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Nishio SY, Usami SI. Frequency of the STRC-CATSPER2 deletion in STRC-associated hearing loss patients. Sci Rep 2022; 12:634. [PMID: 35022556 PMCID: PMC8755823 DOI: 10.1038/s41598-021-04688-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/21/2021] [Indexed: 01/14/2023] Open
Abstract
The STRC gene, located on chromosome 15q15.3, is one of the genetic causes of autosomal recessive mild-to-moderate sensorineural hearing loss. One of the unique characteristics of STRC-associated hearing loss is the high prevalence of long deletions or copy number variations observed on chromosome 15q15.3. Further, the deletion of chromosome 15q15.3 from STRC to CATSPER2 is also known to be a genetic cause of deafness infertility syndrome (DIS), which is associated with not only hearing loss but also male infertility, as CATSPER2 plays crucial roles in sperm motility. Thus, information regarding the deletion range for each patient is important to the provision of appropriate genetic counselling for hearing loss and male infertility. In the present study, we performed next-generation sequencing (NGS) analysis for 9956 Japanese hearing loss patients and analyzed copy number variations in the STRC gene based on NGS read depth data. In addition, we performed Multiplex Ligation-dependent Probe Amplification analysis to determine the deletion range including the PPIP5K1, CKMT1B, STRC and CATSPER2 genomic region to estimate the prevalence of the STRC-CATSPER deletion, which is causative for DIS among the STRC-associated hearing loss patients. As a result, we identified 276 cases with STRC-associated hearing loss. The prevalence of STRC-associated hearing loss in Japanese hearing loss patients was 2.77% (276/9956). In addition, 77.1% of cases with STRC homozygous deletions carried a two copy loss of the entire CKMT1B-STRC-CATSPER2 gene region. This information will be useful for the provision of more appropriate genetic counselling regarding hearing loss and male infertility for the patients with a STRC deletion.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
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2
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Simi A, Perry J, Schindler E, Oza A, Luo M, Hartman T, Krantz ID, Germiller JA, Kawai K, Kenna M. Audiologic Phenotype and Progression in Pediatric STRC-Related Autosomal Recessive Hearing Loss. Laryngoscope 2021; 131:E2897-E2903. [PMID: 34111299 DOI: 10.1002/lary.29680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES Sensorineural hearing loss (SNHL) is a common sensory deficit affecting pediatric populations. The majority of pediatric SNHL is genetic in etiology, with over 123 identified nonsyndromic causative genes. One such gene is STRC, which has been identified as the second most frequent autosomal recessive nonsyndromic gene associated with SNHL in multiple populations. The objective of this study was to investigate the phenotypic presentation and incidence of audiologic progression in pediatric patients with STRC-related hearing loss (HL). METHODS Thirty-nine pediatric patients with confirmed HL and biallelic pathogenic STRC mutations were identified at two pediatric hospitals. A retrospective chart review was completed including demographics, medical history, genetic testing results, and audiologic data. HL progression was assessed using air conduction thresholds from pure-tone audiograms and auditory brain stem responses, and masked bone conduction thresholds from pure-tone audiograms. RESULTS Thirty-six patients had homozygous STRC deletions. Three were compound heterozygotes. All patients had bilateral, symmetric SNHL. Baseline HL was mild in 39% of ears, moderate in 52%, and moderate-severe in 3%. Of the 31 patients for which sufficient data were available to evaluate progression, 18 (58%) had some degree of progressive HL. Among these 31 patients assessed for progression, the mean hearing threshold declined by 0.6 dB per year (95% confidence interval: 0.5, 0.8; P < .001). CONCLUSIONS These biallelic STRC patients displayed HL ranging from mild to moderate-severe at baseline and progressing in 58%. The variability of the STRC phenotype and the possibility of audiologic progression should be considered in the clinical management of pediatric STRC-related SNHL. LEVEL OF EVIDENCE 3 Laryngoscope, 2021.
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Affiliation(s)
- Andrea Simi
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Case Western Reserve University School of Medicine, Cleveland, Ohio, U.S.A
| | - Julia Perry
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A
| | - Emma Schindler
- Department of Otorhinolaryngology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | - Andrea Oza
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, U.S.A
| | - Minjie Luo
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, U.S.A.,Department of Pathology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | - Tiffiney Hartman
- Roberts Individualized Medical Genetics Center, Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, U.S.A
| | - Ian D Krantz
- Roberts Individualized Medical Genetics Center, Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, U.S.A.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A
| | - John A Germiller
- Department of Otorhinolaryngology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, U.S.A.,Division of Otolaryngology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, U.S.A
| | - Kosuke Kawai
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, U.S.A.,Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, U.S.A
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3
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Laurent S, Gehrig C, Nouspikel T, Amr SS, Oza A, Murphy E, Vannier A, Béna FS, Carminho-Rodrigues MT, Blouin JL, Cao Van H, Abramowicz M, Paoloni-Giacobino A, Guipponi M. Molecular characterization of pathogenic OTOA gene conversions in hearing loss patients. Hum Mutat 2021; 42:373-377. [PMID: 33492714 DOI: 10.1002/humu.24167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/02/2020] [Accepted: 12/16/2020] [Indexed: 11/11/2022]
Abstract
Bi-allelic loss-of-function variants of OTOA are a well-known cause of moderate-to-severe hearing loss. Whereas non-allelic homologous recombination-mediated deletions of the gene are well known, gene conversions to pseudogene OTOAP1 have been reported in the literature but never fully described nor their pathogenicity assessed. Here, we report two unrelated patients with moderate hearing-loss, who were compound heterozygotes for a converted allele and a deletion of OTOA. The conversions were initially detected through sequencing depths anomalies at the OTOA locus after exome sequencing, then confirmed with long range polymerase chain reactions. Both conversions lead to loss-of-function by introducing a premature stop codon in exon 22 (p.Glu787*). Using genomic alignments and long read nanopore sequencing, we found that the two probands carry stretches of converted DNA of widely different lengths (at least 9 kbp and around 900 bp, respectively).
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Affiliation(s)
- Sacha Laurent
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Corinne Gehrig
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Thierry Nouspikel
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Sami S Amr
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA
| | - Anne Vannier
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Frédérique Sloan Béna
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Jean-Louis Blouin
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Hélène Cao Van
- Department of Otorhinolaryngology, Head and Neck Surgery, Pediatric Otolaryngology Unit, University Hospitals of Geneva, Geneva, Switzerland
| | - Marc Abramowicz
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ariane Paoloni-Giacobino
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Michel Guipponi
- Department of Diagnostic, Genetic Medicine Unit, University Hospitals of Geneva, Geneva, Switzerland.,Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
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Rentas S, Abou Tayoun A. Utility of droplet digital PCR and NGS-based CNV clinical assays in hearing loss diagnostics: current status and future prospects. Expert Rev Mol Diagn 2021; 21:213-221. [PMID: 33554673 DOI: 10.1080/14737159.2021.1887731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Genetic variants in over 100 genes can cause non-syndromic hearing loss (NSHL). Comprehensive diagnostic testing of these genes requires detecting pathogenic sequence and copy number alterations with economical, scalable and sensitive assays. Here we discuss best practices and effective testing algorithms for hearing-loss-related genes with special emphasis on detection of copy number variants.Areas covered: We review studies that used next-generation sequencing (NGS), chromosomal microarrays, droplet digital PCR (ddPCR), and multiplex ligation-dependent probe amplification (MLPA) for the diagnosis of NSHL. We specifically focus on unique and recurrent copy number changes that affect the GJB2 and STRC genes, two of the most common causes of NSHL.Expert opinion: NGS panels and exome sequencing can detect most pathogenic sequence and copy number variants that cause NSHL; however, GJB2 and STRC currently require additional assays to capture all pathogenic copy number variants. Adoption of genome sequencing may simplify diagnostic workflows, but further investigational studies will be required to evaluate its clinical efficacy.
