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Yamamoto N, Balciuniene J, Hartman T, Diaz-Miranda MA, Bedoukian E, Devkota B, Lawrence A, Golenberg N, Patel M, Tare A, Chen R, Schindler E, Choi J, Kaur M, Charles S, Chen J, Fanning EA, Dechene E, Cao K, Jill MR, Rajagopalan R, Bayram Y, Dulik MC, Germiller J, Conlin LK, Krantz ID, Luo M. Comprehensive Gene Panel Testing for Hearing Loss in Children: Understanding Factors Influencing Diagnostic Yield. J Pediatr 2023; 262:113620. [PMID: 37473993 DOI: 10.1016/j.jpeds.2023.113620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/17/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
OBJECTIVE To evaluate factors influencing the diagnostic yield of comprehensive gene panel testing (CGPT) for hearing loss (HL) in children and to understand the characteristics of undiagnosed probands. STUDY DESIGN This was a retrospective cohort study of 474 probands with childhood-onset HL who underwent CGPT between 2016 and 2020 at a single center. Main outcomes and measures included the association between clinical variables and diagnostic yield and the genetic and clinical characteristics of undiagnosed probands. RESULTS The overall diagnostic yield was 44% (209/474) with causative variants involving 41 genes. While the diagnostic yield was high in the probands with congenital, bilateral, and severe HL, it was low in those with unilateral, noncongenital, or mild HL; cochlear nerve deficiency; preterm birth; neonatal intensive care unit admittance; certain ancestry; and developmental delay. Follow-up studies on 49 probands with initially inconclusive CGPT results changed the diagnostic status to likely positive or negative outcomes in 39 of them (80%). Reflex to exome sequencing on 128 undiagnosed probands by CGPT revealed diagnostic findings in 8 individuals, 5 of whom had developmental delays. The remaining 255 probands were undiagnosed, with 173 (173/255) having only a single variant in the gene(s) associated with autosomal recessive HL and 28% (48/173) having a matched phenotype. CONCLUSION CGPT efficiently identifies the genetic etiologies of HL in children. CGPT-undiagnosed probands may benefit from follow-up studies or expanded testing.
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Affiliation(s)
- Nobuko Yamamoto
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA; Division of Otolaryngology, Department of Surgical Specialties, National Center for Children's Health and Development, Tokyo, Japan; Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; PerkinElmer Genomics, Pittsburgh, PA
| | - Tiffiney Hartman
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maria Alejandra Diaz-Miranda
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Emma Bedoukian
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Batsal Devkota
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Audrey Lawrence
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Netta Golenberg
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maha Patel
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Archana Tare
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Robert Chen
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emma Schindler
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jiwon Choi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maninder Kaur
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah Charles
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jiani Chen
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth A Fanning
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Dechene
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Murrell R Jill
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yavuz Bayram
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - John Germiller
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Otorhinolaryngology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Ian D Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
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Domínguez-Ruiz M, Ruiz-Palmero L, Buonfiglio PI, García-Vaquero I, Gómez-Rosas E, Goñi M, Villamar M, Morín M, Moreno-Pelayo MA, Elgoyhen AB, del Castillo FJ, Dalamón V, del Castillo I. Novel Pathogenic Variants in the Gene Encoding Stereocilin ( STRC) Causing Non-Syndromic Moderate Hearing Loss in Spanish and Argentinean Subjects. Biomedicines 2023; 11:2943. [PMID: 38001944 PMCID: PMC10668944 DOI: 10.3390/biomedicines11112943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Non-syndromic hearing impairment (NSHI) is a very heterogeneous genetic condition, involving over 130 genes. Mutations in GJB2, encoding connexin-26, are a major cause of NSHI (the DFNB1 type), but few other genes have significant epidemiological contributions. Mutations in the STRC gene result in the DFNB16 type of autosomal recessive NSHI, a common cause of moderate hearing loss. STRC is located in a tandem duplicated region that includes the STRCP1 pseudogene, and so it is prone to rearrangements causing structural variations. Firstly, we screened a cohort of 122 Spanish familial cases of non-DFNB1 NSHI with at least two affected siblings and unaffected parents, and with different degrees of hearing loss (mild to profound). Secondly, we screened a cohort of 64 Spanish sporadic non-DFNB1 cases, and a cohort of 35 Argentinean non-DFNB1 cases, all of them with moderate hearing loss. Amplification of marker D15S784, massively parallel DNA sequencing, multiplex ligation-dependent probe amplification and long-range gene-specific PCR followed by Sanger sequencing were used to search and confirm single-nucleotide variants (SNVs) and deletions involving STRC. Causative variants were found in 13 Spanish familial cases (10.7%), 5 Spanish simplex cases (7.8%) and 2 Argentinean cases (5.7%). In all, 34 deleted alleles and 6 SNVs, 5 of which are novel. All affected subjects had moderate hearing impairment. Our results further support this strong genotype-phenotype correlation and highlight the significant contribution of STRC mutations to moderate NSHI in the Spanish population.
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Affiliation(s)
- María Domínguez-Ruiz
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Laura Ruiz-Palmero
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Paula I. Buonfiglio
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
| | - Irene García-Vaquero
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Elena Gómez-Rosas
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Marina Goñi
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Miguel A. Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Ana B. Elgoyhen
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1121ABG, Argentina
| | - Francisco J. del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Viviana Dalamón
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
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Peixoto de Barcelos I, Li D, Watson D, M. McCormick E, Elden L, Aleman TS, O’Neil EC, J. Falk M, Hakonarson H. Multiple Independent Gene Disorders Causing Bardet-Biedl Syndrome, Congenital Hypothyroidism, and Hearing Loss in a Single Indian Patient. Brain Sci 2023; 13:1210. [PMID: 37626566 PMCID: PMC10452740 DOI: 10.3390/brainsci13081210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
We report a 20-year-old, female, adopted Indian patient with over 662 Mb regions of homozy-gosity who presented with intellectual disability, ataxia, schizophrenia, retinal dystrophy, moder-ate-to-severe progressive sensorineural hearing loss (SNHL), congenital hypothyroidism, cleft mi-tral valve with mild mitral valve regurgitation, and dysmorphic features. Exome analysis first on a clinical basis and subsequently on research reanalysis uncovered pathogenic variants in three nu-clear genes following two modes of inheritance that were causal to her complex phenotype. These included (1) compound heterozygous variants in BBS6 potentially causative for Bardet-Biedl syn-drome 6; (2) a homozygous, known pathogenic variant in the stereocilin (STRC) gene associated with nonsyndromic deafness; and (3) a homozygous variant in dual oxidase 2 (DUOX2) gene asso-ciated with congenital hypothyroidism. A variant of uncertain significance was identified in a fourth gene, troponin T2 (TNNT2), associated with cardiomyopathy but not the cleft mitral valve, with mild mitral regurgitation seen in this case. This patient was the product of an apparent first-degree relationship, explaining the multiple independent inherited findings. This case high-lights the need to carefully evaluate multiple independent genetic etiologies for complex pheno-types, particularly in the case of consanguinity, rather than presuming unexplained features are expansions of known gene disorders.
