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Tingaud-Sequeira A, Trimouille A, Sagardoy T, Lacombe D, Rooryck-Thambo C. Oculo-auriculo-vertebral spectrum: new genes and literature review on a complex disease. J Med Genet 2022; 59:417-427. [PMID: 35110414 DOI: 10.1136/jmedgenet-2021-108219] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/30/2021] [Indexed: 12/23/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) or Goldenhar syndrome is due to an abnormal development of first and second branchial arches derivatives during embryogenesis and is characterised by hemifacial microsomia associated with auricular, ocular and vertebral malformations. The clinical and genetic heterogeneity of this spectrum with incomplete penetrance and variable expressivity, render its molecular diagnosis difficult. Only a few recurrent CNVs and genes have been identified as causatives in this complex disorder so far. Prenatal environmental causal factors have also been hypothesised. However, most of the patients remain without aetiology. In this review, we aim at updating clinical diagnostic criteria and describing genetic and non-genetic aetiologies, animal models as well as novel diagnostic tools and surgical management, in order to help and improve clinical care and genetic counselling of these patients and their families.
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Affiliation(s)
- Angèle Tingaud-Sequeira
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France
| | - Aurélien Trimouille
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Thomas Sagardoy
- CHU de Bordeaux, Service d'oto-rhino-laryngologie, de chirurgie cervico-faciale et d'ORL pédiatrique, 33076 Bordeaux, France
| | - Didier Lacombe
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France.,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
| | - Caroline Rooryck-Thambo
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, F-33000 Bordeaux, France .,CHU de Bordeaux, Service de Génétique Médicale, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, F-33076, Bordeaux, France
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Duplications involving the long range HMX1 enhancer are associated with human isolated bilateral concha-type microtia. J Transl Med 2020; 18:244. [PMID: 32552830 PMCID: PMC7302384 DOI: 10.1186/s12967-020-02409-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Microtia is a congenital anomaly of ear that ranges in severity from mild structural abnormalities to complete absence of the outer ears. Concha-type microtia is considered to be a mild form. The H6 family homeobox 1 transcription factor gene (HMX1) plays an important role in craniofacial structures development. Copy number variations (CNVs) of a downstream evolutionarily conserved enhancer region (ECR) of Hmx1 associated with ear and eye abnormalities have been reported in different animals, but not yet in human. To date, no genetic defects responsible for isolated human microtia has been reported except for mutations in HOXA2. Here we recruited five Chinese families with isolated bilateral concha-type microtia, and attempt to identify the underlying genetic causes. Methods Single Nucleotide polymorphism (SNP) array was performed to map the disease locus and detect CNVs on a genome scale primarily in the largest family (F1). Whole genome sequencing was performed to screen all SNVs and CNVs in the candidate disease locus. Array comparative genomic hybridization (aCGH) was then performed to detect CNVs in the other four families, F2-F5. Quantitative real-time polymerase chain reaction (qPCR) was used to validate and determine the extent of identified CNVs containing HMX1-ECR region. Precise breakpoints in F1 and F2 were identified by gap-PCR and sanger sequencing. Dual-luciferase assays were used to detect the enhancer function. qPCR assays were also used to detect HMX1-ECR CNVs in 61 patients with other types mictrotia. Results Linkage and haplotype analysis in F1 mapped the disease locus to a 1.9 Mb interval on 4p16.1 containing HMX1 and its downstream ECR region. Whole genome sequencing detected no potential pathogenic SNVs in coding regions of HMX1 or other genes within the candidate disease locus, but it detected a 94.6 Kb duplication in an intergenic region between HMX1 and CPZ. aCGH and qPCRs also revealed co-segregated duplications in intergenic region downstream of HMX1 in the other four families. The 21.8 Kb minimal overlapping region encompassing the core sequences consensus with mouse ECR of Hmx1. Luciferase assays confirmed the enhancer function in human sequences, and proved that HOXA2 could increase its enhancer activity. No CNVs were detected in HMX1-ECR regions in 61 patients with other type of microtia. Conclusion Duplications involving long range HMX1 enhancers are associated with human isolated bilateral concha-type microtia. We add to evidences in human that copy number variations in HMX1-ECR associates with ear malformations, as in other species. This study also provides an additional example of functional conserved non-coding elements (CNEs) in humans.