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Affiliation(s)
- Stefan Rentas
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, UAE.,Department of Genetics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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5
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Improving the Management of Patients with Hearing Loss by the Implementation of an NGS Panel in Clinical Practice. Genes (Basel) 2020; 11:genes11121467. [PMID: 33297549 PMCID: PMC7762334 DOI: 10.3390/genes11121467] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
A cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss (HL) underwent an exhaustive clinical evaluation. Molecular analysis was performed using targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL. Variants were prioritized according to the minimum allele frequency and classified according to the American College of Medical Genetics and Genomics guidelines. Variant(s) responsible for the disease were detected in a 40% of families including autosomal recessive (AR), autosomal dominant (AD) and X-linked patterns of inheritance. We identified pathogenic or likely pathogenic variants in 26 different genes, 15 with AR inheritance pattern, 9 with AD and 2 that are X-linked. Fourteen of the found variants are novel. This study highlights the clinical utility of targeted NGS for sensorineural hearing loss. The optimal panel for HL must be designed according to the spectrum of the most represented genes in a given population and the laboratory capabilities considering the pressure on healthcare.
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Hildebrandt C, Fulton A, Rodan LH. Homozygous deletion of 21q22.2 in a patient with hypotonia, developmental delay, cortical visual impairment, and retinopathy. Am J Med Genet A 2020; 185:555-560. [PMID: 33170561 DOI: 10.1002/ajmg.a.61969] [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: 05/28/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 11/09/2022]
Abstract
21q22 contains several dosage sensitive genes that are important in neurocognitive development. Determining impacts of gene dosage alterations in this region can be useful in establishing contributions of these genes to human development and disease. We describe a 15-month-old girl with a 1,140 kb homozygous deletion in the Down Syndrome Critical Region at 21q22.2 including 4 genes; B3GALT5, IGSF5, PCP4, DSCAM, and a microRNA (MIR4760). Clinical singleton genome sequencing did not report any candidate gene variants for the patient's phenotype. She presented with hypotonia, global developmental delay, cortical visual impairment, and mild facial dysmorphism. Ophthalmological exam was suggestive of retinopathy. We propose that the absence of DSCAM and PCP4 may contribute to the patient's neurological and retinal phenotype, while the role of absent B3GALT5 and IGSF5 in her presentation remain unclear at this time.
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Affiliation(s)
- Clara Hildebrandt
- Medical Biochemical Fellowship at Boston Children's Hospital, Boston, Massachusetts, USA
| | - Anne Fulton
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lance H Rodan
- Department of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
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Clinical features of hearing loss caused by STRC gene deletions/mutations in Russian population. Int J Pediatr Otorhinolaryngol 2020; 138:110247. [PMID: 32705992 DOI: 10.1016/j.ijporl.2020.110247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/29/2022]
Abstract
UNLABELLED Congenital sensorineural hearing loss is related to mutations in numerous genes encoding the structures of the inner ear in majority of the cases. Mutations in GJB2 gene are the most frequently identified causes of congenital nonsyndromal hearing loss. GJB2 gene testing became a routine clinical tool. For GJB2-negative patients new genetic approaches including methods based on new generation sequencing give a chance to identify mutations in other genes. The frequent reason of mild-to-moderate hearing loss such as the deletions/mutations of the gene STRC encoding stereocilin protein were recognized (OMIM: 606440). OBJECTIVES To evaluate the audiological features in hearing impaired patients with deletions and point mutations in the STRC gene. PATIENTS AND METHODS The group of 28 patients from 21 unrelated families with pathological mutations in the STRC gene underwent audiological examination. The description and analysis of the results of full audiological examination was provided. RESULTS All patients initially had bilateral nonsyndromal sensorineural hearing loss. Among 11 homozygotes of large deletion harboring STRC to CATSPER2 genes were 7 male individuals indicating the presence of male infertility syndrome. In general, 7 children failed audiological screening and 4 children underwent audiological assessment in the age of 3 and 6 months. The most frequently hearing thresholds were registered between 35 and 55 dB that corresponds to mild-to-moderate hearing impairment. The average age of diagnostics was 7.9 years (ranged from 3 months to 45 years). In the majority of patients the audiological profiles were flat or descending with elevation of thresholds at middle and high frequencies and relatively preserved thresholds at low frequencies. Hearing thresholds are symmetric and stable with age. CONCLUSION STRC-linked hearing loss is congenital, of mild and moderate severity. Special clinical and genetic approach for children who failed newborn hearing screening with mild-to-moderate hearing loss is necessary.
