Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness
Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candi...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-12-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.773922/full |
| _version_ | 1818462171589246976 |
|---|---|
| author | Penghui Chen Penghui Chen Penghui Chen Penghui Chen Longhao Wang Longhao Wang Longhao Wang Yongchuan Chai Yongchuan Chai Yongchuan Chai Hao Wu Hao Wu Hao Wu Tao Yang Tao Yang Tao Yang |
| author_facet | Penghui Chen Penghui Chen Penghui Chen Penghui Chen Longhao Wang Longhao Wang Longhao Wang Yongchuan Chai Yongchuan Chai Yongchuan Chai Hao Wu Hao Wu Hao Wu Tao Yang Tao Yang Tao Yang |
| author_sort | Penghui Chen |
| collection | DOAJ |
| description | Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A > T and c.580G > A in EYA4, c.322-57_322-8del in PAX3, c.991-15_991-13del in DFNA5, c.6087-3T > G in PTPRQ and c.164+5G > A in USH1G. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A > T and c.580G > A in EYA4, c.991-15_991-13del in DFNA5), intron retention (c.322-57_322-8del in PAX3), exon skipping and intron retention (c.6087-3T > G in PTPRQ) and shortening of exon (c.164+5G > A in USH1G). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis. |
| first_indexed | 2024-12-14T23:57:48Z |
| format | Article |
| id | doaj.art-b2bf9de49fdc4deeb85d80ab72e4a483 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T23:57:48Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-b2bf9de49fdc4deeb85d80ab72e4a4832022-12-21T22:43:04ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-12-011210.3389/fgene.2021.773922773922Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary DeafnessPenghui Chen0Penghui Chen1Penghui Chen2Penghui Chen3Longhao Wang4Longhao Wang5Longhao Wang6Yongchuan Chai7Yongchuan Chai8Yongchuan Chai9Hao Wu10Hao Wu11Hao Wu12Tao Yang13Tao Yang14Tao Yang15Department of Otolaryngology—Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaEar Institute, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, ChinaDepartment of Otorhinolaryngology—Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaDepartment of Otolaryngology—Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaEar Institute, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, ChinaDepartment of Otolaryngology—Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaEar Institute, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, ChinaDepartment of Otolaryngology—Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaEar Institute, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, ChinaDepartment of Otolaryngology—Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaEar Institute, Shanghai Jiaotong University School of Medicine, Shanghai, ChinaShanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, ChinaSplice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A > T and c.580G > A in EYA4, c.322-57_322-8del in PAX3, c.991-15_991-13del in DFNA5, c.6087-3T > G in PTPRQ and c.164+5G > A in USH1G. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A > T and c.580G > A in EYA4, c.991-15_991-13del in DFNA5), intron retention (c.322-57_322-8del in PAX3), exon skipping and intron retention (c.6087-3T > G in PTPRQ) and shortening of exon (c.164+5G > A in USH1G). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis.https://www.frontiersin.org/articles/10.3389/fgene.2021.773922/fullsplice site mutationRNA splicingminigenehereditary deafnessnext-generation sequencing |
| spellingShingle | Penghui Chen Penghui Chen Penghui Chen Penghui Chen Longhao Wang Longhao Wang Longhao Wang Yongchuan Chai Yongchuan Chai Yongchuan Chai Hao Wu Hao Wu Hao Wu Tao Yang Tao Yang Tao Yang Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness Frontiers in Genetics splice site mutation RNA splicing minigene hereditary deafness next-generation sequencing |
| title | Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness |
| title_full | Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness |
| title_fullStr | Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness |
| title_full_unstemmed | Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness |
| title_short | Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness |
| title_sort | detection and functional verification of noncanonical splice site mutations in hereditary deafness |
| topic | splice site mutation RNA splicing minigene hereditary deafness next-generation sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.773922/full |
| work_keys_str_mv | AT penghuichen detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT penghuichen detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT penghuichen detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT penghuichen detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT longhaowang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT longhaowang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT longhaowang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT yongchuanchai detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT yongchuanchai detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT yongchuanchai detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT haowu detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT haowu detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT haowu detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT taoyang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT taoyang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness AT taoyang detectionandfunctionalverificationofnoncanonicalsplicesitemutationsinhereditarydeafness |