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Affiliation(s)
- Isabella Peixoto de Barcelos
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (I.P.d.B.); (D.L.)
| | - Dong Li
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (I.P.d.B.); (D.L.)
| | - Deborah Watson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (I.P.d.B.); (D.L.)
| | - Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (E.M.M.); (M.J.F.)
| | - Lisa Elden
- Division of Otolaryngology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Thomas S. Aleman
- Division of Ophthalmology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (T.S.A.); (E.C.O.)
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin C. O’Neil
- Division of Ophthalmology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (T.S.A.); (E.C.O.)
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Scheie Eye Institute at the Perelman Center for Advanced Medicine, Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (E.M.M.); (M.J.F.)
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (I.P.d.B.); (D.L.)
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Xiang J, Peng J, Sun X, Lin Z, Li D, Ye H, Wang S, Bai Y, Wang X, Du P, Gao Y, Sun J, Pan S, Peng Z. The Next Generation of Population-Based DFNB16 Carrier Screening and Diagnosis: STRC Copy-Number Variant Analysis from Genome Sequencing Data. Clin Chem 2023:7174048. [PMID: 37207672 DOI: 10.1093/clinchem/hvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing. METHODS We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number. RESULTS The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%-100%) and specificity (98.8%; 95% CI, 97.7%-99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%-2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number. CONCLUSIONS We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.
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Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Zibin Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haodong Ye
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Sibao Wang
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266034, China
| | - Yushi Bai
- Guangdong Zhongyi Forensic Science Center, Shenzhen 518000, China
| | | | - Peina Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Silin Pan
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266034, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Corriols-Noval P, López Simón EC, Cadiñanos J, Diñeiro M, Capín R, González Aguado R, Costales Marcos M, Morales Angulo C, Cabanillas Farpón R. Clinical Impact of Genetic Diagnosis of Sensorineural Hearing Loss in Adults. Otol Neurotol 2022; 43:1125-1136. [PMID: 36190904 DOI: 10.1097/mao.0000000000003706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS Adult genetic sensorineural hearing loss (SNHL) may be underestimated. BACKGROUND The diagnosis of genetic hearing loss is challenging, given its extreme genetic and phenotypic heterogeneity, particularly in adulthood. This study evaluated the utility of next-generation sequencing (NGS) in the etiological diagnosis of adult-onset SNHL. MATERIALS AND METHODS Adults (>16 yr old) with SNHL were recruited at the Otolaryngology Department at Marqués de Valdecilla University Hospital (Spain). Environmental factors, acoustic trauma, endolymphatic hydrops, and age-related hearing loss were excluding criteria. An NGS gene panel was used, including 196 genes (OTOgenics v3) or 229 genes (OTOgenics v4) related to syndromic and nonsyndromic hearing loss. RESULTS Sixty-five patients were included in the study (average age at the onset of SNHL, 41 yr). Fifteen pathogenic/likely pathogenic variants considered to be causative were found in 15 patients (23% diagnostic yield) in TECTA (4), KCNQ4 (3), GJB2 (2), ACTG1 (1), COL2A1 (1), COCH (1), COCH/COL2A1 (1), STRC (1), and ABHD12 (1). Three patients had syndromic associations (20% of patients with genetic diagnosis) that had not been previously diagnosed (two Stickler type I and one polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, cataract syndrome). Seven variants of unknown significance were found in COL11A1 (1), GSMDE (2), DNTM1 (1), SOX10 (1), EYA4 (1), and TECTA (1). CONCLUSION NGS gene panels can provide diagnostic yields greater than 20% for adult SNHL, with a significant proportion of variant of unknown significance that could potentially contribute to increasing diagnostic output. Identifying a genetic cause enables genetic counseling, provides prognostic information and can reveal unrecognized syndromes contributing to an accurate management of their associated manifestations.
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Affiliation(s)
- Patricia Corriols-Noval
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - Eugenia Carmela López Simón
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - Juan Cadiñanos
- Institute of Oncological and Molecular Medicine of Asturias
| | - Marta Diñeiro
- Institute of Oncological and Molecular Medicine of Asturias
| | - Raquel Capín
- Institute of Oncological and Molecular Medicine of Asturias
| | - Rocío González Aguado
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - María Costales Marcos
- Department of Otolaryngology-Head and Neck Surgery, Central University Hospital of Asturias, Asturias, Spain
| | - Carmelo Morales Angulo
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
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Prodanov T, Bansal V. Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing. Nat Commun 2022; 13:3221. [PMID: 35680869 PMCID: PMC9184528 DOI: 10.1038/s41467-022-30930-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
The human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than 150 duplicated genes that overlap LCRs have been implicated in monogenic and complex human diseases. We describe a computational tool, Parascopy, for estimating the aggregate and paralog-specific copy number of duplicated genes using whole-genome sequencing (WGS). Parascopy is an efficient method that jointly analyzes reads mapped to different repeat copies without the need for global realignment. It leverages multiple samples to mitigate sequencing bias and to identify reliable paralogous sequence variants (PSVs) that differentiate repeat copies. Analysis of WGS data for 2504 individuals from diverse populations showed that Parascopy is robust to sequencing bias, has higher accuracy compared to existing methods and enables prioritization of pathogenic copy number changes in duplicated genes.
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Affiliation(s)
- Timofey Prodanov
- Bioinformatics and Systems Biology Graduate Program, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Vikas Bansal
- Department of Pediatrics, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.
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7
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Mutai H, Momozawa Y, Kamatani Y, Nakano A, Sakamoto H, Takiguchi T, Nara K, Kubo M, Matsunaga T. Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes. Orphanet J Rare Dis 2022; 17:114. [PMID: 35248088 PMCID: PMC8898489 DOI: 10.1186/s13023-022-02262-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied.
Results Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Conclusions Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02262-4.
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8
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Corominas J, Smeekens SP, Nelen MR, Yntema HG, Kamsteeg EJ, Pfundt R, Gilissen C. Clinical exome sequencing - mistakes and caveats. Hum Mutat 2022; 43:1041-1055. [PMID: 35191116 PMCID: PMC9541396 DOI: 10.1002/humu.24360] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.
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Affiliation(s)
- Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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9
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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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10
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Han S, Zhang D, Guo Y, Fu Z, Guan G. Prevalence and Characteristics of STRC Gene Mutations (DFNB16): A Systematic Review and Meta-Analysis. Front Genet 2021; 12:707845. [PMID: 34621290 PMCID: PMC8491653 DOI: 10.3389/fgene.2021.707845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the STRC (MIM 606440) gene, inducing DFNB16, are considered a major cause of mild–moderate autosomal recessive non-syndromic hearing loss (ARNSHL). We conducted a systematic review and meta-analysis to determine the global prevalence and characteristics of STRC variations, important information required for genetic counseling. Methods: PubMed, Google Scholar, Medline, Embase, and Web of Science were searched for relevant articles published before January 2021. Results: The pooled prevalence of DFNB16 in GJB2-negative patients with hearing loss was 4.08% (95% CI: 0.0289–0.0573), and the proportion of STRC variants in the mild–moderate hearing loss group was 14.36%. Monoallelic mutations of STRC were 4.84% (95% CI: 0.0343–0.0680) in patients with deafness (non-GJB2) and 1.36% (95% CI: 0.0025–0.0696) in people with normal hearing. The DFNB16 prevalence in genetically confirmed patients (non-GJB2) was 11.10% (95% CI: 0.0716–0.1682). Overall pooled prevalence of deafness–infertility syndrome (DIS) was 36.75% (95% CI: 0.2122–0.5563) in DFNB16. The prevalence of biallelic deletions in STRC gene mutations was 70.85% (95% CI: 0.5824–0.8213). Conclusion: Variants in the STRC gene significantly contribute to mild–moderate hearing impairment. Moreover, biallelic deletions are a main feature of STRC mutations. Copy number variations associated with infertility should be seriously considered when investigating DFNB16.
