9. METHODS In peripheral blood specimens of the index case and his parents, we performed GBanding, Inverted-DAPI Banding, AgNOR staining, Telomere specific Fluorescence in Situ Hybridization (FISH), Molecular karyotyping by Multi-color FISH, whole genome SNP microarrays, sub-telomeric MLPA, and transcription analysis of the expression of KAL1 gene by RT-PCR. RESULTS Multi-color FISH revealed an unbalanced translocation involving the short arm of chromosome X. SNP microarray analysis combined to classical cytogenetics and MLPA demonstrated a de novo 8.796 Mb duplication of Xp22.31-p22.33. Compared to three control specimens, the patient presented significantly elevated expression levels of KAL1 mRNA in peripheral blood, suggesting transcriptional functionality of the duplicated segment. CONCLUSIONS The duplicated segment contains the pseudo-autosomal region PAR1 and more than 30 genes including SHOX, ARSE, STS, KAL1, and FAM9A and is not listed as polymorphic. Our data advocate that duplications of the Xp22.3 region may not be associated with a clinical consequence.
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Affiliation(s)
- Fani-Marlen Roumelioti
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, (BRFAA), Athens, Greece
| | - Eirini Louizou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Spyridon Karras
- Division of Endocrinology and Metabolism, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Rozalia Neroutsou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Voula Velissariou
- Department of Cytogenetics and Molecular Genetics, Bioiatriki, Group of Health Sciences, Athens, Greece
| | - Sarantis Gagos
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, (BRFAA), Athens, Greece.
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16
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Epilepsy phenotype in patients with Xp22.31 microduplication. EPILEPSY & BEHAVIOR CASE REPORTS 2018; 11:31-34. [PMID: 30603611 PMCID: PMC6310737 DOI: 10.1016/j.ebcr.2018.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/05/2018] [Accepted: 10/29/2018] [Indexed: 11/22/2022]
Abstract
The clinical significance of Xp22.31 microduplication is still unclear. We describe a family in which a mother and two children have Xp22.31 microduplication associated with different forms of epilepsy and epileptiform EEG abnormalities. The proband had benign epilepsy with centrotemporal spikes with dysgraphia and dyscalculia (IQ 72), the sister had juvenile myoclonic epilepsy, and both had bilateral talipes anomalies. The mother, who was the carrier of the microduplication, was asymptomatic. The asymptomatic father did not possess the microduplication. These data contribute to delineate the phenotype associated with Xp22.31 microduplication and suggest a potential pathogenic role for an epilepsy phenotype. Developmental disorders are commonly associated with Xp22.31 microduplication. Seizures may occur but specific epileptic syndromes are rare. Xp22.31 microduplication may have an additive role in epilepsy phenotype expression.
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17
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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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18
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Comparative genomic hybridisation as a first option in genetic diagnosis: 1000 cases and a cost–benefit analysis. ANALES DE PEDIATRÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.anpede.2017.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Iourov IY, Zelenova MA, Vorsanova SG, Voinova VV, Yurov YB. 4q21.2q21.3 Duplication: Molecular and Neuropsychological Aspects. Curr Genomics 2018; 19:173-178. [PMID: 29606904 PMCID: PMC5850505 DOI: 10.2174/1389202918666170717161426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/20/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
During the last decades, a large amount of newly described microduplications and microdeletions associated with intellectual disability (ID) and related neuropsychiatric diseases have been discovered. However, due to natural limitations, a significant part of them has not been the focus of multidisciplinary approaches. Here, we address previously undescribed chromosome 4q21.2q21.3 microduplication for gene prioritization, evaluation of cognitive abilities and estimation of genomic mechanisms for brain dysfunction by molecular cytogenetic (cytogenomic) and gene expression (meta-) analyses as well as for neuropsychological assessment. We showed that duplication at 4q21.2q21.3 is associated with moderate ID, cognitive deficits, developmental delay, language impairment, memory and attention problems, facial dysmorphisms, congenital heart defect and dentinogenesis imperfecta. Gene-expression meta-analysis prioritized the following genes: ENOPH1, AFF1, DSPP, SPARCL1, and SPP1. Furthermore, genotype/phenotype correlations allowed the attribution of each gene gain to each phenotypic feature. Neuropsychological testing showed visual-perceptual and fine motor skill deficits, reduced attention span, deficits of the nominative function and problems in processing both visual and aural information. Finally, emerging approaches including molecular cytogenetic, bioinformatic (genome/epigenome meta-analysis) and neuropsychological methods are concluded to be required for comprehensive neurological, genetic and neuropsychological descriptions of new genomic rearrangements/diseases associated with ID.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Ministry of Health, Moscow, Russian Federation
| | - Maria A Zelenova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Svetlana G Vorsanova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Victoria V Voinova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Yuri B Yurov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
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20
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Advani HV, Barrett AN, Evans MI, Choolani M. Challenges in non-invasive prenatal screening for sub-chromosomal copy number variations using cell-free DNA. Prenat Diagn 2017; 37:1067-1075. [PMID: 28950403 DOI: 10.1002/pd.5161] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Accepted: 09/16/2017] [Indexed: 12/14/2022]
Abstract
Non-invasive prenatal screening (NIPS) has revolutionized the approach to prenatal fetal aneuploidy screening. Many commercial providers now offer analyses for sub-chromosomal copy number variations (CNVs). Here, we review the use of NIPS in the context of screening for microdeletions and microduplications, issues surrounding the choice of disorders tested for, and the advantages and disadvantages associated with the inclusion of microdeletions to current NIPS. Several studies have claimed benefits; however, we suggest that microdeletions have not demonstrated a low enough false positive rate to be deemed practical or ethically acceptable, especially considering their low positive predictive values. Because a positive NIPS result should be confirmed using diagnostic techniques, and false positive rates are as high as 90% for some microdeletions, diagnostic testing seems preferable when the goal is to maximize the detection of microdeletion or microduplication syndromes.
