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The use of base editing technology to characterize single nucleotide variants

Computational and Structural Biotechnology Journal, 2022
Single nucleotide variants (SNVs) represent the most common type of polymorphism in the human genome. However, in many cases the phenotypic impacts of such variants are not well understood. Intriguingly, while some SNVs cause debilitating diseases, other variants in the same gene may have no, or limited, impact.
Alexis Komor, Alon Goren
exaly   +4 more sources

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A light-up fluorescence platform based DNA: RNA hybrid G-quadruplet for detecting single nucleotide variant of ctDNA and miRNA-21.

Talanta: The International Journal of Pure and Applied Analytical Chemistry, 2023
The nucleic acid assay is an area of great concern in the diagnosis and treatment of breast cancer. Here, we developed a DNA: RNA hybrid G-quadruplet (HQ) detection platform based on strand displacement amplification (SDA) and Baby Spinach RNA aptamer ...
Gai-Hua Cao, Keyi Long, Yue Qiu, Lan Peng, Hai-Yan Han, Yongzhong Wang, D. Huo, Chang-Jun Hou   +7 more
semanticscholar   +1 more source

Single nucleotide variants in lung cancer

Chinese Medical Journal Pulmonary and Critical Care Medicine
Germline genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), account for interpatient heterogeneity. In the past several decades, genome-wide association studies (GWAS) have identified multiple lung cancer-associated SNVs in Caucasian and Chinese populations.
Zhe Liu, Xiaoling Tian
exaly   +3 more sources

Whole-exome sequencing in a Japanese pedigree implicates a rare non-synonymous single-nucleotide variant in BEST3 as a candidate for mandibular prognathism.

Bone, 2019
Mandibular prognathism is a phenotype of facial deformity seen in populations around the world, but with higher incidence among East Asian populations.
T. Kajii, A. Oka, F. Saito, J. Mitsui, J. Iida   +4 more
semanticscholar   +1 more source

A Method for Predicting Allelic Variants of Single Nucleotide Polymorphisms

Current Topics in Medicinal Chemistry
Introduction: Single nucleotide polymorphisms (SNPs) are pivotal in clinical genetics, serving to link genotypes with disease susceptibility and response to environmental factors, including pharmacogenetics. They also play a crucial role in population genetics for mapping the human genome and localizing genes.
Ekaterina Evgenyevna Tyagunova, Alexander Sergeevich Zakharov, Galina Valerievna Pavlova, Daria Alexandrovna Ogarkova, Natalia Alexandrovna Zhuchenko, Vladimir Alexeyevich Gushchin   +5 more
openaire   +2 more sources

A common single-nucleotide variant in T is strongly associated with chordoma

Nature Genetics, 2012
Chordoma is a rare malignant bone tumor that expresses the transcription factor T. We conducted an association study of 40 individuals with chordoma and 358 ancestry-matched controls, with replication in an independent cohort. Whole-exome and Sanger sequencing of T exons showed strong association of the common nonsynonymous SNP rs2305089 with chordoma ...
Pillay, N., Plagnol, V., Tarpey, P.S., Lobo, S.B., Presneau, N., Szuhai, K., Halai, D., Berisha, F., Cannon, S.R., Mead, S., Kasperaviciute, D., Palmen, J., Talmud, P.J., Kindblom, L.G., Amary, M.F., Tirabosco, R., Flanagan, A.M.   +16 more
openaire   +3 more sources

TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction

Bioinform., 2018
SUMMARY Predicting genetic regulatory variants, most of which locate in non-coding genomic regions, still remain a challenge in genetic research. Among all non-coding regulatory variants, cis-eQTL single nucleotide variants (SNVs) are of particular ...
Li Chen, Ye Wang, Bing Yao, A. Mitra, Xu Wang, Xiao Qin   +5 more
semanticscholar   +1 more source

Understanding the characteristic of single nucleotide variants

2012
This thesis explores a variety of characteristics towards their use in ranking single nucleotide polymorphisms. The thousand genomes project and many similar ongoing large-scale sequencing efforts require new methods to predict functional variants in both coding and non-coding regions in order to understand phenotype and genotype relationships.
openaire   +1 more source

RNA Secondary Structure Alteration Caused by Single Nucleotide Variants

2023
A point mutation in coding RNA can cause not only an amino acid substitution but also a dynamic change of RNA secondary structure, leading to a dysfunctional RNA. Although in silico structure prediction has been used to detect structure-disrupting point mutations known as riboSNitches, exhaustive simulation of long RNAs is needed to detect a ...
Risa Karakida, Kawaguchi, Hisanori, Kiryu   +1 more
openaire   +2 more sources

Single nucleotide variant proportion in genes: a new concept to explore major depression based on DNA sequencing data

Journal of Human Genetics, 2017
Major depressive disorder (MDD) is a common psychiatric illness with significant medical and socioeconomic impact. Genetic factors are likely to play important roles in the development of this condition.
Chenglong Yu, B. Baune, Ma-Li Wong, J. Licinio   +3 more
semanticscholar   +1 more source