Genetic testing for sporadic hearing loss using targeted massively parallel sequencing identifies 10 novel mutations

2014 ◽  
Vol 87 (6) ◽  
pp. 588-593 ◽  
Author(s):  
X. Gu ◽  
L. Guo ◽  
H. Ji ◽  
S. Sun ◽  
R. Chai ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Genetic Testing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Novel Mutations ◽  
Parallel Sequencing

Brief Report of Variants Detected in Hereditary Hearing Loss Cases in Iran over a 3-Year Period

2020 ◽  
Author(s):  
Niloofar BAZAZZADEGAN ◽  
Raheleh VAZEHAN ◽  
Mahsa FADAEE ◽  
Zohreh FATTAHI ◽  
Ayda ABOLHASSANI ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Genetic Testing ◽  
Massively Parallel Sequencing ◽  
Cost Effective ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Hereditary Hearing Loss ◽  
Targeted Genomic Enrichment ◽  
Novel Variants ◽  
Autosomal Recessive Pattern

Background: Diagnosis of hereditary hearing loss (HHL) as a heterogeneous disorder is very important especially in countries with high rates of consanguinity where the autosomal recessive pattern of inheritance is prevalent. Techniques such as next-generation sequencing, a comprehensive genetic test using targeted genomic enrichment and massively parallel sequencing (TGE + MPS), have made the diagnosis more cost-effective. The aim of this study was to determine HHL variants with comprehensive genetic testing in our country. of this study was to determine HHL variants with comprehensive genetic testing in our country. Methods: Fifty GJB2 negative individuals with HHL were referred to the Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, one of the reference diagnostic genetic laboratories in Iran, during a 3-year period between 2014 and 2017. They were screened with the OtoSCOPE test, the targeted genomic enrichment and massively parallel sequencing (TGE + MPS) platform after a detailed history had been taken along with clinical evaluation. Results: Among 32 out of 50 GJB2 negative patients (64%), 34 known pathogenic and novel variants were detected of which 16 (47%) were novel, identified in 10 genes of which the most prevalent were CDH23, MYO7A and MYO15A. Conclusion: These results provide a foundation from which to make appropriate recommendations for the use of comprehensive genetic testing in the evaluation of Iranian patients with hereditary hearing loss.

Novel Mutations in GRXCR1 at DFNB25 Lead to Progressive Hearing Loss and Dizziness

2015 ◽  
Vol 124 (1_suppl) ◽  
pp. 129S-134S ◽  
Author(s):  
Kentaro Mori ◽  
Ikuyo Miyanohara ◽  
Hideaki Moteki ◽  
Shin-ya Nishio ◽  
Yuichi Kurono ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Compound Heterozygous ◽  
Nonsyndromic Hearing Loss ◽  
Novel Mutations ◽  
Progressive Hearing Loss ◽  
Severe Hearing Loss ◽  
Parallel Sequencing ◽  
Targeted Genomic Enrichment

Objective: We identified 2 patients in 1 family who had novel mutations in GRXCR1, which caused progressive hearing loss. Methods: One thousand one hundred twenty Japanese hearing loss patients with sensorineural hearing loss from unrelated families were enrolled in this study. Targeted genomic enrichment with massively parallel sequencing of all known nonsyndromic hearing loss genes was used to identify the genetic causes of hearing loss. Results: In this study, 2 affected individuals with compound heterozygous mutations—c.439C>T (p.R147C) and c.784C>T (p.R262X)—in GRXCR1 were identified. The proband had moderate to severe hearing loss and suffered from dizziness with bilateral canal paralysis. Conclusion: Our cases are the first identified in the Japanese population and are consistent with previously reported cases. The frequency of mutations in GRXCR1 seems to be extremely rare. This study underscores the importance of using comprehensive genetic testing for hearing loss. Furthermore, longitudinal audiologic assessment and precise vestibular testing are necessary for a better understanding of the mechanisms of hearing loss and vestibular dysfunction caused by GRXCR1 mutations.

scholarly journals Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing

2010 ◽  
Vol 107 (49) ◽  
pp. 21104-21109 ◽  
Author(s):  
A. E. Shearer ◽  
A. P. DeLuca ◽  
M. S. Hildebrand ◽  
K. R. Taylor ◽  
J. Gurrola ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Genetic Testing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Hereditary Hearing Loss

scholarly journals USH2A mutations identified by massively parallel sequencing in 3 children with sensorineural hearing loss

2019 ◽  
Vol 62 (3) ◽  
pp. 218-223
Author(s):  
Mayuri Okami ◽  
Momoko Tsukahara ◽  
Kenji Okami ◽  
Masahiro Iida ◽  
Kazumi Takahashi ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Sensorineural Hearing Loss ◽  
Massively Parallel Sequencing ◽  
Sensorineural Hearing ◽  
Massively Parallel ◽  
Parallel Sequencing