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8
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Luo T, Chen HY, Zou QX, Wang T, Cheng YM, Wang HF, Wang F, Jin ZL, Chen Y, Weng SQ, Zeng XH. A novel copy number variation in CATSPER2 causes idiopathic male infertility with normal semen parameters. Hum Reprod 2020; 34:414-423. [PMID: 30629171 DOI: 10.1093/humrep/dey377] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 11/20/2018] [Accepted: 11/30/2018] [Indexed: 12/28/2022] Open
Abstract
STUDY QUESTION Are genetic abnormalities in CATSPER (cation channel of sperm) genes associated with idiopathic male infertility with normal semen parameters and, if so, how do they affect male fertility? SUMMARY ANSWER A novel copy number variation (CNV) in CATSPER2 causes idiopathic male infertility with normal semen parameters by disrupting the ability of sperm to penetrate viscous media, undergo hyperactivation and respond to progesterone. WHAT IS KNOWN ALREADY CATSPER is the principle Ca2+ channel mediating extracellular Ca2+ influx into spermatozoa. Although several case reports have suggested a causal relationship between CATSPER disruption and human male infertility, whether genetic abnormalities in CATSPER genes are associated with idiopathic male infertility with normal semen parameters remains unclear. STUDY DESIGN, SIZE, DURATION Spermatozoa were obtained from men attending the reproductive medical center at Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, China between January 2014 and June 2016. In total, 120 men from infertile couples and 20 healthy male donors were selected to take part in the study, based on their normal semen parameters. PARTICIPANTS/MATERIALS, SETTING, METHODS CATSPER and KSPER currents were assessed using the whole-cell patch-clamp technique. Whole-genome sequencing and TaqMan® CNV assays were performed to identify genetic variations. The expression levels of genes encoding the CATSPER complex were measured by quantitative real-time PCR and Western blot. Sperm motion characteristics and hyperactivation were examined with a computer-aided sperm analysis (CASA) system. Sperm responses to progesterone, assessed as increases in CATSPER current and intercellular Ca2+ concentrations ([Ca2+]i), as well as inducement of penetration ability and acrosome reaction, were examined by means of whole-cell patch-clamp technique, single-sperm [Ca2+]i imaging, penetration into methylcellulose assay and chlortetracycline staining, respectively. MAIN RESULTS AND THE ROLE OF CHANCE An infertile man with complete disruption of CATSPER current was identified. This individual has a novel CNV which disrupts one gene copy in the region 43894500-43950000 in chromosome 15 (GRCh37.p13 Primary Assembly, nsv3067119), containing the whole DNA sequence of CATSPER2. This CNV affected the expression of CATSPER2, resulting in dramatically reduced levels of CATSPER2 proteins in the individual's spermatozoa. Although this individual exhibited normal semen parameters, his spermatozoa showed impaired penetration ability, deficient hyperactivation, and did not respond to progesterone, in terms of monovalent current potentiation, [Ca2+]i increase, penetration ability enhancement and acrosome reaction inducement, which may explain the individual's idiopathic infertility. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Our novel findings require more cases to support the CATSPER2 CNV identified in this study as a common cause of idiopathic male infertility in patients with normal semen parameters. Therefore, caution must be taken when extrapolating the use of this CNV as a potential biomarker for idiopathic male infertility. WIDER IMPLICATIONS OF THE FINDINGS The findings from the unique human CATSPER 'knockout' model in this study not only confirm the essential roles of CATSPER in mediating progesterone response and regulating hyperactivation in human spermatozoa but also reveal that disruption of CATSPER current is a significant factor causing idiopathic male infertility. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by National Natural Science Foundation of China (81771644 and 31400996 to T.L.; 31230034 to X.Z.); National Basic Research Program of China (973 Program, 2015CB943003 to X.Z.); National Key Research and Development Program of China (2016YFC1000905 to T.L.); Natural Science Foundation of Jiangxi, China (20121BBG70021 and GJJ12015 to X.Z.; 20161BAB204167 and 20171ACB21006 to T.L.) and the open project of National Population and Family Planning Key Laboratory of Contraceptives and Devices Research (No. 2016KF07 to T.L.). The authors have no conflicts of interest to declare.
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Affiliation(s)
- Tao Luo
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China.,Key Laboratory of Reproductive Physiology and Pathology in Jiangxi Province, Nanchang, Jiangxi, PR China
| | - Hou-Yang Chen
- Reproductive Medical Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, PR China
| | - Qian-Xing Zou
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Tao Wang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Yi-Min Cheng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Hua-Feng Wang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Fang Wang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Zhong-Lin Jin
- Reproductive Medical Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, PR China
| | - Ying Chen
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Shi-Qi Weng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China
| | - Xu-Hui Zeng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, Jiangxi, PR China.,Key Laboratory of Reproductive Physiology and Pathology in Jiangxi Province, Nanchang, Jiangxi, PR China.,Jiangxi Provincial Collaborative Innovation Center for Cardiovascular, Digestive and Neuropsychiatric Diseases, Nanchang, Jiangxi, PR China
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9
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Ozekin YH, Isner T, Bates EA. Ion Channel Contributions to Morphological Development: Insights From the Role of Kir2.1 in Bone Development. Front Mol Neurosci 2020; 13:99. [PMID: 32581710 PMCID: PMC7296152 DOI: 10.3389/fnmol.2020.00099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/08/2020] [Indexed: 12/21/2022] Open
Abstract
The role of ion channels in neurons and muscles has been well characterized. However, recent work has demonstrated both the presence and necessity of ion channels in diverse cell types for morphological development. For example, mutations that disrupt ion channels give rise to abnormal structural development in species of flies, frogs, fish, mice, and humans. Furthermore, medications and recreational drugs that target ion channels are associated with higher incidence of birth defects in humans. In this review we establish the effects of several teratogens on development including epilepsy treatment drugs (topiramate, valproate, ethosuximide, phenobarbital, phenytoin, and carbamazepine), nicotine, heat, and cannabinoids. We then propose potential links between these teratogenic agents and ion channels with mechanistic insights from model organisms. Finally, we talk about the role of a particular ion channel, Kir2.1, in the formation and development of bone as an example of how ion channels can be used to uncover important processes in morphogenesis. Because ion channels are common targets of many currently used medications, understanding how ion channels impact morphological development will be important for prevention of birth defects. It is becoming increasingly clear that ion channels have functional roles outside of tissues that have been classically considered excitable.
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Affiliation(s)
- Yunus H Ozekin
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Trevor Isner
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Emily A Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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10
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Ito T, Kawashima Y, Fujikawa T, Honda K, Makabe A, Kitamura K, Tsutsumi T. Rapid screening of copy number variations in STRC by droplet digital PCR in patients with mild-to-moderate hearing loss. Hum Genome Var 2019; 6:41. [PMID: 31645979 PMCID: PMC6804619 DOI: 10.1038/s41439-019-0075-5] [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: 04/13/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 11/09/2022] Open
Abstract
Copy number variations (CNVs) are commonly reported in STRC, the causal gene for DFNB16. Various techniques are used clinically for CNV detection, and droplet digital PCR (ddPCR) provides highly precise absolute quantification of DNA copy number. We aimed to validate the feasibility and efficiency of ddPCR in combination with long-range PCR (LR-PCR) in identifying CNVs and mutations in STRC. Additionally, we determined the frequency of CNVs and mutations in STRC in Japanese patients with mild-to-moderate hearing loss. We evaluated 84 unrelated Japanese patients with mild-to-moderate bilateral idiopathic or autosomal recessive nonsyndromic sensorineural hearing loss. The ratio of STRC copy number to the copy number of the internal control RPP30 ranged from 0.949 to 1.009 (0.989 ± 0.017) in 77 patients; it ranged from 0.484 to 0.538 (0.509 ± 0.024) in five patients and was 0.000 in two patients, indicating heterozygous and homozygous deletions, respectively. The copy number deletion prevalence rates were 7.7% and 0.9% in the patients and healthy controls, respectively. In combination with LR-PCR, ddPCR revealed that at least three patients (3.6%) had STRC-related hearing loss. Detecting STRC CNVs by ddPCR was rapid, precise, and cost-effective and facilitated the identification of STRC CNVs.
