scholarly journals Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy

2015 ◽  
Vol 16 (5) ◽  
pp. 769-779 ◽  
Author(s):  
Sabine C. Mueller ◽  
Christina Backes ◽  
Jan Haas ◽  
Hugo A. Katus ◽  
Benjamin Meder ◽  
...  
2021 ◽  
Author(s):  
Chang Li ◽  
Degui Zhi ◽  
Kai Wang ◽  
Xiaoming Liu

We present the pathogenicity prediction models MetaRNN and MetaRNN-indel to help identify and prioritize rare nonsynonymous single nucleotide variants (nsSNVs) and non-frameshift insertion/deletions (nfINDELs) using deep learning and context annotations. Employing independent test datasets, we demonstrate that these new models outperform state-of-the-art competitors and achieve a more interpretable score distribution. MetaRNN executables and precomputed scores are available at http://www.liulab.science/MetaRNN.


2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
GUSTAVO GRELONI ◽  
Federico Varela ◽  
Griselda Bratti ◽  
Guillermo Rosa Diez ◽  
Celia Dos Santos ◽  
...  

Abstract Background and Aims Advances in the past 2 decades have shown atypical hemolytic uremic syndrome (aHUS) to be a disorder of the alternative pathway of complement. Most aHUS cases involve sequence variations in genes encoding complement proteins The term pregnancy associated aHUS (P-aHUS) refer to the thrombotic microangiopathy (TMA) that result from uncontrolled complement activation during pregnancy or the postpartum period. P-aHUS is a devastating systemic disease, with high maternal mortality and morbidity rates, in the pre-eculizumab era. The term ‘C3 glomerulopathy’ (C3GN) encompasses a heterogeneous spectrum of immune-mediated nephropathies that share a common pathological feature, glomerular deposition of C3. This entity may progress to advanced stages of chronic kidney disease and shares a common genetic risk factors with aHUS. Even more, some authors even suggest that C3GN and aHUS represent two forms of a disease spectrum with a common pathogenic principle. Here, we report this rare association and describe the family genetic variants that could cause it Method We describe the clinical and laboratoy data of a patient with the association of aHUS and C3 Glomerulopathy. A genetic study was performed and her available relatives were also screened for mutations/polymorphisms in aHUS-associated complement genes. After extracting gDNA from whole blood (Wizard Genomic DNA Purification Kit, Promega), PCR products of coding sequences and intronic flanking regions of complement genes were sequenced by ABI PRISM 310 Genetic Analyzer (Applied Biosystems). In silico analysis for pathogenicity was completed with Polyphen2-HDIV, PhyloP/Phastcons (MutationTaster), SIFT and PANTHER. All the participants provided informed written consent Results In 3/2012 a 27-year-old patient, with no family history, started his current illness one month after his first natural birth, with acute renal failure and microangiopathic hemolytic anemia, demonstrating a severe TMA in a renal biopsy. Laboratory results showed low C3 serum levels, but C4 were normal, haptoglobine was undetectably low, and all ADAMTS13 parameters were normal. Her urine tests showed also glomerular hematuria and proteinuria in the nephrotic range. She was treated with plasmapheresis and fresh frozen plasma with hematological improvement, but hemodialysis was required for more than 3 months. Despite partial recovery of renal function, six months later reappeared anemia and developed severe arterial hypertension, congestive heart failure and progressive renal insufficiency. Diagnosis of aHUS was made and start treatment with eculizumab with progressive recovery of renal function in the following months. Nevertheless the C3 serum levels persisted low and the proteinuria and hematuria did not change even after long term treatment with eculizumab. Retrospectively, her urynalisis before the pregnant showed proteinuria and hematuria, and a revision of a renal biopsy revealed the presence of dominant C3 deposits in the immunofluorescence, and electrondense deposits in the electronic microscopy, suggesting the diagnostic of C3GN. In a genetic study two novel single nucleotide variants were founded (CFH c.575G>A, p.C192Y (exon 5) (NM_000186), predicted to be pathogenic by 4 of 5 available pathogenicity prediction programs; and CFI c.1189G>T, p.V397L (exon 11) (NM_000204), predicted pathogenic by 0 of 6 available pathogenicity prediction programs). (Figure 1) Conclusion We present here the family genetic bases of a patient who developed a C3GN and a aHUS with a different response to treatment with eculizumab. In this case we identified two novel genetic variants in the CFH and CFI genes in a patient with aHUS, who inherited one variant from each parent. Although the CFI variant is predicted to be benign, the CFH variant is predicted to be damaging. It is located in exon 5, which encodes a portion of the factor H protein implicated in binding to C3b


Author(s):  
Renata Parissi Buainain ◽  
Matheus Negri Boschiero ◽  
Bruno Camporeze ◽  
Paulo Henrique Pires de Aguiar ◽  
Fernando Augusto Lima Marson ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Nayoung Han ◽  
Jung Mi Oh ◽  
In-Wha Kim

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.