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Review of Preferential Suspicious Genes in Microtia Patients Through Various Approaches. J Craniofac Surg 2020; 31:538-541. [PMID: 31977690 DOI: 10.1097/scs.0000000000006244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recently, an increasing trend of the birth prevalence of anotia/microtia is observed in China, contributed by changes of social environment and lifestyle. There seems to be no major breakthroughs in exact pathogenesis of microtia, though the research results related to molecular genetics unceasingly appear. In this review, the authors focus on the results of various research methods which the authors regard as the preferential suspicious gene pool to facilitate the exploration of the pathogenic genes of microtia, knowing that the mechanism of microtia is very complicated. The advantages and limitations of these various approaches will also be systematically delineated. The authors believe that this review will give a deep insight in the genetic research of microtia and help plastic surgeons manage congenital microtia more effectively.
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Wang P, Wang Y, Fan X, Liu Y, Fan Y, Liu T, Chen C, Zhang S, Chen X. Identification of sequence variants associated with severe microtia-astresia by targeted sequencing. BMC Med Genomics 2019; 12:28. [PMID: 30691450 PMCID: PMC6348636 DOI: 10.1186/s12920-019-0475-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
Background Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients. Methods We designed a panel of 131 genes associated with external/middle or inner ear deformity. Targeted genomic capturing combined with next-generation sequencing (NGS) was utilized to screen for mutations in 40 severe microtia-atresia patients. Mutations detected by NGS were filtered and validated. And then mutations were divided into three categories—rare or novel variants, low-frequency variants and common variants—based on their frequency in the public database. The rare or novel mutations were prioritized by pathogenicity analysis. For the low-frequency variants and common variants, we used association studies to explore risk factors of severe microtia-atresia. Results Sixty-five rare heterozygous mutations of 42 genes were identified in 27 (67.5%) severe microtia-atresia patients. Association studies to determine genes that were potentially pathogenic found that PLEC, USH2A, FREM2, DCHS1, GLI3, POMT1 and GBA genes were significantly associated with severe microtia-atresia. Of these, DCHS1 was strongly suggested to cause severe microtia-atresia as it was identified by both low-frequency and common variants association studies. A rare mutation (c.481C > T, p.R161C) in DCHS1 identified in one individual may be deleterious and may cause severe microtia-atresia. Conclusion We identified several genes that were significantly associated with severe microtia-atresia. The findings provide new insights into genetic background of external ear deformities. Electronic supplementary material The online version of this article (10.1186/s12920-019-0475-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pu Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
| | - Yibei Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
| | - Xinmiao Fan
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
| | - Yaping Liu
- Department of Medical Genetics, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Fan
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China
| | - Tao Liu
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Chongjian Chen
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Xiaowei Chen
- Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, China.
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Barber JCK. Reassignment of HMX1 indicates copy number variation within 4p16.1 may be an alternative cause of oculoauricular phenotypes. Am J Med Genet A 2018; 176:2034-2036. [PMID: 30055074 DOI: 10.1002/ajmg.a.40385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 11/07/2022]
Affiliation(s)
- John C K Barber
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
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Aguinaga-Ríos M, Frías S, Arenas-Aranda DJ, Morán-Barroso VF. [Microtia-atresia: clinical, genetic and genomic aspects]. BOLETIN MEDICO DEL HOSPITAL INFANTIL DE MEXICO 2015; 71:387-395. [PMID: 29421636 DOI: 10.1016/j.bmhimx.2014.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/05/2014] [Indexed: 01/13/2023] Open
Abstract
Mexico has a prevalence of microtia of 7.37/10,000 (newborns), 3 times higher than the prevalence reported in other populations (USA 2-3/10,000). Microtia is defined as a congenital malformation of the external ear characterized by a small auricular lobe with an abnormal shape. It is more often unilateral and on the right side. Males are more frequently affected than females. It can occur as an isolated defect or can be associated with other abnormalities such as stenosis of the external auditory canal. In three of the main pediatric hospitals in Mexico, microtia is among the most important causes of attendance in the Genetics Department. Microtia-atresia must be considered as a major malformation with important repercussions in hearing function requiring multidisciplinary medical care in order to limit the disability associated and to provide genetic counseling. Its etiology is complex. Only in a minor number of cases it has been possible to identify a main genetic component (as in monogenic presentations) or a main environmental cause (as in fetal alcohol syndrome or pregestational diabetes). In most cases this malformation is multifactorial. Due to the relevance that the frequency of microtia atresia has in different health services in Mexico, it is important that all medical professionals are aware of its clinical, molecular and inherited characteristics.