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Affiliation(s)
- Taku Ito
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiyuki Kawashima
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Taro Fujikawa
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Honda
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayane Makabe
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Kitamura
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Otorhinolaryngology, Head and Neck Surgery, Chigasaki Chuo Hospital, Chigasaki, Japan
| | - Takeshi Tsutsumi
- 1Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo, Japan
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11
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Shi L, Bai Y, Kharbutli Y, Oza AM, Amr SS, Edelmann L, Mehta L, Scott SA. Prenatal cytogenomic identification and molecular refinement of compound heterozygous STRC deletion breakpoints. Mol Genet Genomic Med 2019; 7:e806. [PMID: 31218851 PMCID: PMC6687617 DOI: 10.1002/mgg3.806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
Here, we report the prenatal detection of a compound heterozygous deletion at chromosome 15q15.3 by clinical chromosomal microarray (CMA) testing that included the CATSPER2 male infertility gene. However, given the low resolution of CMA at this homologous locus, it was unclear if the neighboring STRC hearing loss gene was also affected. Therefore, we developed a novel allele‐specific PCR strategy, which narrowed the proximal breakpoint of the maternally inherited deletion to a 310 bp interval that was 440 bp upstream from the STRC transcription start site.
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Affiliation(s)
- Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Sema4, a Mount Sinai Venture, Stamford, Connecticut
| | - Yan Bai
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Sema4, a Mount Sinai Venture, Stamford, Connecticut
| | - Yara Kharbutli
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Sema4, a Mount Sinai Venture, Stamford, Connecticut
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York.,Sema4, a Mount Sinai Venture, Stamford, Connecticut
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12
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Yokota Y, Moteki H, Nishio SY, Yamaguchi T, Wakui K, Kobayashi Y, Ohyama K, Miyazaki H, Matsuoka R, Abe S, Kumakawa K, Takahashi M, Sakaguchi H, Uehara N, Ishino T, Kosho T, Fukushima Y, Usami SI. Frequency and clinical features of hearing loss caused by STRC deletions. Sci Rep 2019; 9:4408. [PMID: 30867468 PMCID: PMC6416315 DOI: 10.1038/s41598-019-40586-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/19/2019] [Indexed: 12/04/2022] Open
Abstract
Sensorineural hearing loss is a common deficit and mainly occurs due to genetic factors. Recently, copy number variants (CNVs) in the STRC gene have also been recognized as a major cause of genetic hearing loss. We investigated the frequency of STRC deletions in the Japanese population and the characteristics of associated hearing loss. For CNV analysis, we employed a specialized method of Ion AmpliSeqTM sequencing, and confirmed the CNV results via custom array comparative genomic hybridization. We identified 17 probands with STRC homozygous deletions. The prevalence of STRC homozygous deletions was 1.7% in the hearing loss population overall, and 4.3% among mild-to-moderate hearing loss patients. A 2.63% carrier deletion rate was identified in both the hearing loss and the control population with normal hearing. In conclusion, our results show that STRC deletions are the second most common cause of mild-to-moderate hearing loss after the GJB2 gene, which accounts for the majority of genetic hearing loss. The phenotype of hearing loss is congenital and appears to be moderate, and is most likely to be stable without deterioration even after the age of 50. The present study highlights the importance of the STRC gene as a major cause of mild-to-moderate hearing loss.
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Affiliation(s)
- Yoh Yokota
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan. .,Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan.
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan.,Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Yumiko Kobayashi
- Department of Otolaryngology-Head & Neck Surgery, Iwate Medical University, Morioka, Japan
| | - Kenji Ohyama
- Department of Otorhinolaryngology, Tohoku Rosai Hospital, Sendai, Japan
| | - Hiromitsu Miyazaki
- Department of Otorhinolaryngology-Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Japan
| | - Rina Matsuoka
- Department of Otorhinolaryngology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Satoko Abe
- Department of Otorhinolaryngology, Toranomon Hospital, Tokyo, Japan
| | - Kozo Kumakawa
- Department of Otorhinolaryngology, Toranomon Hospital, Tokyo, Japan
| | - Masahiro Takahashi
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama, Japan.,Department of Otorhinolaryngology, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Hirofumi Sakaguchi
- Department of Otorhinolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Natsumi Uehara
- Department of Otolaryngology-Head and Neck Surgery, Kobe University School of Medicine, Kobe, Japan
| | - Takashi Ishino
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Research Center for Support to Advanced Science, Shinshu University, Matsumoto, Japan
| | | | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan.,Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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13
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Morgan A, Lenarduzzi S, Cappellani S, Pecile V, Morgutti M, Orzan E, Ghiselli S, Ambrosetti U, Brumat M, Gajendrarao P, La Bianca M, Faletra F, Grosso E, Sirchia F, Sensi A, Graziano C, Seri M, Gasparini P, Girotto G. Genomic Studies in a Large Cohort of Hearing Impaired Italian Patients Revealed Several New Alleles, a Rare Case of Uniparental Disomy (UPD) and the Importance to Search for Copy Number Variations. Front Genet 2018; 9:681. [PMID: 30622556 PMCID: PMC6309105 DOI: 10.3389/fgene.2018.00681] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 12/07/2018] [Indexed: 11/13/2022] Open
Abstract
Hereditary hearing loss (HHL) is a common disorder characterized by a huge genetic heterogeneity. The definition of a correct molecular diagnosis is essential for proper genetic counseling, recurrence risk estimation, and therapeutic options. From 20 to 40% of patients carry mutations in GJB2 gene, thus, in more than half of cases it is necessary to look for causative variants in the other genes so far identified (~100). In this light, the use of next-generation sequencing technologies has proved to be the best solution for mutational screening, even though it is not always conclusive. Here we describe a combined approach, based on targeted re-sequencing (TRS) of 96 HHL genes followed by high-density SNP arrays, aimed at the identification of the molecular causes of non-syndromic HHL (NSHL). This strategy has been applied to study 103 Italian unrelated cases, negative for mutations in GJB2, and led to the characterization of 31% of them (i.e., 37% of familial and 26.3% of sporadic cases). In particular, TRS revealed TECTA and ACTG1 genes as major players in the Italian population. Furthermore, two de novo missense variants in ACTG1 have been identified and investigated through protein modeling and molecular dynamics simulations, confirming their likely pathogenic effect. Among the selected patients analyzed by SNP arrays (negative to TRS, or with a single variant in a recessive gene) a molecular diagnosis was reached in ~36% of cases, highlighting the importance to look for large insertions/deletions. Moreover, copy number variants analysis led to the identification of the first case of uniparental disomy involving LOXHD1 gene. Overall, taking into account the contribution of GJB2, plus the results from TRS and SNP arrays, it was possible to reach a molecular diagnosis in ~51% of NSHL cases. These data proved the usefulness of a combined approach for the analysis of NSHL and for the definition of the epidemiological picture of HHL in the Italian population.
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Affiliation(s)
- Anna Morgan
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | | | - Vanna Pecile
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | | | - Eva Orzan
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Sara Ghiselli
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Umberto Ambrosetti
- Audiologia, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | | | | | - Enrico Grosso
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Fabio Sirchia
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Alberto Sensi
- Medical Genetics Unit, Department of Clinical Pathology, Azienda Unità Sanitaria Locale (AUSL) della Romagna, Cesena, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Marco Seri
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Paolo Gasparini
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
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14
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Cheung SW, Bi W. Novel applications of array comparative genomic hybridization in molecular diagnostics. Expert Rev Mol Diagn 2018; 18:531-542. [PMID: 29848116 DOI: 10.1080/14737159.2018.1479253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.