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Affiliation(s)
- Shuang Han
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yingyuan Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zeming Fu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guofang Guan
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
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11
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CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations. Genes (Basel) 2021; 12:genes12091427. [PMID: 34573409 PMCID: PMC8472439 DOI: 10.3390/genes12091427] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.
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12
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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13
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Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
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Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
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14
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New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells. J Neurosci 2021; 41:4378-4391. [PMID: 33824189 PMCID: PMC8152607 DOI: 10.1523/jneurosci.2537-20.2021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/19/2021] [Accepted: 03/27/2021] [Indexed: 12/05/2022] Open
Abstract
Transmembrane channel-like protein isoform 1 (TMC1) is a major component of the mechano-electrical transducer (MET) channel in cochlear hair cells and is subject to numerous mutations causing deafness. We report a new dominant human deafness mutation, TMC1 p.T422K, and have characterized the homologous mouse mutant, Tmc1 p.T416K, which caused deafness and outer hair cell (OHC) loss by the fourth postnatal week. MET channels showed decreased Ca2+ permeability and resting open probability, but no change in single-channel conductance or expression. Three adjacent deafness mutations are TMC1 p.L416R, p.G417R, and p.M418K, the last homologous to the mouse Beethoven that exhibits similar channel effects. All substitute a positive for a neutral residue, which could produce charge screening in the channel pore or influence binding of an accessory subunit. Channel properties were compared in mice of both sexes between dominant (Tmc1 p.T416K, Tmc1 p.D569N) and recessive (Tmc1 p.W554L, Tmc1 p.D528N) mutations of residues near the putative pore of the channel. Tmc1 p.W554L and p.D569N exhibit reduced maximum current with no effect on single-channel conductance, implying a smaller number of channels transported to the stereociliary tips; this may stem from impaired TMC1 binding to LHFPL5. Tmc1 p.D528N, located in the pore's narrowest region, uniquely caused large reductions in MET channel conductance and block by dihydrostreptomycin (DHS). For Tmc1 p.T416K and Tmc1 p.D528N, transduction loss occurred between P15 and P20. We propose two mechanisms linking channel mutations and deafness: decreased Ca2+ permeability, common to all mutants, and decreased resting open probability in low Ca2+, confined to dominant mutations. SIGNIFICANCE STATEMENT Transmembrane channel-like protein isoform 1 (TMC1) is thought to be a major component of the mechanotransducer channel in auditory hair cells, but the protein organization and channel structure are still uncertain. We made four mouse lines harboring Tmc1 point mutations that alter channel properties, causing hair cell degeneration and deafness. These include a mouse homolog of a new human deafness mutation pT416K that decreased channel Ca2+ permeability by introducing a positively-charged amino acid in the putative pore. All mutations are consistent with the channel structure predicted from modeling, but only one, p.D528N near the external face of the pore, substantially reduced channel conductance and Ca2+ permeability and virtually abolished block by dihydrostreptomycin (DHS), strongly endorsing its siting within the pore.
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15
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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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16
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Chiereghin C, Robusto M, Mauri L, Primignani P, Castorina P, Ambrosetti U, Duga S, Asselta R, Soldà G. SLC22A4 Gene in Hereditary Non-syndromic Hearing Loss: Recurrence and Incomplete Penetrance of the p.C113Y Mutation in Northwest Africa. Front Genet 2021; 12:606630. [PMID: 33643381 PMCID: PMC7902881 DOI: 10.3389/fgene.2021.606630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Inherited hearing loss is extremely heterogeneous both clinically and genetically. In addition, the spectrum of deafness-causing genetic variants differs greatly among geographical areas and ethnicities. The identification of the causal mutation in affected families allows early diagnosis, clinical follow-up, and genetic counseling. A large consanguineous family of Moroccan origin affected by autosomal recessive sensorineural hearing loss (ARSNHL) was subjected to genome-wide linkage analysis and exome sequencing. Exome-wide variant analysis and prioritization identified the SLC22A4 p.C113Y missense variant (rs768484124) as the most likely cause of ARSNHL in the family, falling within the unique significant (LOD score>3) linkage region on chromosome 5. Indeed, the same variant was previously reported in two Tunisian ARSNHL pedigrees. The variant is present in the homozygous state in all six affected individuals, but also in one normal-hearing sibling, suggesting incomplete penetrance. The mutation is absent in about 1,000 individuals from the Greater Middle East Variome study cohort, including individuals from the North African population, as well as in an additional seven deaf patients from the same geographical area, recruited and screened for mutations in the SLC22A4 gene. This study represents the first independent replication of the involvement of SLC22A4 in ARSNHL, highlighting the importance of the gene, and of the p.C113Y mutation, at least in the Northwest African population.
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Affiliation(s)
| | - Michela Robusto
- Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Lucia Mauri
- S. S. Genetica Medica, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Paola Primignani
- S. S. Genetica Medica, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Pierangela Castorina
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, UO Audiologia, Milan, Italy
| | - Umberto Ambrosetti
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, UO Audiologia, Milan, Italy
| | - Stefano Duga
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Rosanna Asselta
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Giulia Soldà
- Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
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17
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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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18
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Update on next generation sequencing of pharmacokinetics-related genes: Development of the PKseq panel, a platform for amplicon sequencing of drug-metabolizing enzyme and drug transporter genes. Drug Metab Pharmacokinet 2020; 37:100370. [PMID: 33508759 DOI: 10.1016/j.dmpk.2020.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/01/2020] [Accepted: 11/18/2020] [Indexed: 02/08/2023]
Abstract
Genetic variation in pharmacokinetics (PK)-related genes encoding drug metabolizing enzymes or drug transporters is one of the most practical pharmacogenetic biomarkers for the prediction or explanation of an individual's response to drugs. Many pharmacogenomic variations are identified using targeted, whole-exome, and whole-genome sequencing, and the number of known novel variations and alleles in PK-related genes is increasing. The high homology of sequences among PK-related genes is suspected to lead to potential read misalignment and genotyping errors when short-read sequencing was performed. Therefore, highly efficient and accurate next generation sequencing (NGS) platforms for the sequencing of PK-related genes are needed. We have developed PKseq, a targeted sequencing panel based on multiplex PCR, which targets the coding regions of 37 drug transporters, 30 cytochrome P450 isoforms, 10 UDP-glucuronosyltransferases, 5 flavin-containing monooxygenases, 4 glutathione S-transferases, 4 sulfotransferases, and 10 other genes. In this review, we describe the current NGS platforms for the sequencing of PK-related genes. The NGS platforms, including the PKseq panel, will be useful not only for the identification of all the variants of PK-related genes associated with adverse drug reactions and drug efficacy, but also for clinical sequencing to achieve pharmacogenomics-based stratified medicine.