Author(s):  
Pauline Arnaud ◽  
Hélène Morel ◽  
Olivier Milleron ◽  
Laurent Gouya ◽  
Christine Francannet ◽  
...  

Abstract Purpose Individuals with mosaic pathogenic variants in the FBN1 gene are mainly described in the course of familial screening. In the literature, almost all these mosaic individuals are asymptomatic. In this study, we report the experience of our team on more than 5,000 Marfan syndrome (MFS) probands. Methods Next-generation sequencing (NGS) capture technology allowed us to identify five cases of MFS probands who harbored a mosaic pathogenic variant in the FBN1 gene. Results These five sporadic mosaic probands displayed classical features usually seen in Marfan syndrome. Combined with the results of the literature, these rare findings concerned both single-nucleotide variants and copy-number variations. Conclusion This underestimated finding should not be overlooked in the molecular diagnosis of MFS patients and warrants an adaptation of the parameters used in bioinformatics analyses. The five present cases of symptomatic MFS probands harboring a mosaic FBN1 pathogenic variant reinforce the fact that apparently asymptomatic mosaic parents should have a complete clinical examination and a regular cardiovascular follow-up. We advise that individuals with a typical MFS for whom no single-nucleotide pathogenic variant or exon deletion/duplication was identified should be tested by NGS capture panel with an adapted variant calling analysis.


2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Fatao Liu ◽  
Yongsheng Li ◽  
Dongjian Ying ◽  
Shimei Qiu ◽  
Yong He ◽  
...  

AbstractNeuroendocrine carcinoma (NEC) of the gallbladder (GB-NEC) is a rare but extremely malignant subtype of gallbladder cancer (GBC). The genetic and molecular signatures of GB-NEC are poorly understood; thus, molecular targeting is currently unavailable. In the present study, we applied whole-exome sequencing (WES) technology to detect gene mutations and predicted somatic single-nucleotide variants (SNVs) in 15 cases of GB-NEC and 22 cases of general GBC. In 15 GB-NECs, the C > T mutation was predominant among the 6 types of SNVs. TP53 showed the highest mutation frequency (73%, 11/15). Compared with neuroendocrine carcinomas of other organs, significantly mutated genes (SMGs) in GB-NECs were more similar to those in pulmonary large-cell neuroendocrine carcinomas (LCNECs), with driver roles for TP53 and RB1. In the COSMIC database of cancer-related genes, 211 genes were mutated. Strikingly, RB1 (4/15, 27%) and NAB2 (3/15, 20%) mutations were found specifically in GB-NECs; in contrast, mutations in 29 genes, including ERBB2 and ERBB3, were identified exclusively in GBC. Mutations in RB1 and NAB2 were significantly related to downregulation of the RB1 and NAB2 proteins, respectively, according to immunohistochemical (IHC) data (p values = 0.0453 and 0.0303). Clinically actionable genes indicated 23 mutated genes, including ALK, BRCA1, and BRCA2. In addition, potential somatic SNVs predicted by ISOWN and SomVarIUS constituted 6 primary COSMIC mutation signatures (1, 3, 30, 6, 7, and 13) in GB-NEC. Genes carrying somatic SNVs were enriched mainly in oncogenic signaling pathways involving the Notch, WNT, Hippo, and RTK-RAS pathways. In summary, we have systematically identified the mutation landscape of GB-NEC, and these findings may provide mechanistic insights into the specific pathogenesis of this deadly disease.


Transfusion ◽  
2021 ◽  
Author(s):  
Loann Raud ◽  
Marlène Le Tertre ◽  
Léonie Vigneron ◽  
Chandran Ka ◽  
Gaëlle Richard ◽  
...  

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gavin W. Wilson ◽  
Mathieu Derouet ◽  
Gail E. Darling ◽  
Jonathan C. Yeung

AbstractIdentifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to “collapse” molecular duplicates and accurately identify variants and their co-expression. We demonstrate that scSNV is fast, with a reduced false-positive variant call rate, and enables the co-detection of genetic variants and A>G RNA edits across twenty-two samples.


2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Ianthe A. E. M. van Belzen ◽  
Alexander Schönhuth ◽  
Patrick Kemmeren ◽  
Jayne Y. Hehir-Kwa

AbstractCancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.


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