massively parallel sequencing
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Diagnostics ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 207
Author(s):  
Luke Mansard ◽  
Christel Vaché ◽  
Julie Bianchi ◽  
Corinne Baudoin ◽  
Isabelle Perthus ◽  
...  

GSDME, also known as DFNA5, is a gene implicated in autosomal dominant nonsyndromic hearing loss (ADNSHL), affecting, at first, the high frequencies with a subsequent progression over all frequencies. To date, all the GSDME pathogenic variants associated with deafness lead to skipping of exon 8. In two families with apparent ADNSHL, massively parallel sequencing (MPS) integrating a coverage-based method for detection of copy number variations (CNVs) was applied, and it identified the first two causal GSDME structural variants affecting exon 8. The deleterious impact of the c.991-60_1095del variant, which includes the acceptor splice site sequence of exon 8, was confirmed by the study of the proband’s transcripts. The second mutational event is a complex rearrangement that deletes almost all of the exon 8 sequence. This study increases the mutational spectrum of the GSDME gene and highlights the crucial importance of MPS data for the detection of GSDME exon 8 deletions, even though the identification of a causal single-exon CNV by MPS analysis is still challenging.


2021 ◽  
Author(s):  
Sihan Liu ◽  
Yuanyuan Zeng ◽  
Meilin Chen ◽  
Qian Zhang ◽  
Lanchen Wang ◽  
...  

Inspecting concordance between self-reported sex and genotype-inferred sex from genomic data is a significant quality control measure in clinical genetic testing. Numerous tools have been developed to infer sex for genotyping array, whole-exome sequencing, and whole-genome sequencing data. However, improvements in sex inference from targeted gene sequencing panels are warranted. Here, we propose a new tool, seGMM, which applies unsupervised clustering (Gaussian Mixture Model) to determine the gender of a sample from the called genotype data integrated aligned reads. seGMM consistently demonstrated >99% sex inference accuracy in publicly available (1000 Genomes) and our in-house panel dataset, which achieved obviously better sex classification than existing popular tools. Compared to including features only in the X chromosome, our results show that adding additional features from Y chromosomes (e.g. reads mapped to the Y chromosome) can increase sex classification accuracy. Notably, for WES and WGS data, seGMM also has an extremely high degree of accuracy. Finally, we proved the ability of seGMM to infer sex in single patient or trio samples by combining with reference data and pinpointing potential sex chromosome abnormality samples. In general, seGMM provides a reproducible framework to infer sex from massively parallel sequencing data and has great promise in clinical genetics.


2021 ◽  
Vol 17 (12) ◽  
pp. e1009632
Author(s):  
Thomas W. Christy ◽  
Catherine A. Giannetti ◽  
Alain Laederach ◽  
Kevin M. Weeks

SHAPE-JuMP is a concise strategy for identifying close-in-space interactions in RNA molecules. Nucleotides in close three-dimensional proximity are crosslinked with a bi-reactive reagent that covalently links the 2’-hydroxyl groups of the ribose moieties. The identities of crosslinked nucleotides are determined using an engineered reverse transcriptase that jumps across crosslinked sites, resulting in a deletion in the cDNA that is detected using massively parallel sequencing. Here we introduce ShapeJumper, a bioinformatics pipeline to process SHAPE-JuMP sequencing data and to accurately identify through-space interactions, as observed in complex JuMP datasets. ShapeJumper identifies proximal interactions with near-nucleotide resolution using an alignment strategy that is optimized to tolerate the unique non-templated reverse-transcription profile of the engineered crosslink-traversing reverse-transcriptase. JuMP-inspired strategies are now poised to replace adapter-ligation for detecting RNA-RNA interactions in most crosslinking experiments.


2021 ◽  
Vol 22 (24) ◽  
pp. 13294
Author(s):  
Luke Mansard ◽  
David Baux ◽  
Christel Vaché ◽  
Catherine Blanchet ◽  
Isabelle Meunier ◽  
...  