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Affiliation(s)
- Mónica Aguinaga-Ríos
- Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología, México, D.F., México
| | - Sara Frías
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., México
| | - Diego J Arenas-Aranda
- Unidad de Investigación Médica en Genética Humana, Unidad Médica de Alta Especialidad Hospital de Pediatría, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México, D.F., México
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Li X, Hu J, Zhang J, Jin Q, Wang DM, Yu J, Zhang Q, Zhang YB. Genome-wide linkage study suggests a susceptibility locus for isolated bilateral microtia on 4p15.32-4p16.2. PLoS One 2014; 9:e101152. [PMID: 24983964 PMCID: PMC4077761 DOI: 10.1371/journal.pone.0101152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
Microtia is a congenital deformity where the external ear is underdeveloped. Genetic investigations have identified many susceptibility genes of microtia-related syndromes. However, no causal genes were reported for isolated microtia, the main form of microtia. We conducted a genome-wide linkage analysis on a 5-generation Chinese pedigree with isolated bilateral microtia. We identified a suggestive linkage locus on 4p15.32-4p16.2 with parametric LOD score of 2.70 and nonparametric linkage score (Zmean) of 12.28 (simulated occurrence per genome scan equal to 0.46 and 0.47, respectively). Haplotype reconstruction analysis of the 4p15.32-4p16.2 region further confined the linkage signal to a 10-Mb segment located between rs12505562 and rs12649803 (9.65-30.24 cM; 5.54-15.58 Mb). Various human organ developmental genes reside in this 10-Mb susceptibility region, such as EVC, EVC2, SLC2A9, NKX3-2, and HMX1. The coding regions of three genes, EVC known for cartilage development and NKX3-2, HMX1 involved in microtia, were selected for sequencing with 5 individuals from the pedigree. Of the 38 identified sequence variants, none segregates along with the disease phenotype. Other genes or DNA sequences of the 10-Mb region warrant for further investigation. In conclusion, we report a susceptibility locus of isolated microtia, and this finding will encourage future studies on the genetic basis of ear deformity.
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Affiliation(s)
- Xin Li
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Cardiology, Beijing Anzhen Hospital of the Capital University of Medical Sciences, Beijing, P. R. China
| | - Jintian Hu
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Jiao Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Qian Jin
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Duen-Mei Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Qingguo Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Yong-Biao Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
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Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2. Eur J Hum Genet 2013; 22:458-63. [PMID: 24045839 DOI: 10.1038/ejhg.2013.185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 07/04/2013] [Accepted: 07/24/2013] [Indexed: 11/08/2022] Open
Abstract
Copy number variants visible with the light microscope have been described as euchromatic variants (EVs) and EVs with extra G-light material at 8q21.2 have been reported only once before. We report four further patients with EVs of 8q21.2 ascertained for clinical (3) or reproductive reasons (1). Enhanced signal strength from two overlapping bacterial artificial chromosomes (BACs) and microarray analysis mapped the EV to a 284-kb interval in the reference genome. This interval consists of a sequence gap flanked by segmental duplications that contain the 12-kb components of one of the largest Variable Number Tandem Repeat arrays in the human genome. Using digital NanoString technology with a custom probe for the RNA exonuclease 1 homologue (S. cerevisiae)-like 1 (REXO1L1) gene within each 12-kb repeat, significantly enhanced diploid copy numbers of 270 and 265 were found in an EV family and a median diploid copy number of 166 copies in 216 controls. These 8q21.2 EVs are not thought to have clinical consequences as the phenotypes of the probands were inconsistent, those referred for reproductive reasons were otherwise phenotypically normal and the REXO1L1 gene has no known disease association. This EV was found in 4/3078 (1 in 770) consecutive referrals for chromosome analysis and needs to be distinguished from pathogenic imbalances of medial 8q. The REXO1L1 gene product is a marker of hepatitis C virus (HCV) infection and a possible association between REXO1L1 copy number and susceptibility to HCV infection, progression or response to treatment has not yet been excluded.