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19
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Prodanov T, Bansal V. Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications. Nucleic Acids Res 2020; 48:e114. [PMID: 33035301 PMCID: PMC7641771 DOI: 10.1093/nar/gkaa829] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/31/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)—sequence differences between paralogous sequences—to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3–90.6%) and BLASR (82.9–90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. Using DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable, variant calling achieved a higher F1 score and 14 713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlaps with variants and adversely impacts short-read variant calling.
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Affiliation(s)
- Timofey Prodanov
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vikas Bansal
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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20
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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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Markova TG, Alekseeva NN, Mironovich OL, Bliznets EA, Lalayants MR, Polyakov AV, Tavartkiladze GA. [Hearing loss due to mutations or lack of the gene coding protein stereocillin]. Vestn Otorinolaringol 2020; 85:14-20. [PMID: 32476383 DOI: 10.17116/otorino20208502114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The description of a clinical picture and audiological features at the hearing loss caused by changes of a STRC gene, coding protein stereocillin (MIM: 606440). Mutations in the numerous genes responsible for the inner ear proteins are the reason for congenital sensorineural hearing loss. The main cause of congenital bilateral sensorineural hearing loss in the Russian Federation are mutations in GJB2 gene it reaches up 68% of cases identified in infancy. GJB2 gene tests already became routine around the world. Possibilities of new methods based on sequencing of new generation (NGS, next generation sequencing) allow to conduct a research of more rare genes connected with a hearing impairment. The most often among GJB2 negative patients reveal mutations and deletion of a gene of STRC. PATIENTS AND METHODS Full audiological examination of 5 children and one adult with a hearing loss from 2 unrelated families is provided. Mutations in STRC gene were identified. All children are examined aged before 8 years, and 3 children failed universal audiological screening in maternity hospital, to two children screening was not carried out as they were born till 2009. RESULTS The children with the sensorineural hearing loss connected with mutations and deletion of STRC gene failed hearing screening in maternity hospital because of the OAE is not registered, what indicates the congenital nature of a hearing loss. Recently it could not be noticed earlier because of slight increase of hearing thresholds and was regarded only as the early onset. Our data emphasize that the of thresholds from 35 to 60 dB in frequencies 0,5-4 kHz is common for mutations/deletions of STRC gene. CONCLUSION The development of molecular genetics methods confirms the hereditary causes of GJB2-negative patients and expands indications for family counseling. Special approach for child with hearing loss so early revealed is necessary and the consultation of parents frightened of screening results is very important.
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Affiliation(s)
- T G Markova
- National Resarch Center for Audiology and Hearing Rehabilitation, Moscow, Russia.,Russian Medical Academy of Postdoctoral Education of the Ministry of Health of Russia, Moscow, Russia
| | - N N Alekseeva
- National Resarch Center for Audiology and Hearing Rehabilitation, Moscow, Russia.,Russian Medical Academy of Postdoctoral Education of the Ministry of Health of Russia, Moscow, Russia
| | - O L Mironovich
- Academician N.P. Bochkov Medical and Genetic Research Center, Moscow, Russia
| | - E A Bliznets
- Academician N.P. Bochkov Medical and Genetic Research Center, Moscow, Russia
| | - M R Lalayants
- National Resarch Center for Audiology and Hearing Rehabilitation, Moscow, Russia.,Russian Medical Academy of Postdoctoral Education of the Ministry of Health of Russia, Moscow, Russia
| | - A V Polyakov
- Academician N.P. Bochkov Medical and Genetic Research Center, Moscow, Russia
| | - G A Tavartkiladze
- National Resarch Center for Audiology and Hearing Rehabilitation, Moscow, Russia.,Russian Medical Academy of Postdoctoral Education of the Ministry of Health of Russia, Moscow, Russia
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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23
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Rajagopalan R, Murrell JR, Luo M, Conlin LK. A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data. Genome Med 2020; 12:14. [PMID: 32000839 PMCID: PMC6993336 DOI: 10.1186/s13073-020-0712-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Exome sequencing (ES) is a first-tier diagnostic test for many suspected Mendelian disorders. While it is routine to detect small sequence variants, it is not a standard practice in clinical settings to detect germline copy-number variants (CNVs) from ES data due to several reasons relating to performance. In this work, we comprehensively characterized one of the most sensitive ES-based CNV tools, ExomeDepth, against SNP array, a standard of care test in clinical settings to detect genome-wide CNVs. Methods We propose a modified ExomeDepth workflow by excluding exons with low mappability prior to variant calling to drastically reduce the false positives originating from the repetitive regions of the genome, and an iterative variant calling framework to assess the reproducibility. We used a cohort of 307 individuals with clinical ES data and clinical SNP array to estimate the sensitivity and false discovery rate of the CNV detection using exome sequencing. Further, we performed targeted testing of the STRC gene in 1972 individuals. To reduce the number of variants for downstream analysis, we performed a large-scale iterative variant calling process with random control cohorts to assess the reproducibility of the CNVs. Results The modified workflow presented in this paper reduced the number of total variants identified by one third while retaining a higher sensitivity of 97% and resulted in an improved false discovery rate of 11.4% compared to the default ExomeDepth pipeline. The exclusion of exons with low mappability removes 4.5% of the exons, including a subset of exons (0.6%) in disease-associated genes which are intractable by short-read next-generation sequencing (NGS). Results from the reproducibility analysis showed that the clinically reported variants were reproducible 100% of the time and that the modified workflow can be used to rank variants from high to low confidence. Targeted testing of 30 CNVs identified in STRC, a challenging gene to ascertain by NGS, showed a 100% validation rate. Conclusions In summary, we introduced a modification to the default ExomeDepth workflow to reduce the false positives originating from the repetitive regions of the genome, created a large-scale iterative variant calling framework for reproducibility, and provided recommendations for implementation in clinical settings.