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Affiliation(s)
- Sau W Cheung
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Weimin Bi
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Baylor Genetics , Houston , TX , USA
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15
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Krausz C, Cioppi F, Riera-Escamilla A. Testing for genetic contributions to infertility: potential clinical impact. Expert Rev Mol Diagn 2018. [PMID: 29540081 DOI: 10.1080/14737159.2018.1453358] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Male infertility affects about 7% of the general male population, and it is a multifactorial, polygenic pathological condition. Known genetic factors, accounting for about 20-25% of male factor infertility, are present in each etiological category: i) hypothalamic-pituitary axis dysfunction; ii) quantitative and qualitative alterations of spermatogenesis; iii) ductal obstruction/dysfunction. Areas covered: All routinely available genetic tests are described. Indication for testing for chromosomal anomalies and Y chromosome microdeletions is based on sperm count (severe oligozoospermia/azoospermia). Mutation screening in candidate genes is indicated in specific semen/testis phenotypes. In about 40% of infertile patients, the aetiology remains unknown ('idiopathic cases') and whole exome sequencing may reveal novel genetic causes. Expert commentary: Genetic testing is essential for its relevance in clinical decision-making. For instance, it helps to avoid unnecessary surgical or medical treatments and it may provide prediction for testicular sperm retrieval. The highest frequency of genetic anomalies is observed in severe spermatogenic impairment, which can be treated with in vitro fertilization (IVF). Given the risk of transmitting genetic disorders to the future offspring through IVF, the diagnosis of known and the discovery of novel genetic factors in idiopathic infertility is of outmost clinical importance.
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Affiliation(s)
- Csilla Krausz
- a Department of Experimental, Clinical and Biomedical Sciences Mario Serio, Sexual Medicine and Andrology Unit , University of Florence , Florence , Italy
| | - Francesca Cioppi
- a Department of Experimental, Clinical and Biomedical Sciences Mario Serio, Sexual Medicine and Andrology Unit , University of Florence , Florence , Italy
| | - Antoni Riera-Escamilla
- b Andrology Department , Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau) , Barcelona , Spain
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16
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Brabbing-Goldstein D, Reches A, Svirsky R, Bar-Shira A, Yaron Y. Dilemmas in genetic counseling for low-penetrance neuro-susceptibility loci detected on prenatal chromosomal microarray analysis. Am J Obstet Gynecol 2018; 218:247.e1-247.e12. [PMID: 29146387 DOI: 10.1016/j.ajog.2017.11.559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/14/2017] [Accepted: 11/06/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Chromosomal microarray analysis is standard of care in fetuses with malformations, detecting clinically significant copy number variants in 5-7% of cases over conventional karyotyping. However, it also detects variants of uncertain significance in 1.6-4.2% of the cases, some of which are low-penetrance neuro-susceptibility loci. The interpretation of these variants in pregnancy is particularly challenging because the significance is often unclear and the clinical implications may be difficult to predict. OBJECTIVE The purpose of this study was to describe counseling dilemmas regarding low-penetrance neuro-susceptibility loci that are detected by prenatal chromosomal microarray analysis. STUDY DESIGN During the study period (January 2014 to December 2015), 700 prenatal chromosomal microarray analyses were performed. Cases were categorized as "indicated" (n=375) if there were abnormal sonographic findings or suggestive medical history and "patient choice" (n=325) in the presence of a structurally normal fetus with no other particular indication. The laboratory reported on copy number variants ≥400 Kb in size in loci known to be associated with genetic syndromes and ≥1 Mb in other areas of genome. Results were classified as gross aneuploidy, copy number variants, and normal. Copy number variants were categorized according to the American College of Medical Genetics standards and guidelines: pathogenic, variants of uncertain significance, or benign. Variants of uncertain significance were further subdivided into categories of likely pathogenic, variants of uncertain significance with no subclassification, and likely benign. Statistical analysis was performed with the use of Chi square test and Fisher's exact test to compare intergroup differences in incidence of the different result categories and demographic data. RESULTS Patient choice cases became more prevalent with time (35.5% in the beginning of the study, compared with 48.4% at the end of the study period). Clinically significant copy number variants were found in 14 of 375 (3.7%) of indicated cases vs only 2 of 325 (0.6%) of patient choice cases (P=.009). All "likely benign" variants consisted of low-penetrance neuro-susceptibility loci. The incidence thereof was similar between the indicated and patient choice groups (3.7% vs 3.4%; P=.85). In the indicated group, some variants of uncertain significance may have contributed to the abnormal anatomic findings. Conversely, in the patient choice group, the finding of low-penetrance neuro-susceptibility loci was often unexpected and confounding for prospective parents. CONCLUSION Prenatal chromosomal microarray analysis added clinically significant information in both groups. However, it also detected low-penetrance neuro-susceptibility loci in approximately 3.5% of the cases. This fact should be conveyed during pretest counseling to allow patients to make informed choices, particularly when chromosomal microarray is to be performed for patient choice.
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17
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Engraftment of Human Pluripotent Stem Cell-derived Progenitors in the Inner Ear of Prenatal Mice. Sci Rep 2018; 8:1941. [PMID: 29386634 PMCID: PMC5792596 DOI: 10.1038/s41598-018-20277-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/16/2018] [Indexed: 11/08/2022] Open
Abstract
There is, at present, no curative treatment for genetic hearing loss. We have previously reported that transuterine gene transfer of wild type CONNEXIN30 (CX30) genes into otocysts in CX30-deleted mice could restore hearing. Cell transplantation therapy might be another therapeutic option, although it is still unknown whether stem cell-derived progenitor cells could migrate into mouse otocysts. Here, we show successful cell transplantation of progenitors of outer sulcus cell-like cells derived from human-derived induced pluripotent stem cells into mouse otocysts on embryonic day 11.5. The delivered cells engrafted more frequently in the non-sensory region in the inner ear of CX30-deleted mice than in wild type mice and survived for up to 1 week after transplantation. Some of the engrafted cells expressed CX30 proteins in the non-sensory region. This is the first report that demonstrates successful engraftment of exogenous cells in prenatal developing otocysts in mice. Future studies using this mouse otocystic injection model in vivo will provide further clues for developing treatment modalities for congenital hearing loss in humans.