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Van der Aa N, Cheng J, Mateiu L, Zamani Esteki M, Kumar P, Dimitriadou E, Vanneste E, Moreau Y, Vermeesch JR, Voet T. Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains. Nucleic Acids Res 2013; 41:e66. [PMID: 23295674 PMCID: PMC3616740 DOI: 10.1093/nar/gks1352] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Single-cell genomics is revolutionizing basic genome research and clinical genetic diagnosis. However, none of the current research or clinical methods for single-cell analysis distinguishes between the analysis of a cell in G1-, S- or G2/M-phase of the cell cycle. Here, we demonstrate by means of array comparative genomic hybridization that charting the DNA copy number landscape of a cell in S-phase requires conceptually different approaches to that of a cell in G1- or G2/M-phase. Remarkably, despite single-cell whole-genome amplification artifacts, the log2 intensity ratios of single S-phase cells oscillate according to early and late replication domains, which in turn leads to the detection of significantly more DNA imbalances when compared with a cell in G1- or G2/M-phase. Although these DNA imbalances may, on the one hand, be falsely interpreted as genuine structural aberrations in the S-phase cell’s copy number profile and hence lead to misdiagnosis, on the other hand, the ability to detect replication domains genome wide in one cell has important applications in DNA-replication research. Genome-wide cell-type-specific early and late replicating domains have been identified by analyses of DNA from populations of cells, but cell-to-cell differences in DNA replication may be important in genome stability, disease aetiology and various other cellular processes.
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Affiliation(s)
- Niels Van der Aa
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
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Vermeesch JR, Brady PD, Sanlaville D, Kok K, Hastings RJ. Genome-wide arrays: quality criteria and platforms to be used in routine diagnostics. Hum Mutat 2012; 33:906-15. [PMID: 22415865 DOI: 10.1002/humu.22076] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Whole-genome analysis using genome-wide arrays, also called "genomic arrays," "microarrays," or "arrays," has become the first-tier diagnostic test for patients with developmental abnormalities and/or intellectual disabilities. In addition to constitutional anomalies, genomic arrays are also used to diagnose acquired disorders. Despite the rapid implementation of these technologies in diagnostic laboratories, external quality control schemes (such as CEQA, EMQN, UK NEQAS, and the USA QA scheme CAP) and interlaboratory comparisons show that there are huge differences in quality, interpretation, and reporting among laboratories. We offer guidance to laboratories to help assure the quality of array experiments and to standardize minimum detection resolution, and we also provide guidelines to standardize interpretation and reporting.
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Affiliation(s)
- Joris R Vermeesch
- Laboratory for Cytogenetics and Genome Research, Centre for Human Genetics, KU Leuven, University Hospital Leuven, Leuven, Belgium.
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Abstract
Array technology, here termed molecular karyotyping, is an attractive alternative to conventional karyotyping for prenatal diagnosis given the increase in resolution as well as faster report times. We review the benefits and limitations of this technique for the detection of pathogenic genomic imbalances, address the challenges raised in the interpretation of copy number variations, discuss practical considerations for the routine implementation of molecular karyotyping in prenatal diagnosis, and identify areas where more research is desired to enable large scale introduction of the technique(s).
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Lin L, Pan B, Jiang H, Zhuang H, Zhao Y, Guo D, Yu D. Mutational analysis of PACT gene in Chinese patients with microtia. Am J Med Genet A 2011; 155A:906-10. [DOI: 10.1002/ajmg.a.32821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 02/08/2009] [Indexed: 11/07/2022]
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Leung TY, Pooh RK, Wang CC, Lau TK, Choy KW. Classification of pathogenic or benign status of CNVs detected by microarray analysis. Expert Rev Mol Diagn 2010; 10:717-21. [PMID: 20843196 DOI: 10.1586/erm.10.68] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multiple lines of evidence indicated that microarray analysis has a better diagnostic yield of clinically significant genetic changes than do conventional methods in patients with constitutional abnormalities. However, interpretation of microarray data is complicated by the presence of both novel and recurrent copy number variants (CNVs) of unknown significance. To address this issue, Hehir-Kwa et al. described a new computational method for determining the pathogenicity between benign and mental retardation (MR)-associated CNVs among patients with MR. This study demonstrated the value of objectively prioritizing MR-associated CNVs using structural and functional genomic features in diagnostics. In this regard, we discuss an evidence-based summary of how to classify pathogenic or benign status of a CNV in clinical genetics and advocate that there is a need for algorithmic adjustment between constitutional cytogenetic and prenatal diagnosis settings.