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Affiliation(s)
- Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboaratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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24
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Contreras AL, Andal JJL, Lo RM, Ang DC. Pre-analytics, Current Testing Technologies, and Limitations of Testing. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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25
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Otogelin, otogelin-like, and stereocilin form links connecting outer hair cell stereocilia to each other and the tectorial membrane. Proc Natl Acad Sci U S A 2019; 116:25948-25957. [PMID: 31776257 DOI: 10.1073/pnas.1902781116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The function of outer hair cells (OHCs), the mechanical actuators of the cochlea, involves the anchoring of their tallest stereocilia in the tectorial membrane (TM), an acellular structure overlying the sensory epithelium. Otogelin and otogelin-like are TM proteins related to secreted epithelial mucins. Defects in either cause the DFNB18B and DFNB84B genetic forms of deafness, respectively, both characterized by congenital mild-to-moderate hearing impairment. We show here that mutant mice lacking otogelin or otogelin-like have a marked OHC dysfunction, with almost no acoustic distortion products despite the persistence of some mechanoelectrical transduction. In both mutants, these cells lack the horizontal top connectors, which are fibrous links joining adjacent stereocilia, and the TM-attachment crowns coupling the tallest stereocilia to the TM. These defects are consistent with the previously unrecognized presence of otogelin and otogelin-like in the OHC hair bundle. The defective hair bundle cohesiveness and the absence of stereociliary imprints in the TM observed in these mice have also been observed in mutant mice lacking stereocilin, a model of the DFNB16 genetic form of deafness, also characterized by congenital mild-to-moderate hearing impairment. We show that the localizations of stereocilin, otogelin, and otogelin-like in the hair bundle are interdependent, indicating that these proteins interact to form the horizontal top connectors and the TM-attachment crowns. We therefore suggest that these 2 OHC-specific structures have shared mechanical properties mediating reaction forces to sound-induced shearing motion and contributing to the coordinated displacement of stereocilia.
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Abou Tayoun A, Mason-Suares H. Considerations for whole exome sequencing unique to prenatal care. Hum Genet 2019; 139:1149-1159. [PMID: 31701237 DOI: 10.1007/s00439-019-02085-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Whole exome sequencing (WES) is increasingly being used in the prenatal setting. The emerging data support the clinical utility of prenatal WES based on its diagnostic yield, which can be as high as 80% for certain ultrasound findings. However, detailed practice and laboratory guidelines, addressing the indications for prenatal WES and the surrounding technical, interpretation, ethical, and counseling issues, are still lacking. Herein, we review the literature and summarize the most recent findings and applications of prenatal WES. This review offers specialists and clinical genetic laboratorians a body of evidence and expert opinions that can serve as a resource to assist in their practice. Finally, we highlight the emerging technologies that promise a future of prenatal WES without the risks associated with invasive testing.
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Affiliation(s)
| | - Heather Mason-Suares
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Street, Cambridge, MA, 02115, USA.
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27
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O'Leary TJ. The Journal of Molecular Diagnostics: 20 Years of Clinical Innovation. J Mol Diagn 2019; 21:935-937. [PMID: 31635796 DOI: 10.1016/j.jmoldx.2019.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 02/03/2023] Open
Abstract
This guest editorial highlights 20 years of clinical innovation in JMD.
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Affiliation(s)
- Timothy J O'Leary
- Office of Research and Development, Veterans Health Administration, Washington District of Columbia; Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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28
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Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss. Genes (Basel) 2019; 10:genes10090715. [PMID: 31527525 PMCID: PMC6770988 DOI: 10.3390/genes10090715] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/03/2022] Open
Abstract
The OTOA gene (Locus: DFNB22) is reported to be one of the causative genes for non-syndromic autosomal recessive hearing loss. The copy number variations (CNVs) identified in this gene are also known to cause hearing loss, but have not been identified in Japanese patients with hearing loss. Furthermore, the clinical features of OTOA-associated hearing loss have not yet been clarified. In this study, we performed CNV analyses of a large Japanese hearing loss cohort, and identified CNVs in 234 of 2262 (10.3%, 234/2262) patients with autosomal recessive hearing loss. Among the identified CNVs, OTOA gene-related CNVs were the second most frequent (0.6%, 14/2262). Among the 14 cases, 2 individuals carried OTOA homozygous deletions, 4 carried heterozygous deletions with single nucleotide variants (SNVs) in another allele. Additionally, 1 individual with homozygous SNVs in the OTOA gene was also identified. Finally, we identified 7 probands with OTOA-associated hearing loss, so that its prevalence in Japanese patients with autosomal recessive hearing loss was calculated to be 0.3% (7/2262). As novel clinical features identified in this study, the audiometric configurations of patients with OTOA-associated hearing loss were found to be mid-frequency. This is the first study focused on the detailed clinical features of hearing loss caused by this gene mutation and/or gene deletion.
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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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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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31
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Wu X, Gao X, Han P, Zhou Y. Identification of causative variants in patients with non-syndromic hearing loss in the Minnan region, China by targeted next-generation sequencing. Acta Otolaryngol 2019; 139:243-250. [PMID: 30762455 DOI: 10.1080/00016489.2018.1552015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND Due to extreme genetic heterogeneity, targeted next-generation sequencing (NGS) can be an efficient tool for rapid genetic diagnosis of hereditary non-syndromic hearing loss (NSHL). AIMS/OBJECTIVES This study was aiming to identify causative variants in NSHL patients from the Minnan region through targeted NGS. MATERIAL AND METHODS Genomic DNA samples from 90 NSHL subjects were extracted and subjected to SureSelect target enrichment system to capture the entire coding exons and flanking intronic regions of gene GJB2, SLC26A4, and MT-RNR1. The captured DNA was then sequenced by Illumina HiSeq2500. The sequence data was processed and quality-checked using Burrows-Wheeler Alignment, Picard, and GATK, and annotated by SnpEff, SIFT, and GERP++. RESULTS Twenty-six candidate variants in GJB2, SLC26A4, and MT-RNR1 were detected in 57 of 90 NSHL patients. GJB2 c.109G > A was the most frequent variant, followed by GJB2 c.608T > C and c.235delC. Genetic diagnosis was available for 22 NSHL patients, including 19 patients associated with autosomal recessive NSHL, one patients with autosomal dominant NSHL, and two individuals with mitochondrial disorders. CONCLUSIONS AND SIGNIFICANCE Our targeted NGS analysis added supports for the application of NGS in routine diagnosis and provided an overview of genetic variants with allele frequencies in the deaf population from the Minnan region.
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Affiliation(s)
- Xiaohui Wu
- Xiamen Neonatal Hearing Screening and Diagnostic Center, Xiamen Maternity and Child Health Care Hospital, Siming District, Xiamen, China
- Department of Otolaryngology-Head and Neck Surgery, Children’s Hospital of Fudan University; Xiamen Branch; Xiamen Children’s Hospital, Huli District, Xiamen, China
| | - Xingqiang Gao
- Department of Otolaryngology-Head and Neck Surgery, Children’s Hospital of Fudan University; Xiamen Branch; Xiamen Children’s Hospital, Huli District, Xiamen, China
| | - Peng Han
- BGI, BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Yulin Zhou
- Xiamen Neonatal Disease Screening Center, Xiamen Maternity and Child Health Care Hospital, Xiamen, China
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Abstract
HYPOTHESIS We hypothesized that patients with DFNB16 caused hearing loss show characteristical audiological findings depending on genetic results. BACKGROUND Hearing loss belongs to the most frequent congenital diseases. In 50-70% of individuals, hearing loss is caused by genetic defects. DFNB1 (deafness, neurosensory, autosomal-recessive) is the most frequently affected locus. Despite its great genetic heterogeneity, comprehensive analysis of genes like STRC, encoding stereocilin (DFNB16) is possible. The genetic architecture of the DFNB16 locus is challenging and requires a unique molecular genetic testing assay. The aim of the study is a systematic characterization of the audiological phenotype in DFNB16-positive patients. METHODS Since 2011, 290 patients with suspicion of inherited hearing loss received a human genetic exploration. Eighty two DFNB1-negative patients advanced to further testing in the DFNB16 locus. STRC-positive patients obtained complete audiological diagnostic workup. Additionally, epidemiological data was collected. RESULTS Nine of 82 (11%) of the examined patients (mean age 5 yr) showed mutations in the STRC (3 homozygous, 6 compound heterozygous). Aside from a moderate hearing loss in the pure tone audiogram, auditory brainstem response thresholds were 40-50 dB nHL. Otoacoustic emissions were detectable in only one patient. CONCLUSIONS Examination of the DFNB16-locus should be a standard diagnostic test after negative DFNB1-gene screening result. Notably, DFNB16-associated hearing loss can be audiologically characterized as moderate sensorineural hearing loss in the main speech field with absent otoacoustic emissions. Our study is the first to correlate audiological findings with genetic results in patients with hearing loss due to STRC.
