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Hu T, Chen J, Lin X, He W, Liang H, Wang M, Li W, Wu Z, Han M, Jin X, Kristiansen K, Xiao L, Zou Y. Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly. Sci Rep 2024; 14:1292. [PMID: 38221534 PMCID: PMC10788345 DOI: 10.1038/s41598-024-51725-0] [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: 08/11/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024] Open
Abstract
The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
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Affiliation(s)
- Tongyuan Hu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Xiaoqian Lin
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Wenxin He
- BGI Research, Shenzhen, 518083, China
| | - Hewei Liang
- BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | | | - Wenxi Li
- BGI Research, Shenzhen, 518083, China
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
| | - Zhinan Wu
- BGI Research, Shenzhen, 518083, China
| | - Mo Han
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI Research, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
| | - Yuanqiang Zou
- BGI Research, Shenzhen, 518083, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China.
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Wang L, Liu G, Ma D, Zeng H, Wang Y, Luo C, Zhang J, Xu Z. Next-generation sequencing for genetic testing of hearing loss populations. Clin Chim Acta 2024; 552:117693. [PMID: 38056549 DOI: 10.1016/j.cca.2023.117693] [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: 07/14/2023] [Revised: 12/03/2023] [Accepted: 12/03/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND AND AIMS Hearing loss is a common sensorineural disease with genetic heterogeneity. More than 140 genes are known to cause hereditary hearing loss. We aim to uncover the etiologies of hearing loss and provide patients with reasonable reproductive choices. MATERIALS AND METHODS Total 825 participants were recruited, including 74 individuals, 47 couples, and 219 families, to identify the molecular etiologies of hearing loss using next-generation sequencing (NGS). Novel mutations were verified with a minigene splicing assay and the construction of three-dimensional protein models. RESULTS A positive molecular diagnosis was obtained for 244 patients, a rate of 63.05 %. Total 470 mutations were identified in 18 causative genes in positive patients. The most common genes mutated were GJB2 and SLC26A4. 47 novel mutations were identified. Further analysis predicted that two splicing mutations would cause abnormal mRNA splicing and three missense mutations would affect the protein structure. The results of prenatal diagnosis showed that the genotypes of 15 fetuses were the same as the probands. CONCLUSION Our findings expand the mutation spectrum of hearing loss and highlight the importance of genetic diagnosis and prenatal diagnosis to allow accurate and personalized guidance for those at high risk of deafness.
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Affiliation(s)
- Lulu Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Gang Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Dingyuan Ma
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Huasha Zeng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China.
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3
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Cao B, Luo H, Luo T, Li N, Shao K, Wu K, Sahu SK, Li F, Lin C. The performance of whole genome bisulfite sequencing on DNBSEQ-Tx platform examined by different library preparation strategies. Heliyon 2023; 9:e16571. [PMID: 37292292 PMCID: PMC10245168 DOI: 10.1016/j.heliyon.2023.e16571] [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: 10/25/2022] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Background Whole-genome bisulfite sequencing (WGBS) technology can provide comprehensive DNA methylation at a single-base resolution on a genome-wide scale, and is considered to be the gold standard for the detection of 5-methylcytosine (5 mC). However, the International Human Epigenome Consortium propose a full DNA methylome should have at least 30 fold redundant coverage of the reference genome from a single biological replicate. Therefore, it remains cost prohibitive for large-scale studies. To find a solution, the DNBSEQ-Tx sequencing was developed that can generate up to 6 Tb data in a single run for projects involving large-scale sequencing. Results In this study, we provided two WGBS library construction methods DNB_PREBSseq and DNB_SPLATseq optimized for the DNBSEQ-Tx sequencer, and demonstrated the performance of these two methods on the DNBSEQ-Tx platform, using the DNA extracted from four different cell lines. We also compared the sequencing data from these two WGBS library construction methods with HeLa cell line data from ENCODE sequenced on Illumina HiSeq X Ten and WGBS data of two other cell lines sequenced on HiSeq2500. Various quality control (QC) analyses such as the base quality scores, methylation-bias (m-bias), and conversion efficiency indicated that the data sequenced on the DNBSEQ-Tx platform met the WGBS-required quality controls. Meanwhile, our data closely resembled the coverage shown by the data generated by the Illumina platform. Conclusions Our study showed that with our optimized methods, DNBSEQ-Tx could generate high-quality WGBS data with relatively good stability for large-scale WGBS sequencing applications. Thus, we conclude that DNBSEQ-Tx can be used for a wide range of WGBS research.
