scholarly journals Identification and Characterization of Splicing Defects by Single-Molecule Real-Time Sequencing Technology (PacBio)

2020 ◽  
Vol 7 (4) ◽  
pp. 477-481
Author(s):  
Marco Savarese ◽  
Talha Qureshi ◽  
Annalaura Torella ◽  
Pia Laine ◽  
Teresa Giugliano ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Genetic Diseases ◽  
Disease Genes ◽  
Test Results ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Dna Test ◽  
Splicing Defects

Although DNA-sequencing is the most effective procedure to achieve a molecular diagnosis in genetic diseases, complementary RNA analyses are often required. Reverse-Transcription polymerase chain reaction (RT-PCR) is still a valuable option when the clinical phenotype and/or available DNA-test results address the diagnosis toward a gene of interest or when the splicing effect of a single variant needs to be assessed. We use Single-Molecule Real-Time sequencing to detect and characterize splicing defects and single nucleotide variants in well-known disease genes (DMD, NF1, TTN). After proper optimization, the procedure could be used in the diagnostic setting, simplifying the workflow of cDNA analysis.

scholarly journals A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yavor K. Bozhilov ◽  
Damien J. Downes ◽  
Jelena Telenius ◽  
A. Marieke Oudelaar ◽  
Emmanuel N. Olivier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Diseases ◽  
Regulatory Elements ◽  
Base Change ◽  
Dependent Manner ◽  
Globin Genes ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Super Enhancer ◽  
Single Base Change

AbstractMany single nucleotide variants (SNVs) associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements. Some SNVs may also create entirely new regulatory elements which change gene expression, but the mechanism by which they do so is largely unknown. Here we show that a single base change in an otherwise unremarkable region of the human α-globin cluster creates an entirely new promoter and an associated unidirectional transcript. This SNV downregulates α-globin expression causing α-thalassaemia. Of note, the new promoter lying between the α-globin genes and their associated super-enhancer disrupts their interaction in an orientation-dependent manner. Together these observations show how both the order and orientation of the fundamental elements of the genome determine patterns of gene expression and support the concept that active genes may act to disrupt enhancer-promoter interactions in mammals as in Drosophila. Finally, these findings should prompt others to fully evaluate SNVs lying outside of known regulatory elements as causing changes in gene expression by creating new regulatory elements.

scholarly journals Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Dóra Tombácz ◽  
Zsolt Balázs ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
Attila Szűcs ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Long Read

scholarly journals Reference exome data for a Northern Brazilian population

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Alexia L. Weeks ◽  
Richard W. Francis ◽  
Joao I. C. F. Neri ◽  
Nathaly M. C. Costa ◽  
Nivea M. R. Arrais ◽  
...  
Keyword(s):  
Rare Diseases ◽  
Sequence Data ◽  
Genetic Diseases ◽  
Specific Reference ◽  
Single Nucleotide Variants ◽  
Data Set ◽  
Single Nucleotide ◽  
Rare Genetic Diseases ◽  
Genetics And Genomics ◽  
Brazilian Cohort

Abstract Exome sequencing is widely used in the diagnosis of rare genetic diseases and provides useful variant data for analysis of complex diseases. There is not always adequate population-specific reference data to assist in assigning a diagnostic variant to a specific clinical condition. Here we provide a catalogue of variants called after sequencing the exomes of 45 babies from Rio Grande do Nord in Brazil. Sequence data were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 612,761 variants were identified in at least one individual in this Brazilian Cohort, including 559,448 single nucleotide variants (SNVs) and 53,313 insertion/deletions. Of these, 58,111 overlapped with nonsynonymous (nsSNVs) or splice site (ssSNVs) SNVs in dbNSFP. As an aid to clinical diagnosis of rare diseases, we used the American College of Medicine Genetics and Genomics (ACMG) guidelines to assign pathogenic/likely pathogenic status to 185 (0.32%) of the 58,111 nsSNVs and ssSNVs. Our data set provides a useful reference point for diagnosis of rare diseases in Brazil. (169 words).