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Analysis of intragenic USH2A copy number variation unveils broad spectrum of unique and recurrent variants. Eur J Med Genet 2018; 61:621-626. [DOI: 10.1016/j.ejmg.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
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Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype. Eur J Hum Genet 2018; 26:1871-1874. [PMID: 30250054 DOI: 10.1038/s41431-018-0256-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/07/2018] [Accepted: 08/19/2018] [Indexed: 11/08/2022] Open
Abstract
Vestibular disorders comprise a heterogeneous group of diseases with transient or permanent loss of vestibular function. Vestibulopathy is in most cases associated with migraine, Ménière disease, hereditary ataxias, or sensorineural hearing loss. We identified two brothers and their first cousin affected by hearing loss and episodic vertigo. The brothers were homozygous STRC nonsense variant [c.4027 C > T, p.(Q1343*)], whereas their first cousin was compound heterozygous for the STRC nonsense variant and a 97 kb deletion spanning the entire STRC gene. Clinical investigations confirmed pathological vestibular responses in addition to a characteristic DFNB16 hearing loss. The STRC gene encodes Stereocilin in the cochlea and in the vestibular organ where it ensheathes the kinocilium of the otolithic membranes. Stereocilin is associated with the gel overlaying the vestibular kinocilia, suggesting a role for the protein in sensing balance and spatial orientation. Our findings support such a function for Stereocilin in the vestibular organ and expand the phenotype associated with DFNB16.
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Cabanillas R, Diñeiro M, Cifuentes GA, Castillo D, Pruneda PC, Álvarez R, Sánchez-Durán N, Capín R, Plasencia A, Viejo-Díaz M, García-González N, Hernando I, Llorente JL, Repáraz-Andrade A, Torreira-Banzas C, Rosell J, Govea N, Gómez-Martínez JR, Núñez-Batalla F, Garrote JA, Mazón-Gutiérrez Á, Costales M, Isidoro-García M, García-Berrocal B, Ordóñez GR, Cadiñanos J. Comprehensive genomic diagnosis of non-syndromic and syndromic hereditary hearing loss in Spanish patients. BMC Med Genomics 2018; 11:58. [PMID: 29986705 PMCID: PMC6038346 DOI: 10.1186/s12920-018-0375-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation. METHODS We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL. We evaluated the analytical sensitivity and specificity of the panel on 1624 known single nucleotide variants (SNVs) and indels on a mixture of genomic DNA from 10 previously characterized lymphoblastoid cell lines, and analyzed 50 Spanish patients with presumed hereditary SNHL not caused by GJB2/GJB6, OTOF nor MT-RNR1 mutations. RESULTS The analytical sensitivity of the test to detect SNVs and indels on the DNA mixture from the cell lines was > 99.5%, with a specificity > 99.9%. The diagnostic yield on the SNHL patients was 42% (21/50): 47.6% (10/21) with autosomal recessive inheritance pattern (BSND, CDH23, MYO15A, STRC [n = 2], USH2A [n = 3], RDX, SLC26A4); 38.1% (8/21) autosomal dominant (ACTG1 [n = 3; 2 de novo], CHD7, GATA3 [de novo], MITF, P2RX2, SOX10), and 14.3% (3/21) X-linked (COL4A5 [de novo], POU3F4, PRPS1). 46.9% of causative variants (15/32) were not in the databases. 28.6% of genetically diagnosed cases (6/21) had previously undetected syndromes (Barakat, Usher type 2A [n = 3] and Waardenburg [n = 2]). 19% of genetic diagnoses (4/21) were attributable to large deletions/duplications (STRC deletion [n = 2]; partial CDH23 duplication; RDX exon 2 deletion). CONCLUSIONS In the era of precision medicine, obtaining an etiologic diagnosis of SNHL is imperative. Here, we contribute to show that, with the right methodology, NGS can be transferred to the clinical practice, boosting the yield of SNHL genetic diagnosis to 50-60% (including GJB2/GJB6 alterations), improving diagnostic/prognostic accuracy, refining genetic and reproductive counseling and revealing clinically relevant undiagnosed syndromes.
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Affiliation(s)
- Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain.
| | - Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Guadalupe A Cifuentes
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L., Oviedo, Spain
| | | | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Noelia Sánchez-Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Ana Plasencia
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | - Inés Hernando
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | | | - Jordi Rosell
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Nancy Govea
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | | | | | | | | | - María Costales
- Hospital Universitario Central de Asturias, Oviedo, Spain.,Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | | | | | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain.
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Sheppard S, Biswas S, Li MH, Jayaraman V, Slack I, Romasko EJ, Sasson A, Brunton J, Rajagopalan R, Sarmady M, Abrudan JL, Jairam S, DeChene ET, Ying X, Choi J, Wilkens A, Raible SE, Scarano MI, Santani A, Pennington JW, Luo M, Conlin LK, Devkota B, Dulik MC, Spinner NB, Krantz ID. Utility and limitations of exome sequencing as a genetic diagnostic tool for children with hearing loss. Genet Med 2018; 20:1663-1676. [PMID: 29907799 PMCID: PMC6295269 DOI: 10.1038/s41436-018-0004-x] [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: 09/08/2017] [Accepted: 03/20/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Hearing loss (HL) is the most common sensory disorder in children. Prompt molecular diagnosis may guide screening and management, especially in syndromic cases when HL is the single presenting feature. Exome sequencing (ES) is an appealing diagnostic tool for HL as the genetic causes are highly heterogeneous. METHODS ES was performed on a prospective cohort of 43 probands with HL. Sequence data were analyzed for primary and secondary findings. Capture and coverage analysis was performed for genes and variants associated with HL. RESULTS The diagnostic rate using ES was 37.2%, compared with 15.8% for the clinical HL panel. Secondary findings were discovered in three patients. For 247 genes associated with HL, 94.7% of the exons were targeted for capture and 81.7% of these exons were covered at 20× or greater. Further analysis of 454 randomly selected HL-associated variants showed that 89% were targeted for capture and 75% were covered at a read depth of at least 20×. CONCLUSION ES has an improved yield compared with clinical testing and may capture diagnoses not initially considered due to subtle clinical phenotypes. Technical challenges were identified, including inadequate capture and coverage of HL genes. Additional considerations of ES include secondary findings, cost, and turnaround time.