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Affiliation(s)
- Boyang Cao
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huijuan Luo
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Tian Luo
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Nannan Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Kang Shao
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Fuqiang Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Cong Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, China
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4
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Yang JY, Wang WQ, Han MY, Huang SS, Wang GJ, Su Y, Xu JC, Fu Y, Kang DY, Yang K, Zhang X, Liu X, Gao X, Yuan YY, Dai P. Addition of an affected family member to a previously ascertained autosomal recessive nonsyndromic hearing loss pedigree and systematic phenotype-genotype analysis of splice-site variants in MYO15A. BMC Med Genomics 2022; 15:241. [PMCID: PMC9673454 DOI: 10.1186/s12920-022-01368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in MYO15A are known to cause autosomal recessive nonsyndromic hearing loss (ARNSHL), DFNB3. We have previously reported on one ARNSHL family including two affected siblings and identified MYO15A c.5964+3G > A and c.8375 T > C (p.Val2792Ala) as the possible deafness-causing variants. Eight year follow up identified one new affected individual in this family, who also showed congenital, severe to profound sensorineural hearing loss. By whole exome sequencing, we identified a new splice-site variant c.5531+1G > C (maternal allele), in a compound heterozygote with previously identified missense variant c.8375 T > C (p.Val2792Ala) (paternal allele) in MYO15A as the disease-causing variants. The new affected individual underwent unilateral cochlear implantation at the age of 1 year, and 5 year follow-up showed satisfactory speech and language outcomes. Our results further indicate that MYO15A-associated hearing loss is good candidates for cochlear implantation, which is in accordance with previous report. In light of our findings and review of the literatures, 58 splice-site variants in MYO15A are correlated with a severe deafness phenotype, composed of 46 canonical splice-site variants and 12 non-canonical splice-site variants.
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Affiliation(s)
- Jin-Yuan Yang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Wei-Qian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ming-Yu Han
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Sha-Sha Huang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Guo-Jian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Yu Su
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General Hospital Affiliated Hainan Hospital, Jianglin Road, Sanya, 572013 People’s Republic of China ,Hainan Province Clinical Research Center for Otolaryngologic and Head and Neck Diseases, Jianglin Road, Sanya, 572013 People’s Republic of China
| | - Jin-Cao Xu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ying Fu
- grid.27255.370000 0004 1761 1174Department of Otorhinolaryngology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, 266035 Shandong People’s Republic of China
| | - Dong-Yang Kang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Kun Yang
- grid.488137.10000 0001 2267 2324Postgraduate Training Base of Jinzhou Medical University, The PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xin Zhang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Xing Liu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xue Gao
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Yong-Yi Yuan
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Pu Dai
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
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Wang Y, Ye Q, Sun Y, Jiang Y, Meng B, Du J, Chen J, Tugarova AV, Kamnev AA, Huang S. Selenite Reduction by Proteus sp. YS02: New Insights Revealed by Comparative Transcriptomics and Antibacterial Effectiveness of the Biogenic Se0 Nanoparticles. Front Microbiol 2022; 13:845321. [PMID: 35359742 PMCID: PMC8960269 DOI: 10.3389/fmicb.2022.845321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/17/2022] [Indexed: 02/05/2023] Open
Abstract