Usher syndrome is an autosomal recessive disorder characterized by congenital hearing loss combined with retinitis pigmentosa, and in some cases, vestibular areflexia. Three clinical subtypes are distinguished, and MYO7A and USH2A represent the two major causal genes involved in Usher type I, the most severe form, and type II, the most frequent form, respectively. Massively parallel sequencing was performed on a cohort of patients in the context of a molecular diagnosis to confirm clinical suspicion of Usher syndrome. We report here 231 pathogenic MYO7A and USH2A genotypes identified in 73 Usher type I and 158 Usher type II patients. Furthermore, we present the ACMG classification of the variants, which comprise all types. Among them, 68 have not been previously reported in the literature, including 12 missense and 16 splice variants. We also report a new deep intronic variant in USH2A. Despite the important number of molecular studies published on these two genes, we show that during the course of routine genetic diagnosis, undescribed variants continue to be identified at a high rate. This is particularly pertinent in the current era, where therapeutic strategies based on DNA or RNA technologies are being developed.


2021 ◽  
Author(s):  
Hung-Cheng Tsai ◽  
Chik-On Choy ◽  
Tsai-Hung Wu ◽  
Chih-Wei Liu ◽  
Yu-Jen Pan ◽  
...  

Abstract Objectives Rheumatoid Arthritis (RA) is associated with polymorphism in major histocompatibility complex class II genes and dysregulations of CD4+ T cells which cause abnormalities in immune repertoire (iR) expression and intracellular signaling. We monitored nucleotide sequence changes in iR of immunoglobulin heavy chain (IGH), particularly complementarity determining region 3 (CDR3) during the course of treatments in RA patients using massively parallel sequencing technology.Methods CDR3 sequencing was carried out on clinical blood samples from RA patients for disease progress monitoring. The iR of each sample was measured using next generation sequencing (NGS) pipeline. Data analysis was done with a web-based iRweb server. Principal components analysis (PCA) was completed with commercial statistical pipeline. Results Datasets from 14 patients covered VDJ regions of IGH gene. D50 stayed low for all cases (mean D50 = 6.5). A pattern of shared CDR3 sequences was confirmed by a clustering pattern using PCA. Shared profile of 608 CDR3 sequences unique to the disease baseline was identified. D50 analyses revealed clonal diversity would remain low throughout the disease course even after treatment (mean D50 = 11.7 & 8.2 for csDMARD & bDMARD groups respectively) regardless of fluctuated disease activity. PCA has provided a correlation of change in immune diversity along the whole course of RA. Conclusion We have successfully constructed the experimental design, data acquisition, processing, and analysis pipeline of a high throughput massively parallel CDR3 sequences detection to be used to correlate RA disease activity and IGH CDR3 iR during disease progression with or without treatments.


2021 ◽  
Vol 159 ◽  
pp. 52-55
Author(s):  
James R. Marthick ◽  
Kelsie Raspin ◽  
Georgea R. Foley ◽  
Nicholas B. Blackburn ◽  
Annette Banks ◽  
...  

Author(s):  
Ruiyang Tao ◽  
Qiannan Xu ◽  
Shouyu Wang ◽  
Ruocheng Xia ◽  
Qi Yang ◽  
...  

2021 ◽  
Vol 26 (10) ◽  
pp. 4590
Author(s):  
K. V. Savostyanov ◽  
E. N. Basargina ◽  
E. E. Ryabova ◽  
A. A. Pushkov ◽  
I. S. Zhanin ◽  
...  