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Affiliation(s)
- Sarah Sheppard
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sawona Biswas
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mindy H Li
- Division of Genetics, Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA
| | - Vijayakumar Jayaraman
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian Slack
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward J Romasko
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ariella Sasson
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua Brunton
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ramakrishnan Rajagopalan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mahdi Sarmady
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jenica L Abrudan
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sowmya Jairam
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth T DeChene
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiahoan Ying
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiwon Choi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alisha Wilkens
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Raible
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maria I Scarano
- Division of Genetics, Cooper University Health Care, Camden, NY, USA
| | - Avni Santani
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffrey W Pennington
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew C Dulik
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss. Genet Med 2018; 20:1600-1608. [PMID: 29595809 DOI: 10.1038/gim.2018.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/13/2018] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Hereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes. METHODS A tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes. RESULTS ES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis. CONCLUSION The tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.
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Amr SS, Murphy E, Duffy E, Niazi R, Balciuniene J, Luo M, Rehm HL, Abou Tayoun AN. Allele-Specific Droplet Digital PCR Combined with a Next-Generation Sequencing-Based Algorithm for Diagnostic Copy Number Analysis in Genes with High Homology: Proof of Concept Using Stereocilin. Clin Chem 2018; 64:705-714. [PMID: 29339441 DOI: 10.1373/clinchem.2017.280685] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/08/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing. We applied this approach to copy number analysis in STRC, a gene with 98.9% homology to a nonfunctional pseudogene, pSTRC, and characterized its accuracy in detecting different copy number states by use of known samples. RESULTS Using a cohort of 517 patients with hearing loss, we prospectively demonstrated the clinical utility of the approach, which contributed 30 of the 122 total positives (6%) to the diagnostic yield, increasing the overall yield from 17.6% to 23.6%. Positive STRC genotypes included homozygous (n = 15) or compound heterozygous (n = 8) deletions, or heterozygous deletions in trans with pathogenic sequence variants (n = 7). Finally, this approach limited ddPCR testing to cases with NGS copy number findings, thus markedly reducing the number of costly and laborious, albeit specific, ddPCR tests. CONCLUSIONS NGS-based CNV detection followed by allele-specific ddPCR confirmatory testing is a reliable and affordable approach for copy number analysis in medically relevant genes with homology issues.
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Affiliation(s)
- Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Elissa Murphy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA
| | - Elizabeth Duffy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA
| | - Rojeen Niazi
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minjie Luo
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA; .,The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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39
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Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins. Methods Mol Biol 2018; 1840:321-336. [PMID: 30141054 DOI: 10.1007/978-1-4939-8691-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Targeted panel, whole exome, or whole genome DNA sequencing using next-generation sequencing (NGS) allows for extensive high-throughput investigation of molecular machines/systems such as the LINC complex. This includes the identification of genetic variants in humans that cause disease, as is the case for some genes encoding LINC complex proteins. The relatively low cost and high speed of the sequencing process results in large datasets at various stages of analysis and interpretation. For those not intimately familiar with the process, interpretation of the data might prove challenging. This review lays out the most important and most commonly used materials and methods of NGS. It also discusses data analysis and potential pitfalls one might encounter because of peculiarities of the laboratory methodology or data analysis pipelines.
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40
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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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Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers. Genet Med 2017; 20:855-866. [PMID: 29144510 PMCID: PMC6456263 DOI: 10.1038/gim.2017.192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/21/2023] Open
Abstract
PURPOSE: As massively parallel sequencing is increasingly being used for
clinical decision-making, it has become critical to understand parameters
that affect sequencing quality and to establish methods for measuring and
reporting clinical sequencing standards. In this report, we propose a
definition for reduced coverage regions and have
established a set of standards for variant calling in clinical sequencing
applications. METHODS: To enable sequencing centers to assess the regions of poor sequencing
quality in their own data, we optimized and used a tool
(ExCid) to identify reduced coverage loci within genes
or regions of particular interest. We used this framework to examine
sequencing data from 500 patients generated in ten projects from sequencing
centers in the NHGRI/NCI Clinical Sequencing Exploratory Research (CSER)
Consortium. RESULTS: This approach identified reduced coverage regions in clinically
relevant genes, including known clinically relevant loci that were uniquely
missed at individual centers, in multiple centers, and in all centers. CONCLUSIONS: This report provides a process roadmap for clinical sequencing
centers looking to perform similar analyses on their data.
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42
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Almontashiri NAM, Alswaid A, Oza A, Al-Mazrou KA, Elrehim O, Tayoun AA, Rehm HL, Amr SS. Recurrent variants in OTOF are significant contributors to prelingual nonsydromic hearing loss in Saudi patients. Genet Med 2017; 20:536-544. [PMID: 29048421 PMCID: PMC5929117 DOI: 10.1038/gim.2017.143] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/03/2017] [Indexed: 12/01/2022] Open
Abstract
Purpose Hearing loss is more prevalent in the Saudi Arabian population than in other populations; however, the full range of genetic etiologies in this population is unknown. We report the genetic findings from 33 Saudi hearing-loss probands of tribal ancestry, with predominantly prelingual severe to profound hearing loss. Methods Testing was performed over the course of 2012–2016, and involved initial GJB2 sequence and GJB6-D13S1830 deletion screening, with negative cases being reflexed to a next-generation sequencing panel with 70, 71, or 87 hearing-loss genes. Results A “positive” result was reached in 63% of probands, with two recurrent OTOF variants (p.Glu57* and p.Arg1792His) accountable for a third of all “positive” cases. The next most common cause was pathogenic variants in MYO7A and SLC26A4, each responsible for three “positive” cases. Interestingly, only one “positive” diagnosis had a DFNB1-related cause, due to a homozygous GJB6-D13S1830 deletion, and no sequence variants in GJB2 were detected. Conclusion Our findings implicate OTOF as a potential major contributor to hearing loss in the Saudi population, while highlighting the low contribution of GJB2, thus offering important considerations for clinical testing strategies for Saudi patients. Further screening of Saudi patients is needed to characterize the genetic spectrum in this population.