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Affiliation(s)
- Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mark I Evans
- Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, NY, USA.,Comprehensive Genetics and Fetal Medicine Foundation of America, New York, NY, USA
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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21
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Castells-Sarret N, Cueto-González AM, Borregan M, López-Grondona F, Miró R, Tizzano E, Plaja A. [Comparative genomic hybridisation as a first option in genetic diagnosis: 1,000 cases and a cost-benefit analysis]. An Pediatr (Barc) 2017; 89:3-11. [PMID: 28958749 DOI: 10.1016/j.anpedi.2017.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Conventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay/intellectual disability and/or multiple congenital anomalies. The Multiplex Ligation-dependent Probe Amplification increases diagnostic rates from between 2.4 to 5.8%. Currently the comparative genomic hybridisation array or aCGH is the highest performing diagnostic tool in patients with developmental delay/intellectual disability, congenital anomalies and autism spectrum disorders. Our aim is to evaluate the efficiency of the use of aCGH as first-line test in these and other indications (epilepsy, short stature). PATIENTS AND METHOD A total of 1000 patients referred due to one or more of the abovementioned disorders were analysed by aCGH. RESULTS Pathogenic genomic imbalances were detected in 14% of the cases, with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with developmental delay/intellectual disability; 13.7% of multiple congenital anomalies, 9.76% of psychiatric pathologies, 7.02% of patients with epilepsy, and 13.3% of patients with short stature. Within the multiple congenital anomalies, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnoses, respectively. Among the psychiatric disorders, patients with autism spectrum disorders accounted for 8.9% of the diagnoses. CONCLUSIONS Our results demonstrate the effectiveness and efficiency of the use of aCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System.
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Affiliation(s)
- Neus Castells-Sarret
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España.
| | - Anna M Cueto-González
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Facultat de Medicina, Departament de Ciències Morfològiques, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | - Mar Borregan
- Facultat de Medicina, Departament de Ciències Morfològiques, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | | | - Rosa Miró
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | - Eduardo Tizzano
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; CIBERER, Barcelona, España
| | - Alberto Plaja
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
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22
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Madon PF, Athalye AS, Sanghavi K, Parikh FR. Microdeletion Syndromes Detected by FISH – 73 Positive from 374 Cases. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2010.11886080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Prochi F. Madon
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai 400 026, Maharashtra, India E-mail: ,
| | - Arundhati S. Athalye
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai 400 026, Maharashtra, India E-mail: ,
| | - Kunal Sanghavi
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai 400 026, Maharashtra, India E-mail: ,
| | - Firuza R. Parikh
- Department of Assisted Reproduction and Genetics, Jaslok Hospital and Research Centre, Mumbai 400 026, Maharashtra, India E-mail: ,
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23
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Polo-Antúnez A, Arroyo-Carrera I. Severe Neurological Phenotype in a Girl with Xp22.31 Triplication. Mol Syndromol 2017; 8:219-223. [PMID: 28690489 DOI: 10.1159/000475795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
The Xp22.31 duplication is a copy number variant which is challenging to categorize as pathogenic or benign. There is an increasing number of patients with the duplication and a neurobehavioral phenotype, but the duplication is almost always inherited from a parent, who in some cases is phenotypically normal. Also, the duplication is detected in the general population, though in a smaller percentage than in clinically ascertained populations. The Xp22.31 triplication has only been identified in 3 individuals of a large cohort of developmental delay cases but never in the control cohorts or general population. We report a severely affected female with an Xp22.31 tetrasomy, inherited from duplications identified in both phenotypically normal parents. Although our study has limitations, it suggests that the Xp22.31 triplication seems to be more penetrant than the duplication and is associated with a neurological phenotype.
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Affiliation(s)
| | - Ignacio Arroyo-Carrera
- Neonatology Unit, San Pedro de Alcántara Hospital, Cáceres, Spain.,CIBER de Enfermedades Raras (CIBERER) (U724), Instituto de Salud Carlos III, Madrid, Spain
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24
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Lantieri F, Malacarne M, Gimelli S, Santamaria G, Coviello D, Ceccherini I. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. Int J Mol Sci 2017; 18:E609. [PMID: 28287439 PMCID: PMC5372625 DOI: 10.3390/ijms18030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log₂ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log₂ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected.