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Affiliation(s)
- Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR
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A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies. Genet Med 2010; 12:478-85. [PMID: 20734469 DOI: 10.1097/gim.0b013e3181e3914a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
One of the aims of clinical genetics is to identify gene mutations or genomic rearrangements that may underlie complex presentations of phenotypic features, such as multiple congenital malformations and mental retardation. During the decade after publication of the first article on array-based comparative genome hybridization, this technique has supplemented karyotyping as the prime genome-wide screening method in patients with idiopathic multiple congenital malformations and mental retardation. The use of this novel, discovery-based, approach has dramatically increased the detection rate of genomic imbalances. Array-based comparative genome hybridization detects copy number changes in the genome of patients and healthy subjects, some of which may represent phenotypically neutral copy number variations. This prompts the need for properly distinguishing between those copy number changes that may contribute to the clinical phenotype amid a pool of neutral copy number variations. We briefly review the characteristics of copy number changes in relation to their clinical relevance. Second, we discuss several published workflow schemes to identify copy number changes putatively contributing to the phenotype, and third, we propose a three-step procedure aiming to rapidly evaluate copy number changes on a case-by-case basis as to their potential contribution to the phenotype of patients with idiopathic multiple congenital malformations and mental retardation. This workflow is gene-centered and should aid in identification of disease-related candidate genes and in estimating the recurrence risk for the disorder in the family.
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Resumen de la evolución de las técnicas de citogenética y genética molecular para la identificación de las alteraciones genéticas del desarrollo embrionario. Semergen 2010. [DOI: 10.1016/j.semerg.2010.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Monks DC, Jahangir A, Shanske AL, Samanich J, Morrow BE, Babcock M. Mutational analysis of HOXA2 and SIX2 in a Bronx population with isolated microtia. Int J Pediatr Otorhinolaryngol 2010; 74:878-82. [PMID: 20542577 DOI: 10.1016/j.ijporl.2010.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/27/2010] [Accepted: 05/01/2010] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Microtia is a developmental malformation of the external ear with genetic and environmental causes. The prevalence of microtia varies but several studies suggest increased incidence in Hispanic and African American populations. No causal genetic mutations have been identified in these populations. Mutations in the homeobox gene HOXA2 caused microtia in a single Iranian family. Another homeobox gene, SIX2, acts downstream of HOXA2 during development and provides another possible candidate for mutational analysis. METHODS To determine whether mutations in HOXA2 or SIX2 cause sporadic microtia, DNA sequencing analysis was performed on exons in both genes in 8 patients of Hispanic and African descent in the Bronx. Identified variants were assayed in an additional 4 patients and 100 Hispanic control samples using Sequenom MassArray to rule out causality in heterozygous patients. RESULTS No mutations were identified in the coding sequence of HOXA2 or SIX2. Four novel single nucleotide variants were identified among the patient samples. These variants lie in the intron and 3' UTR of HOXA2 and the 5' and 3' UTRs of SIX2. One variant in the intron of HOXA2 lies in a conserved predicted transcription factor binding site for SMARCA3. All four variants are also present at >5% frequency in Hispanic control samples, ruling out these novel variations as causal. CONCLUSIONS Lack of mutations in the coding regions of HOXA2 or SIX2 among the sporadic microtia patients studied indicate different etiologies. Identification of four novel single nucleotide polymorphisms in patients and controls of Hispanic descent, but not of Caucasian populations, points to genetic diversity in an understudied population.
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Affiliation(s)
- Dennis C Monks
- Division of Translational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Center 402, Bronx, NY 10461, USA
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Chafai Elalaoui S, Cherkaoui Jaouad I, Rifai L, Sefiani A. Autosomal dominant microtia. Eur J Med Genet 2010; 53:100-3. [PMID: 20152949 DOI: 10.1016/j.ejmg.2010.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 02/01/2010] [Indexed: 11/29/2022]
Abstract
Microtia (MIM600674) is a congenital malformation which occurs in 1/8000-10000 births. It is characterized by a small, and abnormally shaped pinna. It ranges in severity from a bump of tissue to a partially formed ear cup. Microtia is often associated with atresia of the external auditory canal. Familial microtia with meatal atresia has been reported, either with dominant or recessive inheritance, which makes genetic counselling difficult in sporadic cases. In the present paper, we report the case of a family with congenital microtia and conductive deafness in two generations, suggesting autosomal dominant inheritance with variable expression and incomplete penetrance.
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Affiliation(s)
- S Chafai Elalaoui
- Department of Medical Genetics, National Institute of Health, 27, Avenue Ibn Batouta, B.P. 769 Rabat, Morocco.