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18
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Baux D, Vaché C, Blanchet C, Willems M, Baudoin C, Moclyn M, Faugère V, Touraine R, Isidor B, Dupin-Deguine D, Nizon M, Vincent M, Mercier S, Calais C, García-García G, Azher Z, Lambert L, Perdomo-Trujillo Y, Giuliano F, Claustres M, Koenig M, Mondain M, Roux AF. Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients. Sci Rep 2017; 7:16783. [PMID: 29196752 PMCID: PMC5711943 DOI: 10.1038/s41598-017-16846-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/17/2017] [Indexed: 11/22/2022] Open
Abstract
Hearing loss is the most common sensory disorder and because of its high genetic heterogeneity, implementation of Massively Parallel Sequencing (MPS) in diagnostic laboratories is greatly improving the possibilities of offering optimal care to patients. We present the results of a two-year period of molecular diagnosis that included 207 French families referred for non-syndromic hearing loss. Our multi-step strategy involved (i) DFNB1 locus analysis, (ii) MPS of 74 genes, and (iii) additional approaches including Copy Number Variations, in silico analyses, minigene studies coupled when appropriate with complete gene sequencing, and a specific assay for STRC. This comprehensive screening yielded an overall diagnostic rate of 48%, equally distributed between DFNB1 (24%) and the other genes (24%). Pathogenic genotypes were identified in 19 different genes, with a high prevalence of GJB2, STRC, MYO15A, OTOF, TMC1, MYO7A and USH2A. Involvement of an Usher gene was reported in 16% of the genotyped cohort. Four de novo variants were identified. This study highlights the need to develop several molecular approaches for efficient molecular diagnosis of hearing loss, as this is crucial for genetic counselling, audiological rehabilitation and the detection of syndromic forms.
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Affiliation(s)
- D Baux
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Vaché
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Blanchet
- Service ORL, CHU Montpellier, Montpellier, France.,Centre National de Référence Maladies Rares "Affections Sensorielles Génétiques", CHU Montpellier, Montpellier, France
| | - M Willems
- Génétique Médicale, CHU Montpellier, Montpellier, France
| | - C Baudoin
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - M Moclyn
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - V Faugère
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - R Touraine
- Service de Génétique, CHU-Hôpital Nord, Saint-Etienne, France
| | - B Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - D Dupin-Deguine
- Service de Génétique Médicale, CHU Toulouse, Toulouse, France.,Service d'ORL, Otoneurologie et ORL pédiatrique CHU Toulouse, Toulouse, France
| | - M Nizon
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - M Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - S Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - C Calais
- Service d'ORL, CHU Nantes, Nantes, France
| | - G García-García
- Laboratoire de Génétique de Maladies Rares (LGMR) EA7402, Université de Montpellier, Montpellier, France
| | - Z Azher
- Laboratoire de Génétique de Maladies Rares (LGMR) EA7402, Université de Montpellier, Montpellier, France
| | - L Lambert
- Génétique Médicale, Centre de Compétence des Surdités Génétiques, site constitutif du Centre de Référence des Anomalies du Développement et Syndromes Malformatifs de l'Est, CHRU Nancy, Nancy, France
| | - Y Perdomo-Trujillo
- Service de Génétique Médicale, Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France
| | - F Giuliano
- Service de Génétique Médicale, CHU Nice, Nice, France
| | - M Claustres
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France.,Laboratoire de Génétique de Maladies Rares (LGMR) EA7402, Université de Montpellier, Montpellier, France
| | - M Koenig
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France.,Laboratoire de Génétique de Maladies Rares (LGMR) EA7402, Université de Montpellier, Montpellier, France
| | - M Mondain
- Service ORL, CHU Montpellier, Montpellier, France.,Centre National de Référence Maladies Rares "Affections Sensorielles Génétiques", CHU Montpellier, Montpellier, France
| | - A F Roux
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France. .,Laboratoire de Génétique de Maladies Rares (LGMR) EA7402, Université de Montpellier, Montpellier, France.
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19
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Takeda H, Minoda R, Miwa T, Yamada T, Ise M. Transplanting mouse induced pluripotent stem cells into mouse otocysts in vivo. Neurosci Lett 2017; 647:153-158. [PMID: 28359931 DOI: 10.1016/j.neulet.2017.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/28/2017] [Accepted: 03/10/2017] [Indexed: 12/23/2022]
Abstract
The otocyst is an attractive target for studying treatment strategies for genetic hearing loss and for understanding inner ear development. We have previously reported that trans-uterine supplemental gene therapy in vivo into the otocysts of mice, which had a loss of function mutation in a causative gene of deafness, was able to prevent putative hearing loss. We herein set out to clarify the feasibility of allogenic cell transplantation into the mouse otocysts in vivo. We transplanted naive mouse-derived induced pluripotent stem cells (miPSCs) into the otocysts of wild type mice or connexin (Cx) 30 deficient mice, at embryonic day 11.5 (E11.5). The transplanted m-iPSCs survived in the lumens of the inner ears at E13.5 and E15.5 in wild type mice. In the Cx30 deficient mouse, the transplanted cells survived similarly, with some of the transplanted cells migrating into the lining cells of the lumens of the inner ears at E13.5 and showing tumorigenic cell proliferation at E15.5. In addition, engrafted cells appear to be able to differentiate after the cell transplantation. Our results suggest that otocyst transplanted cells survived and differentiated. A Cx30 deficiency may facilitate cell migration. These findings may offer some hope for cell transplantation therapy for profound genetic hearing loss caused by a Cxs deficiency.
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Affiliation(s)
- Hiroki Takeda
- Department of Otolaryngology-Head and Neck Surgery, Kumamoto University, Graduate School of Medicine, 1-1-1 Honjo, Chuoku, Kumamoto City 860-0811, Japan
| | - Ryosei Minoda
- Department of Otolaryngology-Head and Neck Surgery, Kumamoto University, Graduate School of Medicine, 1-1-1 Honjo, Chuoku, Kumamoto City 860-0811, Japan.