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Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy.
| | - Michela Malacarne
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Bâtiment de Base 8C-3-840.3, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Giuseppe Santamaria
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
| | - Domenico Coviello
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Isabella Ceccherini
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
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25
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Mc Cormack A, Claxton K, Ashton F, Asquith P, Atack E, Mazzaschi R, Moverley P, O'Connor R, Qorri M, Sheath K, Love DR, George AM. Microarray testing in clinical diagnosis: an analysis of 5,300 New Zealand patients. Mol Cytogenet 2016; 9:29. [PMID: 27034718 PMCID: PMC4815202 DOI: 10.1186/s13039-016-0237-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/17/2016] [Indexed: 11/14/2022] Open
Abstract
Background The use of Microarray (array CGH) analysis has become a widely accepted front-line test replacing G banded chromosome studies for patients with an unexplained phenotype. We detail our findings of over 5300 cases. Results Of 5369 pre and postnatal samples, copy number variants (CNVs) were detected in 28.3 %, of which ~40 % were deletions and ~60 % were duplications. 96.8 % of cases with a CNV <5 Mb would not have been detected by G banding. At least 4.9 % were determined to meet the minimum criteria for a known syndrome. Chromosome 17 provided the greatest proportion of pathogenic CNVs with 65 % classified as (likely) pathogenic. X chromosome CNVs were the most commonly detected accounting for 4.2 % of cases, 0.7 % of these being classified as cryptic (likely) pathogenic CNVs. Conclusions Microarray analysis as a primary testing strategy has led to a significant increase in the detection of CNVs (~29 % overall), with ~9 % carrying pathogenic CNVs and one syndromic case identified per 20 referred patients. We suggest these frequencies are consistent with other heterogeneous studies. Conversely, (likely) pathogenic X chromosome CNVs appear to be greater compared with previous studies.
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Affiliation(s)
- Adrian Mc Cormack
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Karen Claxton
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Fern Ashton
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Philip Asquith
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Edward Atack
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Roberto Mazzaschi
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Paula Moverley
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand ; Present address: Pacific Edge Ltd, 87 St David St, North Dunedin, 9016 New Zealand
| | - Rachel O'Connor
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Methat Qorri
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Karen Sheath
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Donald R Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
| | - Alice M George
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, PO Box 110031, Auckland, 1148 New Zealand
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Hardick J, Woelfel R, Gardner W, Ibrahim S. Sequencing ebola and marburg viruses genomes using microarrays. J Med Virol 2016; 88:1303-8. [PMID: 26822839 DOI: 10.1002/jmv.24487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2016] [Indexed: 01/11/2023]
Abstract
Periodic outbreaks of Ebola and Marburg hemorrhagic fevers have occurred in Africa over the past four decades with case fatality rates reaching as high as 90%. The latest Ebola outbreak in West Africa in 2014 raised concerns that these infections can spread across continents and pose serious health risks. Early and accurate identification of the causative agents is necessary to contain outbreaks. In this report, we describe sequencing-by-hybridization (SBH) technique using high density microarrays to identify Ebola and Marburg viruses. The microarrays were designed to interrogate the sequences of entire viral genomes, and were evaluated with three species of Ebolavirus (Reston, Sudan, and Zaire), and three strains of Marburgvirus (Angola, Musoke, and Ravn). The results showed that the consensus sequences generated with four or more hybridizations had 92.1-98.9% accuracy over 95-99% of the genomes. Additionally, with SBH microarrays it was possible to distinguish between different strains of the Lake Victoria Marburgvirus. J. Med. Virol. 88:1303-1308, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Justin Hardick
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Roman Woelfel
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Warren Gardner
- United States Army Research Development and Engineering Command, Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland
| | - Sofi Ibrahim
- United States Army Research Development and Engineering Command, Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland
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27
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Lo K, Karampetsou E, Boustred C, McKay F, Mason S, Hill M, Plagnol V, Chitty L. Limited Clinical Utility of Non-invasive Prenatal Testing for Subchromosomal Abnormalities. Am J Hum Genet 2016; 98:34-44. [PMID: 26708752 DOI: 10.1016/j.ajhg.2015.11.016] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/10/2015] [Indexed: 01/07/2023] Open
Abstract
The use of massively parallel sequencing of maternal cfDNA for non-invasive prenatal testing (NIPT) of aneuploidy is widely available. Recently, the scope of testing has increased to include selected subchromosomal abnormalities, but the number of samples reported has been small. We developed a calling pipeline based on a segmentation algorithm for the detection of these rearrangements in maternal plasma. The same read depth used in our standard pipeline for aneuploidy NIPT detected 15/18 (83%) samples with pathogenic rearrangements > 6 Mb but only 2/10 samples with rearrangements < 6 Mb, unless they were maternally inherited. There were two false-positive calls in 534 samples with no known subchromosomal abnormalities (specificity 99.6%). Using higher read depths, we detected 29/31 fetal subchromosomal abnormalities, including the three samples with maternally inherited microduplications. We conclude that test sensitivity is a function of the fetal fraction, read depth, and size of the fetal CNV and that at least one of the two false negatives is due to a low fetal fraction. The lack of an independent method for determining fetal fraction, especially for female fetuses, leads to uncertainty in test sensitivity, which currently has implications for this technique's future as a clinical diagnostic test. Furthermore, to be effective, NIPT must be able to detect chromosomal rearrangements across the whole genome for a very low false-positive rate. Because standard NIPT can only detect the majority of larger (>6 Mb) chromosomal rearrangements and requires knowledge of fetal fraction, we consider that it is not yet ready for routine clinical implementation.
