Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays

10.1038/9674 ◽  
1999 ◽  
Vol 22 (2) ◽  
pp. 164-167 ◽  
Author(s):  
Joseph G. Hacia ◽  
Jian-Bing Fan ◽  
Oliver Ryder ◽  
Li Jin ◽  
Keith Edgemon ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Oligonucleotide Arrays

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

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 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

scholarly journals MTHFR (methylenetetrahydrofolate reductase: EC 1.5.1.20) SNPs (single-nucleotide polymorphisms) and homocysteine in patients referred for investigation of fertility

2021 ◽  
Author(s):  
Yves Ménézo ◽  
Pasquale Patrizio ◽  
Silvia Alvarez ◽  
Edouard Amar ◽  
Michel Brack ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Methylenetetrahydrofolate Reductase ◽  
Compound Heterozygous ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Men And Women ◽  
Male Gametes ◽  
Folate Cycle ◽  
The Impact

Abstract Purpose MTHFR, one of the major enzymes in the folate cycle, is known to acquire single-nucleotide polymorphisms that significantly reduce its activity, resulting in an increase in circulating homocysteine. Methylation processes are of crucial importance in gametogenesis, involved in the regulation of imprinting and epigenetic tags on DNA and histones. We have retrospectively assessed the prevalence of MTHFR SNPs in a population consulting for infertility according to gender and studied the impact of the mutations on circulating homocysteine levels. Methods More than 2900 patients having suffered at least two miscarriages (2 to 9) or two failed IVF/ICSI (2 to 10) attempts were included for analysis of MTHFR SNPs C677T and A1298C. Serum homocysteine levels were measured simultaneously. Results We observed no difference in the prevalence of different genetic backgrounds between men and women; only 15% of the patients were found to be wild type. More than 40% of the patients are either homozygous for one SNP or compound heterozygous carriers. As expected, the C677T SNP shows the greatest adverse effect on homocysteine accumulation. The impact of MTHFR SNPs on circulating homocysteine is different in men than in women. Conclusions Determination of MTHFR SNPs in both men and women must be seriously advocated in the presence of long-standing infertility; male gametes, from MTHFR SNPs carriers, are not exempted from exerting a hazardous impact on fertility. Patients should be informed of the pleiotropic medical implications of these SNPs for their own health, as well as for the health of future children.

scholarly journals Pairwise Kinship Analysis by the Index of Chromosome Sharing Using High-Density Single Nucleotide Polymorphisms

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0160287 ◽  
Author(s):  
Chie Morimoto ◽  
Sho Manabe ◽  
Takahisa Kawaguchi ◽  
Chihiro Kawai ◽  
Shuntaro Fujimoto ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Kinship Analysis ◽  
Single Nucleotide
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