Biotransformation of selenite by microorganisms is an effective detoxification (in cases of dissimilatory reduction, e.g., to Se0) and assimilation process (when Se is assimilated by cells). However, the current knowledge of the molecular mechanism of selenite reduction remains limited. In this study, a selenite-resistant bacterium was isolated and identified as Proteus sp. YS02. Strain YS02 reduced 93.2% of 5.0 mM selenite to selenium nanoparticles (SeNPs) within 24 h, and the produced SeNPs were spherical and localized intracellularly or extracellularly, with an average dimension of 140 ± 43 nm. The morphology and composition of the isolated and purified SeNPs were characterized using dynamic light scattering (DLS), scanning electron microscopy (SEM) with energy-dispersive X-ray (EDX) spectrometry, and Fourier transform infrared (FTIR) spectroscopy. FTIR spectroscopy indicated the presence of proteins, polysaccharides, and lipids on the surface of the isolated SeNPs. Furthermore, the SeNPs showed excellent antimicrobial activity against several Gram-positive and Gram-negative pathogenic bacteria. Comparative transcriptome analysis was performed to elucidate the selenite reduction mechanism and biosynthesis of SeNPs. It is revealed that 197 genes were significantly upregulated, and 276 genes were significantly downregulated under selenite treatment. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that genes associated with ABC transporters, sulfur metabolism, pentose phosphate pathway (PPP), and pyruvate dehydrogenase were significantly enhanced, indicating selenite is reduced by sulfite reductase with PPP and pyruvate dehydrogenase supplying reducing equivalents and energy. This work suggests numerous genes are involved in the response to selenite stress, providing new insights into the molecular mechanisms of selenite bioreduction with the formation of SeNPs.
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Affiliation(s)
- Yuting Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qing Ye
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yujun Sun
- Institute of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, China
| | - Yulu Jiang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bo Meng
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jun Du
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jingjing Chen
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Anna V. Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
| | - Alexander A. Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
- *Correspondence: Alexander A. Kamnev, ; ; Shengwei Huang,
| | - Shengwei Huang
- Institute of Biomedical and Health Science, School of Life and Health Science, Anhui Science and Technology University, Fengyang, China
- *Correspondence: Alexander A. Kamnev, ; ; Shengwei Huang,
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6
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Zhou C, Xiao Y, Xie H, Wang J, Liu S. Case Report: Novel Compound Heterozygous Variants in TRIOBP Associated With Congenital Deafness in a Chinese Family. Front Genet 2021; 12:766973. [PMID: 34868251 PMCID: PMC8635749 DOI: 10.3389/fgene.2021.766973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Autosomal recessive non-syndromic deafness-28 (DFNB28) is characterized by prelingual, profound sensorineural hearing loss (HL). The disease is related to variants of the TRIOBP gene. TRIO and F-actin binding protein (TRIOBP) plays crucial roles in modulating the assembly of the actin cytoskeleton and are responsible for the proper structure and function of stereocilia in the inner ear. This study aimed to identify pathogenic variants in a patient with HL. Genomic DNA obtained from a 33-year-old woman with HL was evaluated using a disease-targeted gene panel. Using next generation sequencing and bioinformatics analysis, we identified two novel TRIOBP c.1170delC (p.S391Pfs*488) and c.3764C > G (p.S1255*) variants. Both parents of the patient were heterozygous carriers of the gene. The two variants have not been reported in general population databases or published literature. The findings of this study will broaden the spectrum of pathogenic variants in the TRIOBP gene.
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Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hanbing Xie
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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7
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Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes. Biosci Rep 2021; 41:230001. [PMID: 34714320 PMCID: PMC8559308 DOI: 10.1042/bsr20211865] [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: 08/05/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
Hearing loss (HL) 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. The present 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 been reported in NSHL yet, which should be clinically experimented in NSHL. This also indicates this variant's novelty as its association in NSHL. The findings and the analyzed data have delivered some vibrant genetic pathogenesis of NSHL. These data might be used in the diagnostic and prognostic purposes in non-syndromic congenitally deaf children.