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28
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Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB. Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients. Mol Cytogenet 2015; 8:103. [PMID: 26719768 PMCID: PMC4696247 DOI: 10.1186/s13039-015-0202-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/17/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV). RESULTS All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists. CONCLUSIONS As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.
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Affiliation(s)
- Isabel Marques Carreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Eunice Matoso
- CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Laboratório de Citogenética, Hospital Pediátrico de Coimbra, Coimbra, Portugal
| | - Luís Miguel Pires
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - José Ferrão
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Ana Jardim
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Alexandra Mascarenhas
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Marta Pinto
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Nuno Lavoura
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Cláudia Pais
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Patrícia Paiva
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Lúcia Simões
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Margarida Venâncio
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Fabiana Ramos
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Beleza
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sá
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Jorge Saraiva
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
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29
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Abstract
Gene expression is a process of DNA sequence reading into protein synthesis. In cases of problems in DNA repair/apoptosis mechanisms, cells accumulate genomic abnormalities and pass them through generations of cells. The accumulation of mutations causes diseases and even tumors. In addition to cancer, many other neurologic conditions have been associated with genetic mutations. Some trials are testing patients with epigenetic treatments. Epigenetic therapy must be used with caution because epigenetic processes and changes happen constantly in normal cells, giving rise to drug off-target effects. Scientists are making progress in specifically targeting abnormal cells with minimal damage to normal ones.
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Affiliation(s)
- Marina Lipkin Vasquez
- Molecular Biology Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer (IECPN), Rua do Resende 156, 2nd Floor, Centro, Rio de Janeiro CEP 20231-092, Brazil.
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30
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Hinton RB, McBride KL, Bleyl SB, Bowles NE, Border WL, Garg V, Smolarek TA, Lalani SR, Ware SM. Rationale for the Cytogenomics of Cardiovascular Malformations Consortium: A Phenotype Intensive Registry Based Approach. J Cardiovasc Dev Dis 2015; 2:76-92. [PMID: 29371513 PMCID: PMC5753096 DOI: 10.3390/jcdd2020076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/18/2015] [Accepted: 04/22/2015] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular malformations (CVMs) are the most common birth defect, occurring in 1%–5% of all live births. Although the genetic contribution to CVMs is well recognized, the genetic causes of human CVMs are identified infrequently. In addition, a failure of systematic deep phenotyping of CVMs, resulting from the complexity and heterogeneity of malformations, has obscured genotype-phenotype correlations and contributed to a lack of understanding of disease mechanisms. To address these knowledge gaps, we have developed the Cytogenomics of Cardiovascular Malformations (CCVM) Consortium, a multi-site alliance of geneticists and cardiologists, contributing to a database registry of submicroscopic genetic copy number variants (CNVs) based on clinical chromosome microarray testing in individuals with CVMs using detailed classification schemes. Cardiac classification is performed using a modification to the National Birth Defects Prevention Study approach, and non-cardiac diagnoses are captured through ICD-9 and ICD-10 codes. By combining a comprehensive approach to clinically relevant genetic analyses with precise phenotyping, the Consortium goal is to identify novel genomic regions that cause or increase susceptibility to CVMs and to correlate the findings with clinical phenotype. This registry will provide critical insights into genetic architecture, facilitate genotype-phenotype correlations, and provide a valuable resource for the medical community.
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Affiliation(s)
- Robert B Hinton
- Divisions of Cardiology and Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Kim L McBride
- Center for Cardiovascular and Pulmonary Research and Heart Center, Nationwide Children's Hospital and Department of Pediatrics, Ohio State University, Columbus, OH 43205, USA.
| | - Steven B Bleyl
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Neil E Bowles
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - William L Border
- Division of Cardiology, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
| | - Vidu Garg
- Center for Cardiovascular and Pulmonary Research and Heart Center, Nationwide Children's Hospital and Department of Pediatrics, Ohio State University, Columbus, OH 43205, USA.
| | - Teresa A Smolarek
- Divisions of Cardiology and Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Stephanie M Ware
- Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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31
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Quintela I, Fernandez-Prieto M, Gomez-Guerrero L, Resches M, Eiris J, Barros F, Carracedo A. A 6q14.1-q15 microdeletion in a male patient with severe autistic disorder, lack of oral language, and dysmorphic features with concomitant presence of a maternally inherited Xp22.31 copy number gain. Clin Case Rep 2015; 3:415-23. [PMID: 26185640 PMCID: PMC4498854 DOI: 10.1002/ccr3.255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/22/2015] [Indexed: 12/14/2022] Open
Abstract
We report on a male patient with severe autistic disorder, lack of oral language, and dysmorphic features who carries a rare interstitial microdeletion of 4.96 Mb at chromosome 6q14.1-q15. The patient also harbors a maternally inherited copy number gain of 1.69 Mb at chromosome Xp22.31, whose pathogenicity is under debate.
