1
|
Tlili A, Mahfood M, Al Mutery A, Chouchen J. Genetic analysis of 106 sporadic cases with hearing loss in the UAE population. Hum Genomics 2024; 18:59. [PMID: 38844983 PMCID: PMC11157727 DOI: 10.1186/s40246-024-00630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Hereditary hearing loss is a rare hereditary condition that has a significant presence in consanguineous populations. Despite its prevalence, hearing loss is marked by substantial genetic diversity, which poses challenges for diagnosis and screening, particularly in cases with no clear family history or when the impact of the genetic variant requires functional analysis, such as in the case of missense mutations and UTR variants. The advent of next-generation sequencing (NGS) has transformed the identification of genes and variants linked to various conditions, including hearing loss. However, there remains a high proportion of undiagnosed patients, attributable to various factors, including limitations in sequencing coverage and gaps in our knowledge of the entire genome, among other factors. In this study, our objective was to comprehensively identify the spectrum of genes and variants associated with hearing loss in a cohort of 106 affected individuals from the UAE. RESULTS In this study, we investigated 106 sporadic cases of hearing impairment and performed genetic analyses to identify causative mutations. Screening of the GJB2 gene in these cases revealed its involvement in 24 affected individuals, with specific mutations identified. For individuals without GJB2 mutations, whole exome sequencing (WES) was conducted. WES revealed 33 genetic variants, including 6 homozygous and 27 heterozygous DNA changes, two of which were previously implicated in hearing loss, while 25 variants were novel. We also observed multiple potential pathogenic heterozygous variants across different genes in some cases. Notably, a significant proportion of cases remained without potential pathogenic variants. CONCLUSIONS Our findings confirm the complex genetic landscape of hearing loss and the limitations of WES in achieving a 100% diagnostic rate, especially in conditions characterized by genetic heterogeneity. These results contribute to our understanding of the genetic basis of hearing loss and emphasize the need for further research and comprehensive genetic analyses to elucidate the underlying causes of this condition.
Collapse
Affiliation(s)
- Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates.
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates.
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Jihen Chouchen
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| |
Collapse
|
2
|
Zhang L, Yang JY, Wang QQ, Gao X, Wang GJ, Han MY, Kang DY, Han DY, Huang SS, Yuan YY. MPZL2-a common autosomal recessive deafness gene related to moderate sensorineural hearing loss in the Chinese population. BMC Med Genomics 2024; 17:32. [PMID: 38254107 PMCID: PMC10804618 DOI: 10.1186/s12920-023-01786-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Mutations in MPZL2, the characteristic genetic etiology of autosomal recessive deafness loci 111 (DFNB111), cause non-syndromic and moderate sensorineural hearing loss. METHODS In this study, we analyzed the phenotype and genotype of eight pedigrees consisting of 10 hearing loss patients with bi-allelic pathogenic or likely pathogenic variants in MPZL2. These patients were identified from a 3272 Chinese patient cohort who underwent genetic testing. RESULTS Apart from symmetrical and moderate sensorineural hearing loss, the MPZL2-related phenotype was characterized by progressive hearing loss with variation in the onset age (congenital defect to onset at the young adult stage). We determined that in the Chinese population, the genetic load of MPZL2 defects was 0.24% (8/3272) in patients diagnosed with hearing loss and 7.02% (8/114) in patients diagnosed with hereditary moderate sensorineural hearing loss caused by STRC, OTOA, OTOG, OTOGL, TECTA, MPZL2 and others. Three known MPZL2 variants (c.220C > T (p.Gln74*), c.68delC (p.Pro23Leufs*2), c.463delG (p.Ala155Leufs*10)) and a novel start loss variant (c.3G > T (p.Met1?)) were identified. MPZL2 c.220C > T was identified as the hotspot variant in the Chinese population and even in East Asia compared with c.72delA (p.Ile24Metfs*22) in European and West Asia through allele frequency. CONCLUSIONS We concluded that apart from moderate HL, progressive HL is another character of MPZL2-related HL. No specified variant was verified for the progression of HL, the penetrance and expressivity cannot be determined yet. A novel MPZL2 variant at the start codon was identified, enriching the variant spectrum of MPZL2. The hotspot variants of MPZL2 vary in different ethnicities. This study provides valuable data for the diagnosis, prognosis evaluation and genetic counseling of patients with moderate sensorineural hearing loss related to MPZL2.
Collapse
Affiliation(s)
- Lang Zhang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Jin-Yuan Yang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Qiu-Quan Wang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, 100088, Beijing, China
| | - Guo-Jian Wang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Ming-Yu Han
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Dong-Yang Kang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Dong-Yi Han
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China.