Comprehensive preimplantation genetic testing by massively parallel sequencing

2020 ◽  
Author(s):  
Songchang Chen ◽  
Xuyang Yin ◽  
Sijia Zhang ◽  
Jun Xia ◽  
Ping Liu ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genome Sequencing ◽  
Massively Parallel Sequencing ◽  
Science And Technology ◽  
Family Members ◽  
Snp Array ◽  
Massively Parallel ◽  
Preimplantation Genetic Testing ◽  
Parallel Sequencing ◽  
Genome Wide

Abstract STUDY QUESTION Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)? SUMMARY ANSWER Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data. WHAT IS KNOWN ALREADY Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods. STUDY DESIGN, SIZE, DURATION In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated. PARTICIPANTS/MATERIALS, SETTING, METHODS A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed. MAIN RESULTS AND THE ROLE OF CHANCE For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated. LIMITATIONS, REASONS FOR CAUTION The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping. WIDER IMPLICATIONS OF THE FINDINGS WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods. STUDY FUNDING/COMPETING INTEREST(S) This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai ‘Rising Stars of Medical Talent’ Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.

scholarly journals Laboratory Verification of a BRCA1 and BRCA2 Massively Parallel Sequencing Assay from Wet Bench to Bioinformatics for Germline DNA Analysis

2021 ◽  
Author(s):  
Kok-Siong Poon ◽  
Lily Chiu ◽  
Karen Mei-Ling Tan
Keyword(s):  
Genetic Testing ◽  
Sanger Sequencing ◽  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Brca1 And Brca2 ◽  
Clinical Diagnostic Laboratory ◽  
Parallel Sequencing ◽  
Miseq Platform ◽  
Brca Genetic Testing

Abstract Introduction A robust genetic test for BRCA1 and BRCA2 genes is necessary for the diagnosis, prognosis, and treatment of patients with hereditary breast and ovarian cancer. We evaluated a commercial amplicon-based massively parallel sequencing (MPS) assay, BRCA MASTR Plus on the MiSeq platform, for germline BRCA genetic testing. Methods This study was performed on 31 DNA from cell lines and proficiency testing samples to establish the accuracy of the assay. A reference cell line DNA, NA12878 was used to determine the reproducibility of the assay. Discordant MPS result was resolved orthogonally by the current gold-standard Sanger sequencing method. Results The analytical accuracy, sensitivity, and specificity for variant detection were 93.55, 92.86, and 100.00%, respectively. Both sequencing depth and variant allele frequencies were highly reproducible by comparing the NA12878 DNA tested in three separate runs. The single discordant result, later confirmed by Sanger sequencing was due to the inability of the MASTR Reporter software to identify a 40-bp deletion in BRCA1. Conclusion The BRCA MASTR Plus assay on the MiSeq platform is accurate and reproducible for germline BRCA genetic testing, making it suitable for use in a clinical diagnostic laboratory. However, Sanger sequencing may still serve as a confirmatory method to improve diagnostic capability of the MPS assay.

Non-ocular Stickler Syndrome With a Novel Mutation in COL11A2 Diagnosed by Massively Parallel Sequencing in Japanese Hearing Loss Patients

2015 ◽  
Vol 124 (1_suppl) ◽  
pp. 111S-117S ◽  
Author(s):  
Yoh-ichiro Iwasa ◽  
Hideaki Moteki ◽  
Mitsuru Hattori ◽  
Ririko Sato ◽  
Shin-ya Nishio ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Clinical Symptoms ◽  
Massively Parallel Sequencing ◽  
Novel Mutation ◽  
Genetic Diagnosis ◽  
Analysis Data ◽  
Massively Parallel ◽  
Stickler Syndrome ◽  
Parallel Sequencing ◽  
First Case

Objectives: This study aims to document the clinical features of patients with COL11A2 mutations and to describe the usefulness of massively parallel sequencing. Methods: One thousand one hundred twenty (1120) Japanese hearing loss patients from 53 ENT departments nationwide participated in this study. Massively parallel sequencing of 63 genes implicated in hearing loss was performed to identify the genetic causes in the Japanese hearing loss patients. Results: A novel mutation in COL11A2 (c.3937_3948delCCCCCAGGGCCA) was detected in an affected family, and it was segregated in all hearing loss individuals. The clinical findings of this family were compatible with non-ocular Stickler syndrome. Orofacial features of mid-facial hypoplasia and slowly progressive mild to moderate hearing loss were also presented. Audiological examinations showed favorable auditory performance with hearing aid(s). Conclusion: This is the first case report of the genetic diagnosis of a non-ocular Stickler syndrome family in the Japanese population. We suggest that it is important to take both genetic analysis data and clinical symptoms into consideration to make an accurate diagnosis.

Sign in / Sign up

Export Citation Format

Share Document