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Affiliation(s)
- Ines Quintela
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Montse Fernandez-Prieto
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Lorena Gomez-Guerrero
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Mariela Resches
- Departamento de Psicologia Evolutiva y de la Educacion, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Jesus Eiris
- Unidad de Neurologia Pediatrica, Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Universidade de Santiago de Compostela Santiago de Compostela, Spain ; Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain ; Center of Excellence in Genomic Medicine Research, King Abdulaziz University Jeddah, Saudi Arabia
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32
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Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2014.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Lay-Son G, Espinoza K, Vial C, Rivera JC, Guzmán ML, Repetto GM. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. J Pediatr (Rio J) 2015; 91:189-95. [PMID: 25458876 DOI: 10.1016/j.jped.2014.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/28/2014] [Accepted: 07/09/2014] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan™ HD Array, Affymetrix, Inc., Santa Clara, CA, USA). Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs) were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting.
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Affiliation(s)
- Guillermo Lay-Son
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile.
| | - Karena Espinoza
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Juan C Rivera
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - María L Guzmán
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
| | - Gabriela M Repetto
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
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Kloosterman WP, Hochstenbach R. Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease. Mol Cytogenet 2014; 7:100. [PMID: 25606056 PMCID: PMC4299681 DOI: 10.1186/s13039-014-0100-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 01/14/2023] Open
Abstract
Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient's phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, P.O. Box 85060, 3508 AB Utrecht, The Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Genome Diagnostics, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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Large cryptic genomic rearrangements with apparently normal karyotypes detected by array-CGH. Mol Cytogenet 2014; 7:82. [PMID: 25435912 PMCID: PMC4247713 DOI: 10.1186/s13039-014-0082-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/29/2014] [Indexed: 12/18/2022] Open
Abstract
Background Conventional karyotyping (550 bands resolution) is able to identify chromosomal aberrations >5-10 Mb, which represent a known cause of intellectual disability/developmental delay (ID/DD) and/or multiple congenital anomalies (MCA). Array-Comparative Genomic Hybridization (array-CGH) has increased the diagnostic yield of 15-20%. Results In a cohort of 700 ID/DD cases with or without MCA, including 15 prenatal diagnoses, we identified a subgroup of seven patients with a normal karyotype and a large complex rearrangement detected by array-CGH (at least 6, and up to 18 Mb). FISH analysis could be performed on six cases and showed that rearrangements were translocation derivatives, indistinguishable from a normal karyotype as they involved a similar band pattern and size. Five were inherited from a parent with a balanced translocation, whereas two were apparently de novo. Genes spanning the rearrangements could be associated with some phenotypic features in three cases (case 3: DOCK8; case 4: GATA3, AKR1C4; case 6: AS/PWS deletion, CHRNA7), and in two, likely disease genes were present (case 5: NR2F2, TP63, IGF1R; case 7: CDON). Three of our cases were prenatal diagnoses with an apparently normal karyotype. Conclusions Large complex rearrangements of up to 18 Mb, involving chromosomal regions with similar size and band appearance may be overlooked by conventional karyotyping. Array-CGH allows a precise chromosomal diagnosis and recurrence risk definition, further confirming this analysis as a first tier approach to clarify molecular bases of ID/DD and/or MCA. In prenatal tests, array-CGH is confirmed as an important tool to avoid false negative results due to karyotype intrinsic limit of detection.
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Liu N, Yan J, Chen X, Song J, Wang B, Yao Y. Prenatal diagnosis of a de novo interstitial deletion of 11q (11q22.3 → q23.3) associated with abnormal ultrasound findings by array comparative genomic hybridization. Mol Cytogenet 2014; 7:62. [PMID: 25298785 PMCID: PMC4189608 DOI: 10.1186/s13039-014-0062-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background Conventional G-band karyotyping offers low-resolution detection of chromosome abnormalities and cannot provide information about the involved genomic content. On the other hand, array comparative genomic hybridization can offer a rapid and comprehensive detection of genomewide gains and losses with higher resolution, thus providing the genetic basis for prenatal diagnosis of fetal abnormalities. Case presentation A 35-year-old primigravid underwent cordocentesis at 28 weeks gestation due to the presence of polyhydramnios, intrauterine growth retardation, persistent right umbilical vein and mild stenosis of aortic arch at the ultrasound scan. Conventional G-band chromosome analysis revealed an apparently normal karyotype whereas the array CGH detected a de novo 8.97 Mb deletion at chromosome 11q22.3 → q23.3 and offered a precise characterization of the genetic defect. Conclusions The array CGH detected a de novo interstitial 11q deletion with its precise location and size which could be missed or confused by G-band chromosome analysis. The breakpoint was close to the folate sensitive rare fragile site FRA11B and the aphidicolin inducible common fragile site FRA11G, the co-localization fragile site could have caused instability and constitutional chromosomal breakage. This case study indicates that array CGH is a useful technique for detecting small unbalanced chromosomal abnormalities and should be an integral part of prenatal diagnosis for fetal malformations.
