Panel-based NGS reveals disease-causing mutations in hearing loss patients using BGISEQ-500 platform

Sun, Yan; Yuan, Jing; Wu, Limin; Li, Min; Cui, Xiaoli; Yan, Chengbin; Du, Liangcheng; Mao, Liangwei; Man, Jianfen; Li, Wei; Kristiansen, Karsten; Wu, Xuan; Pan, Weijun; Yang, Yun

doi:10.1097/md.0000000000014860

Cited by 13 publications

(9 citation statements)

References 26 publications

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“…The diagnostic yield of the targeted NGS genetic examination is approaching the reported ratio (i.e., one-half to two-thirds) of HHI in pediatric SNHI [4]. To date, several NGS-based diagnostic panels for HHI, including ours, have been designed [4,45,46,47,48,49]. There is solid evidence that the use of the NGS technique can significantly increase the diagnostic yield of genetic examination for HHI and facilitate the genetic counseling for the affected families.…”

Section: Discussionmentioning

confidence: 99%

Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population

Tsai

Lin

et al. 2019

Genes

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Hereditary hearing impairment (HHI) is a common but heterogeneous clinical entity caused by mutations in a plethora of deafness genes. Research over the past few decades has shown that the genetic epidemiology of HHI varies significantly across populations. In this study, we used different genetic examination strategies to address the genetic causes of HHI in a large Taiwanese cohort composed of >5000 hearing-impaired families. We also analyzed the clinical features associated with specific genetic mutations. Our results demonstrated that next-generation sequencing-based examination strategies could achieve genetic diagnosis in approximately half of the families. Common deafness-associated genes in the Taiwanese patients assessed, in the order of prevalence, included GJB2, SLC26A4, OTOF, MYO15A, and MTRNR1, which were similar to those found in other populations. However, the Taiwanese patients had some unique mutations in these genes. These findings may have important clinical implications for refining molecular diagnostics, facilitating genetic counseling, and enabling precision medicine for the management of HHI.

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Section: Discussionmentioning

confidence: 99%

Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population

Tsai

Lin

et al. 2019

Genes

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“…For example, the MGISEQ-2000 currently generates 1.44 TB of sequence data in a single run with a running cost of 10 USD/GB. Several recent studies have compared the performance of BGI sequencers with Illumina’s sequencers and showed that the BGI sequencers produced high-quality sequence data at lower or similar prices in studies of whole-exome [2,3], whole-genome [4][1], transcriptome [5,6], single-cell transcriptome [2,78], metagenome [9], and small RNA sequencing [10].…”

Section: Introductionmentioning

confidence: 99%

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

et al. 2019

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Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGIS-EQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGIS-EQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

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“…Though GJB2 is the most common mutation worldwide in different populations, other important genes include SLC26A4, GJB3, GJB6, MYO15A, MYO7A, TMC1, CDH23 etc. were also identified in the pathogenesis of NSHL [24][25][26][27][28]. This study reviewed all the described target genes identified experimentally in NSHL during the period between 2009 and 2020 and attempted to study the interactions between them through functional network analysis and identify the possible deleterious variants.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes

2021

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Hearing loss is a significant public health problem and causes the most frequent congenital disability in developed societies. The genetic analysis of non-syndromic hearing loss (NSHL) may be considered as a complement to the existent plethora of diagnostic modalities available. This study focuses on exploring more target genes with respective non-synonymous single nucleotide polymorphisms (nsSNPs) involved in the development of NSHL. The functional network analysis and variant study have successfully been carried out from the gene pool retrieved from reported research articles of the last decade. The analyses have been done through STRING. According to predicted biological processes, various variant analysis tools have successfully classified the NSHL causative genes and identified the deleterious nsSNPs, respectively. Among the predicted pathogenic nsSNPs with rsIDs rs80356586 (I515T), rs80356596 (L1011P), rs80356606 (P1987R) in OTOF have been reported in NSHL earlier. The rs121909642 (P722S), rs267606805 (P722H) in FGFR1, rs121918506 (E565A) and rs121918509 (A628T, A629T) in FGFR2 have not reported in NSHL yet, which should be clinically experimented in NSHL. This also which indicates this variant's novelty as its association in NSHL. The findings and the analysed data have delivered some vibrant genetic pathogenesis of NSHL. This data might be used in the diagnostic and prognostic purposes in non-syndromic congenitally deaf children.

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Panel-based NGS reveals disease-causing mutations in hearing loss patients using BGISEQ-500 platform

Abstract: Supplemental Digital Content is available in the text

Cited by 13 publications

References 26 publications

Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population

Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes

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