Toehold probe-based interrogation for haplotype phasing of long nucleic acid strands

2020 ◽  
Vol 12 (34) ◽  
pp. 4185-4190
Author(s):  
Xinyu Zhuang ◽  
Henson L. Lee Yu ◽  
I-Ming Hsing
Keyword(s):  
Nucleic Acid ◽  
Single Nucleotide Polymorphisms ◽  
Disease Risk ◽  
Accurate Determination ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Haplotype Phasing ◽  
Haplotype Phase

The arrangement of multiple single nucleotide polymorphisms (SNPs) in a gene, called a haplotype phase, is increasingly recognized as critical for accurate determination of disease risk and severity.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide

Association between Single-Nucleotide Polymorphisms of the hOGG1,NEIL1,APEX1, FEN1,LIG1, and LIG3 Genes and Alzheimer's Disease Risk

2016 ◽  
Vol 73 (2) ◽  
pp. 98-107 ◽  
Author(s):  
Dominik Kwiatkowski ◽  
Piotr Czarny ◽  
Monika Toma ◽  
Anna Korycinska ◽  
Katarzyna Sowinska ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Nucleotide Polymorphisms ◽  
Disease Risk ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Analysis of the genetic diversity of Phalaenopsis orchids with single nucleotide polymorphisms and snap markers derived from the Pto gene

2021 ◽  
Vol 53 (4) ◽  
pp. 620-631
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Functional Link ◽  
Single Nucleotide ◽  
Functional Changes ◽  
Interspecies Variability

The Pto gene is a plant gene that has been reported to be involved in resistance to bacterial pathogens. A partial genomic sequence corresponding to Pto (~449 bp) was isolated from 16 species and four hybrids of Phalaenopsis during 2017 at the Department of Agronomy and Horticulture, IPB University, Bogor, Indonesia. Multiple sequence analysis was performed to find putative single nucleotide polymorphisms (SNPs) and design the corresponding single nucleotide-amplified polymorphism (SNAP) markers, which were in turn used to estimate the genetic diversity of 25 Phalaenopsis species. In total, 20 SNPs, of which 14 were nonsynonymous, were identified from the partial Pto sequences. Eighteen SNAP primers were then developed based on these 14 nonsynonymous and four synonymous SNPs. Validation results showed that 15 SNAP primers showed a polymorphism information content exceeding 0.3, suggesting the existence of more than two alleles for this locus. Upon their use, the SNAP markers described 86% of all interspecies variability. The Pto 52, Pto 349, Pto 229, and Pto 380 SNAP markers were very informative in the determination of genetic diversity. Notably, the existence of these nonsynonymous SNPs implied the possibility of functional changes within the amino acid sequence of the putative PTO protein. Thus, the resulting differences in the activity of the PTO protein may be used to breed tolerance to pathogen infection. Further work may be required to establish a functional link between tolerance to pathogens and the presence of Pto-SNAP markers in Phalaenopsis properly.

scholarly journals An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Ying Wang ◽  
Jidong Ru ◽  
Tao Jin ◽  
Ming Sun ◽  
Lizhu Jia ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Single Nucleotide Polymorphisms ◽  
Disease Risk ◽  
Software Tool ◽  
Mature Mirnas ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
1000 Genomes ◽  
Mirna Sequencing

MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual’s samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.

scholarly journals Residues 155 and 348 Contribute to the Determination of P2X7Receptor Function via Distinct Mechanisms Revealed by Single-nucleotide Polymorphisms

2011 ◽  
Vol 286 (10) ◽  
pp. 8176-8187 ◽  
Author(s):  
Helen J. Bradley ◽  
Jocelyn M. Baldwin ◽  
G. Ranjan Goli ◽  
Brian Johnson ◽  
Jie Zou ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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