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Affiliation(s)
- Nian Liu
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jiong Yan
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Xinlin Chen
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jieping Song
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Bo Wang
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Yanyi Yao
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
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Khan AO, Nagl S, Bergmann C, Bolz HJ. Limited ocular motility in a child with 3q23 microdeletion ("blepharophimosis syndrome plus"). J Pediatr Ophthalmol Strabismus 2014; 51 Online:e51-4. [PMID: 25032695 DOI: 10.3928/01913913-20140709-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 11/20/2022]
Abstract
Blepharophimosis syndrome is a recognizable ocular phenotype (blepharophimosis, telecanthus, ptosis, and epicanthus inversus) caused by heterozygous (dominant) intragenic mutation in FOXL2 (chromosome 3q23), which can also cause premature ovarian failure. A deletion that involves not only FOXL2 but also adjacent genes can result in additional clinical features ("blepharophimosis syndrome plus"). Studies of such patients are useful because observed additional clinical features suggest potential functions of genes adjacent to FOXL2. The authors describe a boy with blepharophimosis syndrome plus from a de novo heterozygous 3q22.3-q24 11.2 Mb microdeletion. Among his additional clinical features was bilateral limitation of abduction and supraduction, which suggests that the deleted area includes a gene responsible for ocular motility.
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Esplin ED, Li B, Slavotinek A, Novelli A, Battaglia A, Clark R, Curry C, Hudgins L. Nine patients with Xp22.31 microduplication, cognitive deficits, seizures, and talipes anomalies. Am J Med Genet A 2014; 164A:2097-103. [DOI: 10.1002/ajmg.a.36598] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 04/13/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Edward D. Esplin
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
| | - Ben Li
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics; University of California San Francisco; San Francisco California
| | - Antonio Novelli
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza Hospital; San Giovanni Rotondo (FG) Italy
| | - Agatino Battaglia
- The Stella Maris Clinical Research Institute for Child and Adolescent Neurology and Psychiatry; Calambrone (Pisa) Italy
| | - Robin Clark
- Division of Medical Genetics, Department of Pediatrics; Loma Linda University; Loma Linda California
| | - Cynthia Curry
- Division of Medical Genetics, Department of Pediatrics; UCSF Fresno; Fresno California
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics; Stanford University School of Medicine; Stanford California
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Abstract
Eye brows are essential for esthetic and functional purposes. Various kinds of eye brows are found in human species. Protective function is one of the important functions of eye brows. Double eye brow is a very rare condition found in human. This case report describes one of the rare cases of double eye brow.
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Affiliation(s)
- Sudipta Kar
- Department of Pedodontics and Preventive Dentistry, Guru Nanak Institute of Dental Science and Research, Panihati, Kolkata, West Bengal, India
| | - Chiranjit Ghosh
- Department of Pedodontics and Preventive Dentistry, Guru Nanak Institute of Dental Science and Research, Panihati, Kolkata, West Bengal, India
| | - Badruddin Ahamed Bazmi
- Department of Pedodontics and Preventive Dentistry, Guru Nanak Institute of Dental Science and Research, Panihati, Kolkata, West Bengal, India
| | - Subrata Sarkar
- Department of Pedodontics and Preventive Dentistry, Guru Nanak Institute of Dental Science and Research, Panihati, Kolkata, West Bengal, India
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Bernhardt BA, Kellom K, Barbarese A, Faucett WA, Wapner RJ. An exploration of genetic counselors' needs and experiences with prenatal chromosomal microarray testing. J Genet Couns 2014; 23:938-47. [PMID: 24569858 DOI: 10.1007/s10897-014-9702-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/05/2014] [Indexed: 11/28/2022]
Abstract
Because of the higher yield over traditional chromosomal analysis, chromosomal microarray analysis (CMA) is being used increasingly in prenatal diagnosis. Unfortunately, the clinical implication of many copy number variants found on prenatal CMA is uncertain, complicating genetic counseling. Recognizing that uncertain results will be encountered frequently as more of the genome is assayed prenatally, we set out to understand the experiences and needs of genetic counselors when counseling patients about uncertain prenatal microarray results, their comfort with various aspects of prenatal genetic counseling, and their interest in additional education and training about prenatal microarray testing. We first interviewed 10 genetic counselors about their experiences of providing pre- and post-test genetic counseling about prenatal CMA. Based on the findings from the counselor interviews, we developed items for a survey to assess the prevalence of genetic counselors' attitudes towards, experience and comfort with, and educational needs regarding prenatal CMA. Based on surveys completed by 193 prenatal genetic counselors, we found that when there is an uncertain CMA result, only 59% would be comfortable providing genetic counseling and only 43% would be comfortable helping a patient make a decision about pregnancy termination. Being less comfortable was associated with seeing fewer patients having prenatal CMA testing. Respondents expressed a high degree of interest in additional education about prenatal CMA and counseling about uncertain results. Further genetic counselor education and training aimed at improving counselors' personal comfort with uncertain results and communicating about them with patients is needed.