| | - Toru Miwa
- Department of Otolaryngology-Head and Neck Surgery, Kumamoto University, Graduate School of Medicine, 1-1-1 Honjo, Chuoku, Kumamoto City 860-0811, Japan
| | - Takao Yamada
- Department of Otolaryngology-Head and Neck Surgery, Kumamoto University, Graduate School of Medicine, 1-1-1 Honjo, Chuoku, Kumamoto City 860-0811, Japan
| | - Momoko Ise
- Department of Otolaryngology-Head and Neck Surgery, Kumamoto University, Graduate School of Medicine, 1-1-1 Honjo, Chuoku, Kumamoto City 860-0811, Japan
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20
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Mehta D, Noon SE, Schwartz E, Wilkens A, Bedoukian EC, Scarano I, Crenshaw EB, Krantz ID. Outcomes of evaluation and testing of 660 individuals with hearing loss in a pediatric genetics of hearing loss clinic. Am J Med Genet A 2016; 170:2523-30. [PMID: 27480936 DOI: 10.1002/ajmg.a.37855] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/07/2016] [Indexed: 11/11/2022]
Abstract
Hearing loss is a relatively common condition in children, occurring in approximately 2 out of every 1,000 births with approximately 50% of reported diagnoses having a primary genetic etiology. Given the prevalence and genetic component of hearing loss, coupled with a trend toward early diagnosis with the institution of universal newborn hearing screening, The Genetics of Hearing Loss Clinic was established at The Children's Hospital of Philadelphia to manage the diagnosis, testing, and genetic counseling for individuals and families. This paper described a cohort of 660 individuals with a diagnosis of hearing loss evaluated between July 2008 and July 2015 in the Genetics of Hearing Loss Clinic. To elucidate the cause of hearing loss in this cohort for better management and prognostication, testing included single nucleotide polymorphism chromosomal microarray, hearing loss next generation sequencing panel, and additional clinical tests inclusive of thyroid and renal function studies, temporal bone magnetic resonance imaging, and electrocardiogram. Of those evaluated, most had bilateral sensorineural hearing loss, occurring in 489/660 (74%). Additionally, 612/660 (93%) of patients presented with a nonsyndromic form of hearing loss (no other observed clinical findings at the time of exam), of which pathogenic mutations in GJB2 were most prevalent. Of the individuals with syndromic manifestations (48/660), Usher and Waardenburg syndrome were most commonly observed. A family history of hearing loss (first degree relative) was present in 12.6% of families with available information. Through molecular analyses, clinical examination, and laboratory testing, a definitive etiologic diagnosis was established in 157/660 (23.8%) of individuals. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Devanshi Mehta
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah E Noon
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Emily Schwartz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alisha Wilkens
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Emma C Bedoukian
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Irene Scarano
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - E Bryan Crenshaw
- Center for Childhood Communication, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Otorhinolaryngology: Head and Neck Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. .,The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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Moteki H, Azaiez H, Sloan-Heggen CM, Booth K, Nishio SY, Wakui K, Yamaguchi T, Kolbe DL, Iwasa YI, Shearer AE, Fukushima Y, Smith RJH, Usami SI. Detection and Confirmation of Deafness-Causing Copy Number Variations in the STRC Gene by Massively Parallel Sequencing and Comparative Genomic Hybridization. Ann Otol Rhinol Laryngol 2016; 125:918-923. [PMID: 27469136 DOI: 10.1177/0003489416661345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Copy number variations (CNVs), a major cause of genetic hearing loss, most frequently involve the STRC gene, located on chr15q15.3 and causally related to autosomal recessive non-syndromic hearing loss (ARNSHL) at the DFNB16 locus. The interpretation of STRC sequence data can be challenging due to the existence of a virtually identical pseudogene, pSTRC, that promotes complex genomic rearrangements in this genomic region. Targeted genomic enrichment with massively parallel sequencing (TGE+MPS) has emerged as the preferred method by which to provide comprehensive genetic testing for hearing loss. We aimed to identify CNVs in the STRC region using established and validated bioinformatics methods. METHODS We used TGE+MPS to identify the genetic cause of hearing loss. The CNV results were confirmed with customized array comparative genomic hybridization (array CGH). RESULTS Three probands with progressive mild to moderate hearing loss were found among 40 subjects with ARNSHL to segregate homozygous STRC deletions and gene to pseudogene conversion. Array CGH showed that the deletions/conversions span multiple genes outside of the exons captured by TGE+MPS. CONCLUSION These data further validate the necessity to integrate the detection of both simple variant changes and complex genomic rearrangements in the clinical diagnosis of genetic hearing loss.
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Affiliation(s)
- Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Hela Azaiez
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Christina M Sloan-Heggen
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Kevin Booth
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Diana L Kolbe
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Yoh-Ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Eliot Shearer
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Yoshimitsu Fukushima
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Richard J H Smith
- Molecular Otolaryngology & Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Hospital and Clinics, Iowa, USA
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
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22
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Genetic Testing for Deaf and Hard of Hearing Individuals: Genetic Counseling. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet 2016; 135:441-450. [PMID: 26969326 PMCID: PMC4796320 DOI: 10.1007/s00439-016-1648-8] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/14/2016] [Indexed: 12/11/2022]
Abstract
Hearing loss is the most common sensory deficit in humans, affecting 1 in 500 newborns. Due to its genetic heterogeneity, comprehensive diagnostic testing has not previously been completed in a large multiethnic cohort. To determine the aggregate contribution inheritance makes to non-syndromic hearing loss, we performed comprehensive clinical genetic testing with targeted genomic enrichment and massively parallel sequencing on 1119 sequentially accrued patients. No patient was excluded based on phenotype, inheritance or previous testing. Testing resulted in identification of the underlying genetic cause for hearing loss in 440 patients (39 %). Pathogenic variants were found in 49 genes and included missense variants (49 %), large copy number changes (18 %), small insertions and deletions (18 %), nonsense variants (8 %), splice-site alterations (6 %), and promoter variants (<1 %). The diagnostic rate varied considerably based on phenotype and was highest for patients with a positive family history of hearing loss or when the loss was congenital and symmetric. The spectrum of implicated genes showed wide ethnic variability. These findings support the more efficient utilization of medical resources through the development of evidence-based algorithms for the diagnosis of hearing loss.
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24
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Rosenberg C, Freitas ÉL, Uehara DT, Auricchio MTBM, Costa SS, Oiticica J, Silva AG, Krepischi AC, Mingroni-Netto RC. Genomic copy number alterations in non-syndromic hearing loss. Clin Genet 2015; 89:473-477. [DOI: 10.1111/cge.12683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - É. L. Freitas
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - D. T. Uehara
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - M. T. B. M. Auricchio
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - S. S. Costa
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - J. Oiticica
- Department of Otorhinolaryngology, Medical School; University of São Paulo; São Paulo Brazil
| | - A. G. Silva
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - A. C. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - R. C. Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
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25
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Shearer AE, Smith RJH. Massively Parallel Sequencing for Genetic Diagnosis of Hearing Loss: The New Standard of Care. Otolaryngol Head Neck Surg 2015; 153:175-82. [PMID: 26084827 PMCID: PMC4743024 DOI: 10.1177/0194599815591156] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/22/2015] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To evaluate the use of new genetic sequencing techniques for comprehensive genetic testing for hearing loss. DATA SOURCES Articles were identified from PubMed and Google Scholar databases using pertinent search terms. REVIEW METHODS Literature search identified 30 studies as candidates that met search criteria. Three studies were excluded, and 8 studies were found to be case reports. Twenty studies were included for review analysis, including 7 studies that evaluated controls and 16 studies that evaluated patients with unknown causes of hearing loss; 3 studies evaluated both controls and patients. CONCLUSIONS In the 20 studies included in the review analysis, 426 control samples and 603 patients with unknown causes of hearing loss underwent comprehensive genetic diagnosis for hearing loss using massively parallel sequencing. Control analysis showed a sensitivity and specificity >99%, sufficient for clinical use of these tests. The overall diagnostic rate was 41% (range, 10%-83%) and varied based on several factors, including inheritance and prescreening prior to comprehensive testing. There were significant differences in platforms available with regard to the number and type of genes included and whether copy number variations were examined. Based on these results, comprehensive genetic testing should form the cornerstone of a tiered approach to clinical evaluation of patients with hearing loss along with history, physical examination, and audiometry and can determine further testing that may be required, if any. IMPLICATIONS FOR PRACTICE Comprehensive genetic testing has become the new standard of care for genetic testing for patients with sensorineural hearing loss.