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8
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Usami SI, Nishio SY. The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K patients. Hum Genet 2021; 141:665-681. [PMID: 34599366 PMCID: PMC9035015 DOI: 10.1007/s00439-021-02371-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
Etiological studies have shown genetic disorders to be a major cause of sensorineural hearing loss, but there are a limited number of comprehensive etiological reports based on genetic analysis. In the present study, the same platform using a diagnostic DNA panel carrying 63 deafness genes and the same filtering algorithm were applied to 10,047 samples obtained from social health insurance-based genetic testing of hearing loss. The most remarkable result obtained in this comprehensive study was that the data first clarified the genetic epidemiology from congenital/early-onset deafness to late-onset hearing loss. The overall diagnostic rate was 38.8%, with the rate differing for each age group; 48.6% for the congenital/early-onset group (~5y.o.), 33.5% for the juvenile/young adult-onset group, and 18.0% for the 40+ y.o. group. Interestingly, each group showed a different kind of causative gene. With regard to the mutational spectra, there are certain recurrent variants that may be due to founder effects or hot spots. A series of haplotype studies have shown many recurrent variants are due to founder effects, which is compatible with human migration. It should be noted that, regardless of differences in the mutational spectrum, the clinical characteristics caused by particular genes can be considered universal. This comprehensive review clarified the detailed clinical characteristics (onset age, severity, progressiveness, etc.) of hearing loss caused by each gene, and will provide useful information for future clinical application, including genetic counseling and selection of appropriate interventions.
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Affiliation(s)
- Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
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Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, Kim SY. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics 2021; 43:713-724. [PMID: 33864614 DOI: 10.1007/s13258-021-01096-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencing instruments. OBJECTIVE In this study, we compared the performance of the two platform's major sequencing instruments-Illumina's NovaSeq 6000 and MGI's MGISEQ-2000 and DNBSEQ-T7-to test whether the MGISEQ-2000 and DNBSEQ-T7 sequencing instruments are also suitable for whole genome sequencing. METHODS We sequenced two pairs of normal and tumor tissues from Korean lung cancer patients using the three platforms. Then, we called single nucleotide variants (SNVs) and insertion and deletion (indels) for somatic and germline variants to compare the performance among the three platforms. RESULTS In quality control analysis, all of the three platforms showed high-quality scores and deep coverages. Comparison among the three platforms revealed that MGISEQ-2000 is most concordant with NovaSeq 6000 for germline SNVs and indels, and DNBSEQ-T7 is most concordant with NovaSeq 6000 for somatic SNVs and indels. CONCLUSIONS These results suggest that the performances of the MGISEQ-2000 and DNBSEQ-T7 platforms are comparable to that of the Illumina NovaSeq 6000 platform and support the potential applicability of the MGISEQ-2000 and DNBSEQ-T7 platforms in actual genome analysis fields.
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Affiliation(s)
- Sol A Jeon
- Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea.,Department of Bioscience, University of Science and Technology, 34113, Daejeon, South Korea
| | - Jong Lyul Park
- Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea
| | - Seung-Jin Park
- Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea.,Department of Bioscience, University of Science and Technology, 34113, Daejeon, South Korea
| | - Jeong Hwan Kim
- Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea
| | - Sung-Ho Goh
- National Cancer Center, Goyang-si, Republic of Korea
| | - Ji-Youn Han
- National Cancer Center, Goyang-si, Republic of Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea. .,Department of Bioscience, University of Science and Technology, 34113, Daejeon, South Korea.