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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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Askree SH, Chin ELH, Bean LH, Coffee B, Tanner A, Hegde M. Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genet 2013; 14:116. [PMID: 24304607 PMCID: PMC4235222 DOI: 10.1186/1471-2156-14-116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022] Open
Abstract
Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered.
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Affiliation(s)
| | | | | | | | | | - Madhuri Hegde
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, 2165 N Decatur Road, Decatur, GA 30033, USA.
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Xq28 (MECP2) microdeletions are common in mutation-negative females with Rett syndrome and cause mild subtypes of the disease. Mol Cytogenet 2013; 6:53. [PMID: 24283533 PMCID: PMC4176196 DOI: 10.1186/1755-8166-6-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 01/13/2023] Open
Abstract
Background Rett syndrome (RTT) is an X-linked neurodevelopmental disease affecting predominantly females caused by MECP2 mutations. Although RTT is classically considered a monogenic disease, a stable proportion of patients, who do not exhibit MECP2 sequence variations, does exist. Here, we have attempted at uncovering genetic causes underlying the disorder in mutation-negative cases by whole genome analysis using array comparative genomic hybridization (CGH) and a bioinformatic approach. Results Using BAC and oligonucleotide array CGH, 39 patients from RTT Russian cohort (in total, 354 RTT patients), who did not bear intragenic MECP2 mutations, were studied. Among the individuals studied, 12 patients were those with classic RTT and 27 were those with atypical RTT. We have detected five 99.4 kb deletions in chromosome Xq28 affecting MECP2 associated with mild manifestations of classic RTT and five deletions encompassing MECP2 spanning 502.428 kb (three cases), 539.545 kb (one case) and 877.444 kb (one case) associated with mild atypical RTT. A case has demonstrated somatic mosaicism. Regardless of RTT type and deletion size, all the cases exhibited mild phenotypes. Conclusions Our data indicate for the first time that no fewer than 25% of RTT cases without detectable MECP2 mutations are caused by Xq28 microdeletions. Furthermore, Xq28 (MECP2) deletions are likely to cause mild subtypes of the disease, which can manifest as both classical and atypical RTT.
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Lee CG, Park SJ, Yun JN, Ko JM, Kim HJ, Yim SY, Sohn YB. Array-based comparative genomic hybridization in 190 Korean patients with developmental delay and/or intellectual disability: a single tertiary care university center study. Yonsei Med J 2013; 54:1463-70. [PMID: 24142652 PMCID: PMC3809862 DOI: 10.3349/ymj.2013.54.6.1463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE This study analyzed and evaluated the demographic, clinical, and cytogenetic data [G-banded karyotyping and array-based comparative genomic hybridization (array CGH)] of patients with unexplained developmental delay or intellectual disability at a single Korean institution. MATERIALS AND METHODS We collected clinical and cytogenetic data based on retrospective charts at Ajou University Medical Center, Suwon, Korea from April 2008 to March 2012. RESULTS A total of 190 patients were identified. Mean age was 5.1±1.87 years. Array CGH yielded abnormal results in 26 of 190 patients (13.7%). Copy number losses were about two-fold more frequent than gains. A total of 61.5% of all patients had copy number losses. The most common deletion disorders included 22q11.2 deletion syndrome, 15q11.2q12 deletion and 18q deletion syndrome. Copy number gains were identified in 34.6% of patients, and common diseases among these included Potocki-Lupski syndrome, 15q11-13 duplication syndrome and duplication 22q. Abnormal karyotype with normal array CGH results was exhibited in 2.6% of patients; theses included balanced translocation (n=2), inversion (n=2) and low-level mosaicism (n=1). Facial abnormalities (p<0.001) and failure to thrive were (p<0.001) also more frequent in the group of patients with abnormal CGH findings. CONCLUSION Array CGH is a useful diagnostic tool in clinical settings in patients with developmental delay or intellectual disability combined with facial abnormalities or failure to thrive.
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Affiliation(s)
- Cha Gon Lee
- Department of Medical Genetics, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 443-380, Korea.
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Callaway JLA, Shaffer LG, Chitty LS, Rosenfeld JA, Crolla JA. The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature. Prenat Diagn 2013; 33:1119-23. [PMID: 23983223 PMCID: PMC4285999 DOI: 10.1002/pd.4209] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
ABSTRACT The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
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Key Informants’ Perspectives of Implementing Chromosomal Microarrays Into Clinical Practice in Australia. Twin Res Hum Genet 2013; 16:833-9. [DOI: 10.1017/thg.2013.43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
High-resolution genomic tests have the potential to revolutionize healthcare by vastly improving mutation detection. The use of chromosomal microarray (CMA) represents one of the earliest examples of these new genomic tests being introduced and disseminated in the clinic. While CMA has clear advantages over traditional karyotyping in terms of mutation detection, little research has investigated the process by which CMA was implemented in clinical settings. Fifteen key informants, six clinicians, and nine laboratory scientists from four Australian states were interviewed about their experiences during and in the time since CMA was adopted for clinical use. Participants discussed challenges such as result interpretation and communication. Strengths were also highlighted, including the collaborative approaches of some centers. Clinical experiences and opinions can inform larger studies with a range of stakeholders, including patients. The historical perspectives from this retrospective study can be helpful in guiding the implementation of future genomic technologies such as whole exome/genome sequencing.