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Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Richard J H Smith
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa, USA Department of Molecular Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa, USA
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26
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Potential treatments for genetic hearing loss in humans: current conundrums. Gene Ther 2015; 22:603-9. [PMID: 25781649 DOI: 10.1038/gt.2015.27] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/24/2015] [Accepted: 02/12/2015] [Indexed: 12/18/2022]
Abstract
Genetic defects are a major cause of hearing loss in newborns. Consequently, hearing loss has a profound negative impact on human daily living. Numerous causative genes for genetic hearing loss have been identified. However, presently, there are no truly curative treatments for this condition. There have been several recent reports on successful treatments in mice using embryonic gene therapy, neonatal gene therapy and neonatal antisense oligonucleotide therapy. Herein, we describe state-of-the-art research on genetic hearing loss treatment through gene therapy and discuss the obstacles to overcome in curative treatments of genetic hearing loss in humans.
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27
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Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology. J Mol Diagn 2014; 16:639-47. [PMID: 25157971 DOI: 10.1016/j.jmoldx.2014.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/21/2014] [Accepted: 06/18/2014] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized genetic testing by enabling simultaneous analysis of unprecedented numbers of genes. However, genes with high-sequence homology pose challenges to current NGS technologies. Because diagnostic sequencing is moving toward exome analysis, knowledge of these homologous genes is essential to avoid false positive and negative results. An example is the STRC gene, one of >70 genes known to contribute to the genetic basis of hearing loss. STRC is 99.6% identical to a pseudogene (pSTRC) and therefore inaccessible to standard NGS methodologies. The STRC locus is also known to be a common site for large deletions. Comprehensive diagnostic testing for inherited hearing loss therefore necessitates a combination of several approaches to avoid pseudogene interference. We have developed a clinical test that combines standard NGS and NGS-based copy number assessment supplemented with a long-range PCR-based Sanger or MiSeq assay to eliminate pseudogene contamination. By using this combination of assays we could identify biallelic STRC variants in 14% (95% CI, 8%-24%) of individuals with isolated nonsyndromic hearing loss who had previously tested negative on our 70-gene hearing loss panel, corresponding to a detection rate of 11.2% (95% CI, 6%-19%) for previously untested patients. This approach has broad applicability because medically significant genes for many disease areas include genes with high-sequence homology.
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28
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Shearer AE, Kolbe DL, Azaiez H, Sloan CM, Frees KL, Weaver AE, Clark ET, Nishimura CJ, Black-Ziegelbein EA, Smith RJH. Copy number variants are a common cause of non-syndromic hearing loss. Genome Med 2014; 6:37. [PMID: 24963352 PMCID: PMC4067994 DOI: 10.1186/gm554] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/14/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Copy number variants (CNVs) are a well-recognized cause of genetic disease; however, methods for their identification are often gene-specific, excluded as 'routine' in screens of genetically heterogeneous disorders, and not implemented in most next-generation sequencing pipelines. For this reason, the contribution of CNVs to non-syndromic hearing loss (NSHL) is most likely under-recognized. We aimed to incorporate a method for CNV identification as part of our standard analysis pipeline and to determine the contribution of CNVs to genetic hearing loss. METHODS We used targeted genomic enrichment and massively parallel sequencing to isolate and sequence all exons of all genes known to cause NSHL. We completed testing on 686 patients with hearing loss with no exclusions based on type of hearing loss or any other clinical features. For analysis we used an integrated method for detection of single nucleotide changes, indels and CNVs. CNVs were identified using a previously published method that utilizes median read-depth ratios and a sliding-window approach. RESULTS Of 686 patients tested, 15.2% (104) carried at least one CNV within a known deafness gene. Of the 38.9% (267) of individuals for whom we were able to determine a genetic cause of hearing loss, a CNV was implicated in 18.7% (50). We identified CNVs in 16 different genes including 7 genes for which no CNVs have been previously reported. CNVs of STRC were most common (73% of CNVs identified) followed by CNVs of OTOA (13% of CNVs identified). CONCLUSION CNVs are an important cause of NSHL and their detection must be included in comprehensive genetic testing for hearing loss.
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Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Diana L Kolbe
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA ; Iowa Institute of Human Genetics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
| | - Hela Azaiez
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Christina M Sloan
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Kathy L Frees
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Amy E Weaver
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Erika T Clark
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Carla J Nishimura
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA ; Iowa Institute of Human Genetics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
| | - E Ann Black-Ziegelbein
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA ; Iowa Institute of Human Genetics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
| | - Richard J H Smith
- Department of Otolaryngology - Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA ; Iowa Institute of Human Genetics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA ; Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa 52242, USA
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29
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Vona B, Hofrichter MAH, Neuner C, Schröder J, Gehrig A, Hennermann JB, Kraus F, Shehata-Dieler W, Klopocki E, Nanda I, Haaf T. DFNB16 is a frequent cause of congenital hearing impairment: implementation of STRC mutation analysis in routine diagnostics. Clin Genet 2014; 87:49-55. [PMID: 26011646 PMCID: PMC4302246 DOI: 10.1111/cge.12332] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/26/2013] [Accepted: 12/12/2013] [Indexed: 11/29/2022]
Abstract
Increasing attention has been directed toward assessing mutational fallout of stereocilin (STRC), the gene underlying DFNB16. A major challenge is due to a closely linked pseudogene with 99.6% coding sequence identity. In 94 GJB2/GJB6-mutation negative individuals with non-syndromic sensorineural hearing loss (NSHL), we identified two homozygous and six heterozygous deletions, encompassing the STRC region by microarray and/or quantitative polymerase chain reaction (qPCR) analysis. To detect smaller mutations, we developed a Sanger sequencing method for pseudogene exclusion. Three heterozygous deletion carriers exhibited hemizygous mutations predicted as negatively impacting the protein. In 30 NSHL individuals without deletion, we detected one with compound heterozygous and two with heterozygous pathogenic mutations. Of 36 total patients undergoing STRC sequencing, two showed the c.3893A>G variant in conjunction with a heterozygous deletion or mutation and three exhibited the variant in a heterozygous state. Although this variant affects a highly conserved amino acid and is predicted as deleterious, comparable minor allele frequencies (MAFs) (around 10%) in NSHL individuals and controls and homozygous variant carriers without NSHL argue against its pathogenicity. Collectively, six (6%) of 94 NSHL individuals were diagnosed with homozygous or compound heterozygous mutations causing DFNB16 and five (5%) as heterozygous mutation carriers. Besides GJB2/GJB6 (DFNB1), STRC is a major contributor to congenital hearing impairment.
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Affiliation(s)
- B Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - M A H Hofrichter
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - C Neuner
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - J Schröder
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - A Gehrig
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - J B Hennermann
- Department of Pediatric Endocrinology, Gastroenterology and Metabolic Diseases, Charité Universitätsmedizin, Berlin, Germany
| | - F Kraus
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital, Würzburg, Germany
| | - W Shehata-Dieler
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital, Würzburg, Germany
| | - E Klopocki
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - I Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - T Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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