scholarly journals Development and Validation of a Next-Generation Sequencing Panel for Syndromic and Nonsyndromic Hearing Loss

2020 ◽  
Vol 5 (3) ◽  
pp. 467-479 ◽  
Author(s):  
Malinda Butz ◽  
Amber McDonald ◽  
Patrick A Lundquist ◽  
Melanie Meyer ◽  
Sean Harrington ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Copy Number Variants ◽  
Analytical Sensitivity ◽  
Nonsyndromic Hearing Loss ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Small Indels ◽  
Syndromic Hearing Loss ◽  
Generation Sequencing

Abstract Background Deafness and hearing loss are common conditions that can be seen independently or as part of a syndrome and are often mediated by genetic causes. We sought to develop and validate a hereditary hearing loss panel (HHLP) to detect single nucleotide variants (SNVs), insertions and deletions (indels), and copy number variants (CNVs) in 166 genes related to nonsyndromic and syndromic hearing loss. Methods We developed a custom-capture next-generation sequencing (NGS) reagent to detect all coding regions, ±10 flanking bp, for the 166 genes related to nonsyndromic and syndromic hearing loss. Our validation consisted of testing 52 samples to establish accuracy, reproducibility, and analytical sensitivity. In addition to NGS, supplementary methods, including multiplex ligation-dependent probe amplification, long-range PCR, and Sanger sequencing, were used to ensure coverage of regions that had high complexity or homology. Results We observed 100% positive and negative percentage agreement for detection of SNVs (n = 362), small indels (1–22 bp, n = 25), and CNVs (gains, n = 8; losses, n = 17). Finally, we showed that this assay was able to detect variants with a variant allele frequency ≥20% for SNVs and indels and ≥30% to 35% for CNVs. Conclusions We validated an HHLP that detects SNVs, indels, and CNVs in 166 genes related to syndromic and nonsyndromic hearing loss. The results of this assay can be utilized to confirm a diagnosis of hearing loss and related syndromic disorders associated with known causal genes.

scholarly journals Design and validation of a next generation sequencing assay for hereditaryBRCA1andBRCA2mutation testing

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2162 ◽  
Author(s):  
Hyunseok P. Kang ◽  
Jared R. Maguire ◽  
Clement S. Chu ◽  
Imran S. Haque ◽  
Henry Lai ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variants ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Cancer Syndrome ◽  
Cancer Screen ◽  
Inherited Cancer ◽  
Increased Risk ◽  
Large Rearrangements ◽  
Generation Sequencing

Hereditary breast and ovarian cancer syndrome, caused by a germline pathogenic variant in theBRCA1orBRCA2(BRCA1/2) genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have aBRCA1/2mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in theBRCA1andBRCA2genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 114-sample validation set consisting of samples from cell lines and deidentified patient samples, including 36 samples withBRCA1/2pathogenic germline mutations.

scholarly journals Clinical and genetic study of twelve Chinese Han families with non-syndromic deafness

2019 ◽  
Author(s):  
Di Wu ◽  
Weiyuan Huang ◽  
Shuo Li ◽  
Jie Zhang ◽  
Xiaohua Chen ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Accurate Diagnosis ◽  
Next Generation ◽  
Phenotype Correlation ◽  
Chinese Han ◽  
Targeted Next Generation Sequencing ◽  
Whole Exome ◽  
Syndromic Hearing Loss ◽  
Generation Sequencing

Abstract BACKGROUND: Non-syndromic hearing loss is clinically and genetically heterogeneous. In this study, we characterized the clinical features of twelve Chinese Han deaf families in which mutations in common deafness genes GJB2 , SLC26A4 and MT-RNR1 were excluded. RESULTS: Targeted next-generation sequencing of 147 known deafness genes was performed in probands of ten families, while whole-exome sequencing was applied in those of the rest two. Pathogenic mutations in a total of 11 rare deafness genes, OTOF , CDH23 , PCDH15 , PDZD7 , ADGRV1 , KARS , OTOG , GRXCR2 , MYO6 , GRHL2 , and POU3F4 , were identified in all 12 probands, with 17 mutations being novel. Intrafamilial co-segregation of the mutations and the deafness phenotype were confirmed by Sanger sequencing. CONCLUSIONS: Our results expanded the mutation spectrum and genotype-phenotype correlation of non-syndromic hearing loss in Chinese Hans and also emphasized the importance of combining both next-generation sequencing and detailed auditory evaluation to achieve a more accurate diagnosis for non-syndromic hearing loss.

Identifying the distant metastasis genes by next-generation sequencing panel in nasopharyngeal carcinoma.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e18547-e18547
Author(s):  
Man Hu ◽  
Jinming Yu ◽  
Zihan Zhou ◽  
Peifeng Li ◽  
Xianbin Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nasopharyngeal Carcinoma ◽  
Distant Metastasis ◽  
Copy Number Variants ◽  
Intensity Modulated Radiotherapy ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Chi Square ◽  
Exact Test ◽  
Generation Sequencing

e18547 Background: Even though local and regional controls have been substantially improved in nasopharyngeal carcinoma (NPC) in the contemporary era of intensity-modulated radiotherapy with extensive use of combined chemotherapy, the distant metastasis becomes the major cause of treatment failure and cancer-related death. To date, the genes contributed to metastasis of NPC is still unclear. The aim of this study was to identify the genes which lead to distant metastasis. Methods: A total of forty primary nonkeratinizing NPC patients were diagnosed at Shandong Cancer Hospital in this study. The formaldehyde-fixed paraffin embedded (FFPE) taken from primary sites or metastatic lymph nodes were performed next-generation sequencing (NGS) panel (Shanghai OrigiMed Co., Ltd.) to determine variated genes, such as single nucleotide variants (SNV), copy number variants (CNV) and rearrangement. These patients were followed up until Febr. 8, 2020. The genes related to distant metastasis were identified by logistic regression. Moreover, this study compared the frequency of mutated gene between our data and Catalog of Somatic Mutations in Cancer (COSMIC) database by the Chi-square test or Fisher’s exact test. Results: The study included 31 men and 9 women. The median age of the patients at diagnosis was 47 years (range 15–71 years). With the median follow-up of 10.6 months (range 16.8–72.3 months), 7 patients had distant metastasis and 1 undergone recurrent. Notably, EMSY and MCL1 variants were contributed to NPC distant metastasis (OR = 31, P = 0.049). The top eight SNV of genes in our study were CYLD, KMT2D, BAP1, EP300, TP53, ATM, NFKBIA and SPEN. When compared to COSMIC database, the mutant frequencies of CYLD, EP300 and BAP1 in our study were significantly higher than that of COSMIC database. However, the mutant frequencies of IDH2 and KMT2C were significantly lower than COSMIC database. Conclusions: This is the first study which suggests that EMSY and MCL1 variants were involved in the metastasis of NPC. The study identified 5 genes, which mutation frequency is significantly different from the COSMIC database. The study provided a molecular basis for a comprehensive understanding of, and exploring targeted therapies for nasopharyngeal carcinoma.

Next generation sequencing study in a cohort of Italian patients with syndromic hearing loss

2019 ◽  
Vol 381 ◽  
pp. 107769 ◽  
Author(s):  
Stefania Lenarduzzi ◽  
Anna Morgan ◽  
Flavio Faletra ◽  
Stefania Cappellani ◽  
Marcello Morgutti ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Syndromic Hearing Loss ◽  
Generation Sequencing
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