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Min J, Mao B, Wang Y, He X, Gao S, Wang H. A Heterozygous Novel Mutation in TFAP2A Gene Causes Atypical Branchio-Oculo-Facial Syndrome With Isolated Coloboma of Choroid: A Case Report. Front Pediatr 2020; 8:380. [PMID: 32766183 PMCID: PMC7379893 DOI: 10.3389/fped.2020.00380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Branchio-oculo-facial syndrome (BOFS) is a rare congenital developmental disorder with highly variable clinical phenotypes in autosomal dominant inheritance. The aim of this study is to identify disease-causing mutations in a Chinese family with predominant coloboma of choroid. Case report: We described a family (a mother and her daughter) with unclear clinical diagnosis. The mother (proband) presented with bilateral coloboma of choroid, whereas her daughter had a relatively severe phenotype and presented with larger bilateral choroid coloboma and high-vaulted arch. We applied the next generation sequencing (NGS) panel and analyzed 776 genes related to inherited ocular disorders on the proband. Four candidate heterozygous variants in four genes, respectively, were detected in the proband. Validation of these variants were subsequently performed in the family using Sanger sequencing. Among these variants, a novel nonsense mutation c.912C>A, p.(Cys304*) (NM_001042425.2) which in exon 6 of the conserved helix-span-helix domain in TFAP2A results in a premature termination codon. It may trigger nonsense-mediated mRNA decay (NMD). Both the affected mother and daughter had this variant, whereas it was absent in the asymptomatic father. Together with the silicon tools and clinical features, we concluded that the variant c.912C>A, p.(Cys304*), was the second reported nonsense mutation in TFAP2A gene, which was the disease-causing mutation of the family. Conclusion: There are many hereditary diseases accompanied by ocular anomalies. For instance, BOFS, patients with atypical features are always at risk of being under-diagnosed. NGS is a powerful method to identify the genetic cause and improve genetic counseling for less clarified hereditary ocular diseases.
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Affiliation(s)
- Jie Min
- Department of Obstetrics and Gynecology, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Mao
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Wang
- Wuhan Aier Eye Hospital, Aier School of Ophthalmology, Central South University, Wuhan, China
| | - Xuelian He
- Department of Obstetrics and Gynecology, Wuhan Medical and Health Center for Women and Children, Wuhan, China
| | | | - Hairong Wang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
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Wu CC, Tsai CY, Lin YH, Chen PY, Lin PH, Cheng YF, Wu CM, Lin YH, Lee CY, Erdenechuluun J, Liu TC, Chen PL, Hsu CJ. Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population. Genes (Basel) 2019; 10:genes10100772. [PMID: 31581539 PMCID: PMC6826657 DOI: 10.3390/genes10100772] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
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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Affiliation(s)
- Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan.
| | - Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
| | - Pey-Yu Chen
- Department of Otolaryngology, Mackay Memorial Hospital, Taipei 10449, Taiwan.
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital Yunlin Branch, Yunlin 64041, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
| | - Che-Ming Wu
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Linkou 33302, Taiwan.
| | - Yin-Hung Lin
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan.
| | - Chee-Yee Lee
- Department of Otolaryngology, Buddhist Tzuchi General Hospital, Taichung Branch, Taichung 42743, Taiwan.
| | - Jargalkhuu Erdenechuluun
- Department of Otolaryngology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia.
- The EMJJ Otolaryngology Hospital, Ulaanbaatar 14210, Mongolia.
- Department of Otolaryngology, National Center for Maternal and Child Health, Ulaanbaatar 16060, Mongolia.
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan.
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan.
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
- Department of Otolaryngology, Buddhist Tzuchi General Hospital, Taichung Branch, Taichung 42743, Taiwan.
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Jeon SA, Park JL, Kim JH, Kim JH, Kim YS, Kim JC, Kim SY. Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing. Genomics Inform 2019; 17:e32. [PMID: 31610628 PMCID: PMC6808641 DOI: 10.5808/gi.2019.17.3.e32] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/20/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023] Open
Abstract
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 MGISEQ-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 MGISEQ-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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Affiliation(s)
- Sol A Jeon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jong Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jong-Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jeong Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yong Sung Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jin Cheon Kim
- Department of Surgery, University of Ulsan College of Medicine, Seoul, Korea
- Department of Cancer Research, Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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