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Fiorentino F, Napoletano S, Caiazzo F, Sessa M, Bono S, Spizzichino L, Gordon A, Nuccitelli A, Rizzo G, Baldi M. Chromosomal microarray analysis as a first-line test in pregnancies with a priori low risk for the detection of submicroscopic chromosomal abnormalities. Eur J Hum Genet 2013; 21:725-30. [PMID: 23211699 PMCID: PMC3722951 DOI: 10.1038/ejhg.2012.253] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this study, we aimed to explore the utility of chromosomal microarray analysis (CMA) in groups of pregnancies with a priori low risk for detection of submicroscopic chromosome abnormalities, usually not considered an indication for testing, in order to assess whether CMA improves the detection rate of prenatal chromosomal aberrations. A total of 3000 prenatal samples were processed in parallel using both whole-genome CMA and conventional karyotyping. The indications for prenatal testing included: advanced maternal age, maternal serum screening test abnormality, abnormal ultrasound findings, known abnormal fetal karyotype, parental anxiety, family history of a genetic condition and cell culture failure. The use of CMA resulted in an increased detection rate regardless of the indication for analysis. This was evident in high risk groups (abnormal ultrasound findings and abnormal fetal karyotype), in which the percentage of detection was 5.8% (7/120), and also in low risk groups, such as advanced maternal age (6/1118, 0.5%), and parental anxiety (11/1674, 0.7%). A total of 24 (0.8%) fetal conditions would have remained undiagnosed if only a standard karyotype had been performed. Importantly, 17 (0.6%) of such findings would have otherwise been overlooked if CMA was offered only to high risk pregnancies.The results of this study suggest that more widespread CMA testing of fetuses would result in a higher detection of clinically relevant chromosome abnormalities, even in low risk pregnancies. Our findings provide substantial evidence for the introduction of CMA as a first-line diagnostic test for all pregnant women undergoing invasive prenatal testing, regardless of risk factors.
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McNamee K, Dawood F, Farquharson RG. Evaluation of array comparative genomic hybridization in recurrent miscarriage. Br J Hosp Med (Lond) 2013; 74:36-40. [PMID: 23593676 DOI: 10.12968/hmed.2013.74.1.36] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- K McNamee
- Department of Gynaecology, Liverpool Women's Hospital, Liverpool L8 7SS.
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Connor JA, Hinton RB, Miller EM, Sund KL, Ruschman JG, Ware SM. Genetic Testing Practices in Infants with Congenital Heart Disease. CONGENIT HEART DIS 2013; 9:158-67. [DOI: 10.1111/chd.12112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Jessica A. Connor
- Division of Human Genetics; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
| | - Robert B. Hinton
- Heart Institute; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
| | - Erin M. Miller
- Heart Institute; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
| | - Kristen L. Sund
- Division of Human Genetics; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
| | - Jennifer G. Ruschman
- Division of Human Genetics; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
| | - Stephanie M. Ware
- Division of Human Genetics; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
- Heart Institute; Cincinnati Children's Hospital Medical Center; Cincinnati Ohio USA
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Shimada S, Okamoto N, Ito M, Arai Y, Momosaki K, Togawa M, Maegaki Y, Sugawara M, Shimojima K, Osawa M, Yamamoto T. MECP2 duplication syndrome in both genders. Brain Dev 2013; 35:411-9. [PMID: 22877836 DOI: 10.1016/j.braindev.2012.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/07/2012] [Accepted: 07/15/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND Duplications involving the methyl-CpG-binding protein 2 gene (MECP2) locus at Xq28 have been frequently identified in male patients who exhibit a phenotype unique from that of Rett syndrome, which is mainly characterized by severe mental retardation, recurrent infections, and epilepsy. This combination of features is recognized as MECP2 duplication syndrome. METHODS Genomic copy number was investigated for patients with unexplained mental retardation, and phenotypic features of the patients having interstitial duplications including MECP2 were analyzed. RESULTS Three male and one female patients with MECP2 duplication were identified. The phenotypic features of all the four patients were compatible with MECP2 duplication syndrome. The X-chromosome inactivation (XCI) pattern was analyzed in the female patient, identifying a skewed XCI that activated the X-chromosome containing the MECP2 duplication. Her mother possessed the same MECP2 duplication and a random XCI pattern but exhibited no phenotypic features, indicating a nonsymptomatic carrier. The brain magnetic resonance imaging revealed periventricular cystic lesions in all four patients, including the female patient. CONCLUSION This study suggested clinical implications of the MECP2 duplication syndrome not only in the male but also in female patients with unexplained mental retardation.
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Affiliation(s)
- Shino Shimada
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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