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Affiliation(s)
- Naif A M Almontashiri
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | | | - Andrea Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Khalid A Al-Mazrou
- Department of Otolaryngology, King Saud University, Riyadh, Saudi Arabia
| | - Omnia Elrehim
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmad Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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Santani A, Murrell J, Funke B, Yu Z, Hegde M, Mao R, Ferreira-Gonzalez A, Voelkerding KV, Weck KE. Development and Validation of Targeted Next-Generation Sequencing Panels for Detection of Germline Variants in Inherited Diseases. Arch Pathol Lab Med 2017; 141:787-797. [PMID: 28322587 DOI: 10.5858/arpa.2016-0517-ra] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - The number of targeted next-generation sequencing (NGS) panels for genetic diseases offered by clinical laboratories is rapidly increasing. Before an NGS-based test is implemented in a clinical laboratory, appropriate validation studies are needed to determine the performance characteristics of the test. OBJECTIVE - To provide examples of assay design and validation of targeted NGS gene panels for the detection of germline variants associated with inherited disorders. DATA SOURCES - The approaches used by 2 clinical laboratories for the development and validation of targeted NGS gene panels are described. Important design and validation considerations are examined. CONCLUSIONS - Clinical laboratories must validate performance specifications of each test prior to implementation. Test design specifications and validation data are provided, outlining important steps in validation of targeted NGS panels by clinical diagnostic laboratories.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Karen E Weck
- From the Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Dr Santani); the Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Drs Santani, Murrell, and Yu); the Department of Pathology, MGH/Harvard Medical School, Boston, Massachusetts (Dr Funke); the Laboratory for Molecular Medicine at Partners HealthCare, Personalized Medicine, Cambridge, Massachusetts (Dr Funke); the Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia (Dr Hegde); the Department of Pathology, ARUP Laboratories Institute for Clinical and Experimental Pathology (Dr Mao) and the Department of Pathology (Dr Voelkerding), University of Utah School of Medicine, Salt Lake City; the Division of Molecular Diagnostics, Department of Pathology, Virginia Commonwealth University, Richmond (Dr Ferreira-Gonzalez); Genomics and Bioinformatics, ARUP Laboratories, Salt Lake City, Utah (Dr Voelkerding); and the Department of Pathology and Laboratory Medicine and Genetics, University of North Carolina at Chapel Hill (Dr Weck)
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Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16:987-99. [PMID: 27388938 DOI: 10.1080/14737159.2016.1209411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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Mandelker D, Schmidt RJ, Ankala A, McDonald Gibson K, Bowser M, Sharma H, Duffy E, Hegde M, Santani A, Lebo M, Funke B. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing. Genet Med 2016; 18:1282-1289. [PMID: 27228465 DOI: 10.1038/gim.2016.58] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 03/24/2016] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) is now routinely used to interrogate large sets of genes in a diagnostic setting. Regions of high sequence homology continue to be a major challenge for short-read technologies and can lead to false-positive and false-negative diagnostic errors. At the scale of whole-exome sequencing (WES), laboratories may be limited in their knowledge of genes and regions that pose technical hurdles due to high homology. We have created an exome-wide resource that catalogs highly homologous regions that is tailored toward diagnostic applications. METHODS This resource was developed using a mappability-based approach tailored to current Sanger and NGS protocols. RESULTS Gene-level and exon-level lists delineate regions that are difficult or impossible to analyze via standard NGS. These regions are ranked by degree of affectedness, annotated for medical relevance, and classified by the type of homology (within-gene, different functional gene, known pseudogene, uncharacterized noncoding region). Additionally, we provide a list of exons that cannot be analyzed by short-amplicon Sanger sequencing. CONCLUSION This resource can help guide clinical test design, supplemental assay implementation, and results interpretation in the context of high homology.Genet Med 18 12, 1282-1289.
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Affiliation(s)
- Diana Mandelker
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA.,Current affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA (D.M.); Medical Genetics, Invitae Corporation, San Francisco, California, USA (K.M.G.)
| | - Ryan J Schmidt
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kristin McDonald Gibson
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Current affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA (D.M.); Medical Genetics, Invitae Corporation, San Francisco, California, USA (K.M.G.)
| | - Mark Bowser
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Himanshu Sharma
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Elizabeth Duffy
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Madhuri Hegde
- Emory Genetics Lab, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Lebo
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Birgit Funke
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School/Massachusetts General Hospital, Boston, Massachusetts, USA
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García-García G, Baux D, Faugère V, Moclyn M, Koenig M, Claustres M, Roux AF. Assessment of the latest NGS enrichment capture methods in clinical context. Sci Rep 2016; 6:20948. [PMID: 26864517 PMCID: PMC4750071 DOI: 10.1038/srep20948] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022] Open
Abstract
Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.
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Affiliation(s)
- Gema García-García
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Valérie Faugère
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mélody Moclyn
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Michel Koenig
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de génétique de maladies rares, EA 7402, Université de Montpellier, Montpellier, France
- Laboratoire de génétique moléculaire, CHRU Montpelier, Montpellier, France
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Pugh TJ, Amr SS, Bowser MJ, Gowrisankar S, Hynes E, Mahanta LM, Rehm HL, Funke B, Lebo MS. VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data. Genet Med 2015; 18:712-9. [PMID: 26681316 PMCID: PMC4940431 DOI: 10.1038/gim.2015.156] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/15/2015] [Indexed: 01/10/2023] Open
Abstract
Purpose: To develop and validate VisCap, a software program targeted to clinical laboratories for inference and visualization of germ-line copy-number variants (CNVs) from targeted next-generation sequencing data. Genet Med18 7, 712–719. Methods: VisCap calculates the fraction of overall sequence coverage assigned to genomic intervals and computes log2 ratios of these values to the median of reference samples profiled using the same test configuration. Candidate CNVs are called when log2 ratios exceed user-defined thresholds. Genet Med18 7, 712–719. Results: We optimized VisCap using 14 cases with known CNVs, followed by prospective analysis of 1,104 cases referred for diagnostic DNA sequencing. To verify calls in the prospective cohort, we used droplet digital polymerase chain reaction (PCR) to confirm 10/27 candidate CNVs and 72/72 copy-neutral genomic regions scored by VisCap. We also used a genome-wide bead array to confirm the absence of CNV calls across panels applied to 10 cases. To improve specificity, we instituted a visual scoring system that enabled experienced reviewers to differentiate true-positive from false-positive calls with minimal impact on laboratory workflow. Genet Med18 7, 712–719. Conclusions: VisCap is a sensitive method for inferring CNVs from targeted sequence data from targeted gene panels. Visual scoring of data underlying CNV calls is a critical step to reduce false-positive calls for follow-up testing. Genet Med18 7, 712–719.
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Affiliation(s)
- Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Sivakumar Gowrisankar
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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Nagy PL, Mansukhani M. The role of clinical genomic testing in diagnosis and discovery of pathogenic mutations. Expert Rev Mol Diagn 2015. [PMID: 26202666 DOI: 10.1586/14737159.2015.1071667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Next-generation sequencing in clinical practice allows for a critical review of the literature to evaluate disease relatedness of specific genes and pathogenicity of individual mutations, while providing an important discovery tool for new disease genes and disease-causing mutations. Data obtained from large panels, whole exome or whole genome sequencing, performed for constitutional or cancer cases, need to be managed in a transparent, yet powerful analytical framework. Assessment of reported pathogenic potential of a variant or disease association of a gene requires careful consideration of population allele frequency, variant data from parents, and precise, yet concise phenotypic description of the entire family and other individuals or families that have the same variant. The full potential for discovery can only be realized if there is data sharing between clinicians performing the interpretation worldwide and structural biologists, analytical chemists and cell biologists interested and knowledgeable of the structure and function of the genes involved.
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Affiliation(s)
- Peter L Nagy
- a Department of Pathology and Cell Biology, Columbia University, Laboratory of Personalized Genomic Medicine, 630 West 168 Street, 10032, New York, NY, USA
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