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Choy KW, Setlur SR, Lee C, Lau TK. The impact of human copy number variation on a new era of genetic testing. BJOG 2010; 117:391-8. [DOI: 10.1111/j.1471-0528.2009.02470.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Sharp AJ. Emerging themes and new challenges in defining the role of structural variation in human disease. Hum Mutat 2009; 30:135-44. [DOI: 10.1002/humu.20843] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kakinuma H, Sato H. Copy-number variations associated with autism spectrum disorder. Pharmacogenomics 2009; 9:1143-54. [PMID: 18681787 DOI: 10.2217/14622416.9.8.1143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous developmental disorder with a strong genetic component. Rare genetic disorders and various chromosomal abnormalities are thought to account for approximately 10% of people with ASD. The etiology of the remaining cases remains unknown. Recent advances in array-based technology have increased the resolution in detecting submicroscopic deletions and duplications, referred to as copy-number variations. ASD-associated copy-number variations, which are considered to be present in individuals with ASD but not in unaffected individuals, have been extensively investigated. These data will provide us with an opportunity not only to search for genes causing or contributing to ASDs but also to understand the genetics of ASD.
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Affiliation(s)
- Hiroaki Kakinuma
- Department of Pediatrics, Kanazawa Medical University, 1-1 Uchinada, Kahoku-gun, Ishikawa 920-293, Japan.
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Hollox EJ, Barber JCK, Brookes AJ, Armour JAL. Defensins and the dynamic genome: what we can learn from structural variation at human chromosome band 8p23.1. Genome Res 2009; 18:1686-97. [PMID: 18974263 DOI: 10.1101/gr.080945.108] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past four years, genome-wide studies have uncovered numerous examples of structural variation in the human genome. This includes structural variation that changes copy number, such as deletion and duplication, and structural variation that does not change copy number, such as orientation and positional polymorphism. One region that contains all these types of variation spans the chromosome band 8p23.1. This region has been studied in some depth, and the focus of this review is to examine our current understanding of the variation of this region. We also consider whether this region is a good model for other structurally variable regions in the genome and what the implications of this variation are for clinical studies. Finally, we discuss the bioinformatics challenges raised, discuss the evolution of the region, and suggest some future priorities for structural variation research.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom.
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Molekulare Karyotypisierung in der klinischen Anwendung. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Zusammenfassung
In den vergangenen Jahren hat sich die Anwendung der Mikroarraytechnologie für die Detektion von putativ pathologischen submikroskopischen Copy-Number-Variationen (CNV) einen festen Platz in der molekularen Zytogenetik erobert. Neben der Identifikation somatischer CNV in der onkologischen Diagnostik wird diese Technologie nunmehr für die Analyse von konstitutionellen CNV bei Patienten mit mentaler Retardierung genutzt. Arraybasierte genomische Hybridisierungen zeigen eine deutliche Verbesserung zu der bereits seit Jahren angewendeten komparativen genomischen Hybridisierung (CGH). Insbesondere weisen die dazugehörigen Technologien eine verbesserte Auflösung von weniger als 100 kb für Deletionen und Duplikationen auf und haben damit eine deutlich bessere Aufklärungsrate von Krankheiten mit Behinderungen ungeklärter Ursache. In einigen Zentren gehört die Arraytechnologie daher bereits zur Routinetechnologie der Syndromabklärung. Im vorliegenden Beitrag soll deshalb auch auf die Gemeinsamkeiten bzw. Unterschiede der verschiedenen Basistechnologien der Arraytechnik eingegangen werden.
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Qin J, Jones RC, Ramakrishnan R. Studying copy number variations using a nanofluidic platform. Nucleic Acids Res 2008; 36:e116. [PMID: 18710881 PMCID: PMC2566873 DOI: 10.1093/nar/gkn518] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). All these approaches are limited in resolution and can at best distinguish a twofold (or 50%) difference in copy number. We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. We have evaluated the digital array's performance using a model system, to show that this technology is exquisitely sensitive, capable of differentiating as little as a 15% difference in gene copy number (or between 6 and 7 copies of a target gene). We have also analyzed commercial DNA samples for their CYP2D6 copy numbers and confirmed that our results were consistent with those obtained independently using conventional techniques. In a screening experiment with breast cancer and normal DNA samples, the ERBB2 gene was found to be amplified in about 35% of breast cancer samples. The use of the digital array enables accurate measurement of gene copy numbers and is of significant value in CNV studies.
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Affiliation(s)
- Jian Qin
- Fluidigm Corporation, South San Francisco, CA 94080, USA
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