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China.
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Sha-Sha Huang
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China.
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China.
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Yong-Yi Yuan
- College of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Otolaryngologic Diseases, Sixth Medical Center of the PLA General Hospital, Chinese PLA Medical School, 6# Fucheng Road, Beijing, 100048, China.
- State Key Lab of Hearing Science, Ministry of Education, Beijing, China.
- Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China.
| |
Collapse
|
3
|
Steyaert W, Haer-Wigman L, Pfundt R, Hellebrekers D, Steehouwer M, Hampstead J, de Boer E, Stegmann A, Yntema H, Kamsteeg EJ, Brunner H, Hoischen A, Gilissen C. Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation. Nat Commun 2023; 14:6845. [PMID: 37891200 PMCID: PMC10611741 DOI: 10.1038/s41467-023-42531-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.
Collapse
Affiliation(s)
- Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Debby Hellebrekers
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Elke de Boer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Alexander Stegmann
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
| | - Han Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Maastricht University Medical Center + , Department of Clinical Genetics, Maastricht, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
- Radboud University Medical Center, Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525, GA, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands.
| |
Collapse
|
4
|
Xiang J, Zhang H, Sun X, Zhang J, Xu Z, Sun J, Peng Z. Utility of Whole Genome Sequencing for Population Screening of Deafness-Related Genetic Variants and Cytomegalovirus Infection in Newborns. Front Genet 2022; 13:883617. [PMID: 35571039 PMCID: PMC9099144 DOI: 10.3389/fgene.2022.883617] [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: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hearing loss affects approximately two out of every 1,000 newborns. Genetic factors and congenital cytomegalovirus (CMV) infections account for around 90% of the etiology. The purpose of this study was to develop and test a whole genome sequencing (WGS) approach to detect deafness-related genetic variants and CMV infections simultaneously in newborns.Method: Deafness-related genes causing congenital or childhood hearing loss were curated and selected for newborn screening. Nine dried blood spots from newborns with known genetic variants (n = 6) or CMV infections (n = 3) were employed to develop and validate the WGS testing and analytic pipeline. We then pilot tested the WGS analysis on 51 de-identified clinical samples.Results: 92 gene-disease pairs were selected for screening hearing loss in newborns. In the validation test, WGS accurately detected all types of genetic variants, including single nucleotide variations, insertions/deletions, and copy number variations in the nuclear or mitochondrial genome. Sequence reads mapping to the CMV reference genome were discovered in CMV infected samples. In the pilot test, WGS identified nine out of 51 (18%) newborns carrying pathogenic variants associated with deafness.Conclusion: WGS can simultaneously detect genetic variants and CMV infections in dried blood spot specimens from newborns. Our study provides proof of principle that genome sequencing can be a promising alternative for newborn screening of hearing loss.
Collapse
Affiliation(s)
- Jiale Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenpeng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Zhiyu Peng,
| |
Collapse
|
5
|
Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet 2021; 141:387-400. [PMID: 34811589 DOI: 10.1007/s00439-021-02365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
Structural variation includes a change in copy number, orientation, or location of a part of the genome. Copy number variants (CNVs) are a common cause of genetic hearing loss, comprising nearly 20% of diagnosed cases. While large deletions involving the gene STRC are the most common pathogenic CNVs, a significant proportion of known hearing loss genes also contain pathogenic CNVs. In this review, we provide an overview of currently used methods for detection of CNVs in genes known to cause hearing loss including molecular techniques such as multiplex ligation probe amplification (MLPA) and digital droplet polymerase chain reaction (ddPCR), array-CGH and single-nucleotide polymorphism (SNP) arrays, as well as techniques for detection of CNVs using next-generation sequencing data analysis including targeted gene panel, exome, and genome sequencing data. In addition, in this review, we compile published data on pathogenic hearing loss CNVs to provide an up-to-date overview. We show that CNVs have been identified in 29 different non-syndromic hearing loss genes. An understanding of the contribution of CNVs to genetic hearing loss is critical to the current diagnosis of hearing loss and is crucial for future gene therapies. Thus, evaluation for CNVs is required in any modern pipeline for genetic diagnosis of hearing loss.
