scholarly journals Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness

2021 ◽  
Vol 12 ◽  
Author(s):  
Penghui Chen ◽  
Longhao Wang ◽  
Yongchuan Chai ◽  
Hao Wu ◽  
Tao Yang
Keyword(s):  
Next Generation Sequencing ◽  
Splice Site ◽  
Negative Impact ◽  
Intron Retention ◽  
Exon Skipping ◽  
Next Generation Sequencing Data ◽  
Functional Verification ◽  
Next Generation ◽  
Hereditary Deafness ◽  
Generation Sequencing

Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A > T and c.580G > A in EYA4, c.322-57_322-8del in PAX3, c.991-15_991-13del in DFNA5, c.6087-3T > G in PTPRQ and c.164+5G > A in USH1G. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A > T and c.580G > A in EYA4, c.991-15_991-13del in DFNA5), intron retention (c.322-57_322-8del in PAX3), exon skipping and intron retention (c.6087-3T > G in PTPRQ) and shortening of exon (c.164+5G > A in USH1G). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis.

Targeted DNA- and RNA-based next-generation sequencing for identifying MET exon 14 alterations in pulmonary sarcomatoid carcinoma.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e20591-e20591
Author(s):  
Jianming Ying ◽  
Lianju Gao ◽  
Yan Li ◽  
Bing Liu ◽  
Lamei Deng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Splice Site ◽  
Point Mutations ◽  
Sarcomatoid Carcinoma ◽  
Exon Skipping ◽  
Performance Comparison ◽  
Next Generation ◽  
Dna And Rna ◽  
Pulmonary Sarcomatoid Carcinoma ◽  
Generation Sequencing

e20591 Background:Highly diverse somatic splice site alteration at MET exon 14 ( METex14) result in exon skipping, which is supposed to be a therapeutic target in NSCLC. Here we report detection of METex14 alterations using targeted DNA- and RNA-based Next-Generation Sequencing (NGS) in pulmonary sarcomatoid carcinoma (PSC) with a high frequency of METex14 skipping. Methods: Tumor specimens were collected from 100 Chinese PSC patients. DNA and RNA were subject to targeted NGS, allowing the detection of somatic splice site alterations and intragenic METex14 skipping respectively. Then, somatic mutations that lead to METex14 skipping were recognized. Meanwhile, cross-platform performance comparison for detecting MET exon 14 skipping was achieved. Moreover, Sanger sequencing was also performed on the METex14-positive specimens. Results: So far, we have detected genetic aberrations in 34 FFPE samples. For RNA-based NGS, METex14 skipping was identified in 8 (23.5%) of 34 patient cases. The population frequency was accordant to the reported percent of 22% (PMID: 26215952). And 5 (62.5%) of 8 METex14-positive patients were detected somatic splice site mutations by DNA-based NGS, including 4 cases with known point mutations at the 3’ splice region and one case with a novel deletion (chr7: 116412027- 116412042) at MET exon14 region, which is newly discovered. No somatic mutation was found at the splice junctions of METex14 in the remaining 3 samples using DNA-based NGS. Conclusions: Mutational events of MET leading to exon 14 skipping are frequent occurred in Chinese PSC patients. Our study also suggests that RNA-based NGS could identify more METex14 skipping, and thus provide more accurate results than DNA-based NGS.

scholarly journals NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

2021 ◽  
Author(s):  
Anne Krogh Nøhr ◽  
Kristian Hanghøj ◽  
Genis Garcia Erill ◽  
Zilong Li ◽  
Ida Moltke ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Software Tool ◽  
Estimation Methods ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C ++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

scholarly journals recoup: flexible and versatile signal visualization from next generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Panagiotis Moulos
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Special Focus ◽  
Next Generation ◽  
Sequencing Data ◽  
User Friendliness ◽  
Computational Environment ◽  
Level Data ◽  
Data Signal ◽  
Generation Sequencing

Abstract Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.

scholarly journals BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

2011 ◽  
Vol 9 (6) ◽  
pp. 238-244 ◽  
Author(s):  
Tongwu Zhang ◽  
Yingfeng Luo ◽  
Kan Liu ◽  
Linlin Pan ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quality Assessment ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing
Sign in / Sign up

Export Citation Format

Share Document