Dataset Information

Whole Exome Sequencing Reveals Pathogenic Variants in MYO3A, MYO15A and COL9A3, and Differential Frequencies in Ancestral Alleles in Hearing Impairment Genes Among Individuals from Cameroon.

ABSTRACT: There is scarcity of known gene variants of Hearing Impairment (HI) in African populations. This knowledge deficit is ultimately affecting the development of genetic diagnoses. We used whole exome sequencing to investigate gene variants, pathways of interactive genes, and the fractions of ancestral over derived alleles for 159 HI genes, among 18 Cameroonian patients with non-syndromic HI (NSHI), and 129 ethnically matched controls. Pathogenic and likely pathogenic (PLP) variants were found in MYO3A, MYO15A and COL9A3, with a resolution rate of 50% (9/18 patients). The study identified significant genetic differentiation in novel population specific gene variants at FOXD4L2, DHRS2L6, RPL3L and VTN, between HI patients and controls. These gene variants are found in functional/co-expressed interactive networks with other known HI associated genes; and in the same pathways with VTN being a hub protein, i.e. focal adhesion pathway and regulation of the actin cytoskeleton (p values

SUBMITTER: Wonkam A

PROVIDER: S-EPMC7861016 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon.

Wonkam Ambroise A Manyisa Noluthando N Bope Christian D CD Dandara Collet C Chimusa Emile R ER

Human molecular genetics 20210201 23

There is scarcity of known gene variants of hearing impairment (HI) in African populations. This knowledge deficit is ultimately affecting the development of genetic diagnoses. We used whole exome sequencing to investigate gene variants, pathways of interactive genes and the fractions of ancestral overderived alleles for 159 HI genes among 18 Cameroonian patients with non-syndromic HI (NSHI) and 129 ethnically matched controls. Pathogenic and likely pathogenic (PLP) variants were found in MYO3A, ...[more]

PMID: 33078831

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Project description:BACKGROUND:MYO15A variants are responsible for human non-syndromic autosomal recessive deafness (DFNB3). The majority of MYO15A variants are associated with a congenital severe-to-profound hearing loss phenotype, except for MYO15A variants in exon 2, which cause a milder auditory phenotype, suggesting a genotype-phenotype correlation of MYO15A. However, MYO15A variants not in exon 2 related to a milder phenotype have also been reported, indicating that the genotype-phenotype correlation of MYO15A is complicated. This study aimed to provide more cases of MYO15A variation with diverse phenotypes to analyse this complex correlation. METHODS:Fifteen Chinese autosomal recessive non-syndromic hearing loss (ARNSHL) individuals with MYO15A variants (8 males and 7 females) from 14 unrelated families, identified by targeted gene capture of 127 known candidate deafness genes, were recruited. Additionally, we conducted a review of the literature to further analyses all reported MYO15A genotype-phenotype relationships worldwide. RESULTS:We identified 16 novel variants and 12 reported pathogenic MYO15A variants in 15 patients, two of which presented with a milder phenotype. Interestingly, one of these cases carried two reported pathogenic variants in exon 2, while the other carried two novel variants not in exon 2. Based on our literature review, MYO15A genotype-phenotype correlation analysis showed that almost all domains were reported to be correlated with a milder phenotype. However, variants in the N-terminal domain were more likely to cause a milder phenotype. Using next-generation sequencing (NGS), we also found that the number of known MYO15A variants with milder phenotypes in Southeast Asia has increased in recent years. CONCLUSION:Our work extended the MYO15A variant spectrum, enriched our knowledge of auditory phenotypes, and tried to explore the genotype-phenotype correlation in different populations in order to investigate the cause of the complex MYO15A genotype-phenotype correlation.

Dataset Information

Whole Exome Sequencing Reveals Pathogenic Variants in MYO3A, MYO15A and COL9A3, and Differential Frequencies in Ancestral Alleles in Hearing Impairment Genes Among Individuals from Cameroon.

Publications

Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon.

Similar Datasets

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