Aim. To identify the proportion of restrictive cardiomyopathy (RCM), as well as cardiomyopathy (CMP) with a restrictive type of hemodynamics among all cases of genetic CMP and to determine the relative frequencies and spectrum of nucleotide variants in Russian children with RCM, as well as to search for phenogenotypic correlations.Material and methods. The study included 689 children with CMPs. All children underwent a molecular genetic testing of the target regions of 419 genes responsible for various cardiomyopathies and channelopathies using the method of massively parallel sequencing (MPS).Results. In 668 (97,0%) children, pathogenic, likely pathogenic nucleotide variants, as well as nucleotide variants with unknown clinical significance, were identified. Of these, 45 (6,7%) patients were selected to determine the molecular genetic characteristics of RCM, 20 of whom had clinical symptoms and morphofunctional structure of RCMP (3,0%), while the remaining 25 (3,7%) children were diagnosed with another CMP type with a restrictive type of hemodynamics. In total, these patients had 41 nucleotide variants in 15 different genes, while 19 (46,3%) variants were pathogenic, 12 (29,3%) — likely pathogenic, 10 (24,4%) — uncertain clinical significance. Pathogenic and likely pathogenic variants were identified in a total of 38 (84,4%) patients, while in 19 (42,2%) patients, the pathogenic variants described earlier were found. The most common genetic marker of RCM in Russian children was TNNI3 gene mutations. In total, they were identified in 12 (25%) children: with RCP — 8 (40%) patients; with CMP with a restrictive type of hemodynamics — 4 (16%) patients. At the same time, the most common mutation of the TNNI3 gene was the nucleotide variant c.575G>A, leading to the amino acid variant p.R192H, described earlier in patients with RCM and identified by us in three (15%) unrelated children with RCM. In addition, a significant difference was found between the averaged values of N-terminal pro-brain natriuretic peptide in patients with mutations in the MYH7 and TNNI3 genes (0,0039, p<0,05), as well as between the peak flow gradient values in children with mutations in TNNI3 and FLNC genes (0,0016, p<0,05), TNNI3 and MYH7 genes (0,039, p<0,05).Conclusion. The results of this study indicate a significant genetic heterogeneity of RCM in Russian children and the need for further research aimed at finding genotype-phenotype associations in order to predict the course of the disease and select the proper therapy.


2021 ◽  
Author(s):  
Xing Zou ◽  
Guanglin He ◽  
Jing Liu ◽  
Lirong Jiang ◽  
Mengge Wang ◽  
...  

Genetic findings suggested that ethnolinguistically diverse populations in China harbor differentiated genetic structure and complex evolutionary admixture history, which provide the genetic basis and theoretical foundation for forensic biogeographical ancestry inference (BGAI). Forensic assays for BGAI among intracontinental eastern Eurasians were previously conducted mainly based on the SNPs or InDels. Microhaplotypes, as a set of closely linked SNPs within 200 base pairs, possess the advantages of both STR and SNP and have great potential in forensic ancestry inference. However, the developed forensic assay based on the ancestry informative microhaplotypes in the BGAI remained to be comprehensively explored, especially in China with enriching genetic diversity. Here, we described a new BGAI panel based on 21 novel identified ancestry informative microhaplotypes that focused on dissected finer-scale ancestry composition of Chinese populations. We initially screened all possible microhaplotypes with high Fst values among five East Asian populations and finally employed 21 candidate microhaplotypes in two multiplex SNaPshot assays. Forensic amplification efficiency and statistically/physically phased haplotypes of the 21 microhaplotypes were validated using both SNaPshot and massively parallel sequencing (MPS) platforms. Followingly, we validated the efficiency of these microhaplotypes for BGAI in 764 individuals from ten Chinese populations. Fine-scale ancestry source and ancestry proportion estimated by the principal component analysis (PCA), multidimensional scaling (MDS), phylogenetic tree and model-based STRUCTURE among worldwide populations and East Asians showed that our customized panel could provide a higher discrimination resolution in both continental population stratification and East Asian regional substructure. East Asian populations could be further classified into linguistically/geographically different intracontinental subpopulations (Tibeto-Burman, Tai-Kadai and others). Finally, we obtained a higher estimated accuracy using training and tested datasets in the microhaplotype-based panel than traditional SNP-based panels. Generally, the above results demonstrated that this microhaplotype panel was robust and suitable for forensic BGAI in Chinese populations, which not only provided a high discriminatory power for continental populations but also discriminated East Asians into linguistically restricted subpopulations.


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