Collapse
|
6
|
Compound Heterozygosity for OTOA Truncating Variant and Genomic Rearrangement Cause Autosomal Recessive Sensorineural Hearing Loss in an Italian Family. Audiol Res 2021; 11:443-451. [PMID: 34562879 PMCID: PMC8482239 DOI: 10.3390/audiolres11030041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022] Open
Abstract
Hearing loss (HL) affects 1–3 newborns per 1000 and, in industrialized countries, recognizes a genetic etiology in more than 80% of the congenital cases. Excluding GJB2 and GJB6, OTOA is one of the leading genes associated with autosomal recessive non-syndromic HL. Allelic heterogeneity linked to OTOA also includes genomic rearrangements facilitated by non-allelic homologous recombination with the neighboring OTOAP1 pseudogene. We present a couple of Italian siblings affected by moderate to severe sensorineural hearing loss (SNHL) due to compound heterozygosity at the OTOA locus. Multigene panel next-generation sequencing identified the c.2223G>A, p.(Trp741*) variant transmitted from the unaffected mother. Assuming the existence of a second paternal deleterious variant which evaded detection at sequencing, genomic array analysis found a ~150 Kb microdeletion of paternal origin and spanning part of OTOA. Both deleterious alleles were identified for the first time. This study demonstrates the utility of an integrated approach to solve complex cases and allow appropriate management to affected individuals and at-risk relatives.
Collapse
|
7
|
Van Heurck R, Carminho-Rodrigues MT, Ranza E, Stafuzza C, Quteineh L, Gehrig C, Hammar E, Guipponi M, Abramowicz M, Senn P, Guinand N, Cao-Van H, Paoloni-Giacobino A. Benefits of Exome Sequencing in Children with Suspected Isolated Hearing Loss. Genes (Basel) 2021; 12:genes12081277. [PMID: 34440452 PMCID: PMC8391342 DOI: 10.3390/genes12081277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose: Hearing loss is characterized by an extensive genetic heterogeneity and remains a common disorder in children. Molecular diagnosis is of particular benefit in children, and permits the early identification of clinically-unrecognized hearing loss syndromes, which permits effective clinical management and follow-up, including genetic counselling. Methods: We performed whole-exome sequencing with the analysis of a panel of 189 genes associated with hearing loss in a prospective cohort of 61 children and 9 adults presenting mainly with isolated hearing loss. Results: The overall diagnostic rate using exome sequencing was 47.2% (52.5% in children; 22% in adults). In children with confirmed molecular results, 17/32 (53.2%) showed autosomal recessive inheritance patterns, 14/32 (43.75%) showed an autosomal dominant condition, and one case had X-linked hearing loss. In adults, the two patients showed an autosomal dominant inheritance pattern. Among the 32 children, 17 (53.1%) had nonsyndromic hearing loss and 15 (46.7%) had syndromic hearing loss. One adult was diagnosed with syndromic hearing loss and one with nonsyndromic hearing loss. The most common causative genes were STRC (5 cases), GJB2 (3 cases), COL11A1 (3 cases), and ACTG1 (3 cases). Conclusions: Exome sequencing has a high diagnostic yield in children with hearing loss and can reveal a syndromic hearing loss form before other organs/systems become involved, allowing the surveillance of unrecognized present and/or future complications associated with these syndromes.
Collapse
Affiliation(s)
- Roxane Van Heurck
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Maria Teresa Carminho-Rodrigues
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Emmanuelle Ranza
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Caterina Stafuzza
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Lina Quteineh
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Corinne Gehrig
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Eva Hammar
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Michel Guipponi
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Marc Abramowicz
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Pascal Senn
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Nils Guinand
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Helene Cao-Van
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Ariane Paoloni-Giacobino
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
- Correspondence:
| |
Collapse
|
8
|
de Bruijn SE, Fadaie Z, Cremers FPM, Kremer H, Roosing S. The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. Int J Mol Sci 2021; 22:2943. [PMID: 33799353 PMCID: PMC7998853 DOI: 10.3390/ijms22062943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
The identification of pathogenic variants in monogenic diseases has been of interest to researchers and clinicians for several decades. However, for inherited diseases with extremely high genetic heterogeneity, such as hearing loss and retinal dystrophies, establishing a molecular diagnosis requires an enormous effort. In this review, we use these two genetic conditions as examples to describe the initial molecular genetic identification approaches, as performed since the early 90s, and subsequent improvements and refinements introduced over the years. Next, the history of DNA sequencing from conventional Sanger sequencing to high-throughput massive parallel sequencing, a.k.a. next-generation sequencing, is outlined, including their advantages and limitations and their impact on identifying the remaining genetic defects. Moreover, the development of recent technologies, also coined "third-generation" sequencing, is reviewed, which holds the promise to overcome these limitations. Furthermore, we outline the importance and complexity of variant interpretation in clinical diagnostic settings concerning the massive number of different variants identified by these methods. Finally, we briefly mention the development of novel approaches such as optical mapping and multiomics, which can help to further identify genetic defects in the near future.
Collapse
Affiliation(s)
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Hannie Kremer
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| |
Collapse
|