Identification and characterization of human xylosyltransferase II promoter single nucleotide variants

2015 ◽  
Vol 458 (4) ◽  
pp. 901-907
Author(s):  
Isabel Faust ◽  
Kai Oliver Böker ◽  
Christina Eirich ◽  
Dagmar Akkermann ◽  
Joachim Kuhn ◽  
...  
Keyword(s):  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Identification And Characterization

scholarly journals Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

2011 ◽  
Vol 40 (4) ◽  
pp. e29-e29 ◽  
Author(s):  
Tyson A. Clark ◽  
Iain A. Murray ◽  
Richard D. Morgan ◽  
Andrey O. Kislyuk ◽  
Kristi E. Spittle ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Dna Methyltransferase

scholarly journals Characterization of single nucleotide variants of OPN3 gene in melanocytic nevi and melanoma

2021 ◽  
pp. 100006
Author(s):  
Wei Zhang ◽  
Jianglong Feng ◽  
Wen Zeng ◽  
Zhixu Zhou ◽  
Yu Wang ◽  
...  
Keyword(s):  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Melanocytic Nevi

scholarly journals The integrity of the U12 snRNA 3′ stem–loop is necessary for its overall stability

2021 ◽  
Vol 49 (5) ◽  
pp. 2835-2847
Author(s):  
Antto J Norppa ◽  
Mikko J Frilander
Keyword(s):  
Steady State ◽  
Early Onset ◽  
Human Population ◽  
Genetic Diseases ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Stem Loop ◽  
Snrna Gene ◽  
Small Nuclear Rnas ◽  
Overall Stability

Abstract Disruption of minor spliceosome functions underlies several genetic diseases with mutations in the minor spliceosome-specific small nuclear RNAs (snRNAs) and proteins. Here, we define the molecular outcome of the U12 snRNA mutation (84C>U) resulting in an early-onset form of cerebellar ataxia. To understand the molecular consequences of the U12 snRNA mutation, we created cell lines harboring the 84C>T mutation in the U12 snRNA gene (RNU12). We show that the 84C>U mutation leads to accelerated decay of the snRNA, resulting in significantly reduced steady-state U12 snRNA levels. Additionally, the mutation leads to accumulation of 3′-truncated forms of U12 snRNA, which have undergone the cytoplasmic steps of snRNP biogenesis. Our data suggests that the 84C>U-mutant snRNA is targeted for decay following reimport into the nucleus, and that the U12 snRNA fragments are decay intermediates that result from the stalling of a 3′-to-5′ exonuclease. Finally, we show that several other single-nucleotide variants in the 3′ stem-loop of U12 snRNA that are segregating in the human population are also highly destabilizing. This suggests that the 3′ stem-loop is important for the overall stability of the U12 snRNA and that additional disease-causing mutations are likely to exist in this region.

scholarly journals DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning

2021 ◽  
Author(s):  
Azza Althagafi ◽  
Lamia Alsubaie ◽  
Nagarajan Kathiresan ◽  
Katsuhiko Mineta ◽  
Taghrid Aloraini ◽  
...  
Keyword(s):  
Research Group ◽  
Genetic Diseases ◽  
Computational Method ◽  
Structural Variants ◽  
Single Nucleotide Variants ◽  
Structural Genomic ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Molecular Features ◽  
Gene Functions

AbstractMotivationStructural genomic variants account for much of human variability and are involved in several diseases. Structural variants are complex and may affect coding regions of multiple genes, or affect the functions of genomic regions in different ways from single nucleotide variants. Interpreting the phenotypic consequences of structural variants relies on information about gene functions, haploinsufficiency or triplosensitivity, and other genomic features. Phenotype-based methods to identifying variants that are involved in genetic diseases combine molecular features with prior knowledge about the phenotypic consequences of altering gene functions. While phenotype-based methods have been applied successfully to single nucleotide variants, as well as short insertions and deletions, the complexity of structural variants makes it more challenging to link them to phenotypes. Furthermore, structural variants can affect a large number of coding regions, and phenotype information may not be available for all of them.ResultsWe developed DeepSVP, a computational method to prioritize structural variants involved in genetic diseases by combining genomic information with information about gene functions. We incorporate phenotypes linked to genes, functions of gene products, gene expression in individual celltypes, and anatomical sites of expression, and systematically relate them to their phenotypic consequences through ontologies and machine learning. DeepSVP significantly improves the success rate of finding causative variants in several benchmarks and can identify novel pathogenic structural variants in consanguineous families.Availabilityhttps://github.com/bio-ontology-research-group/[email protected]

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