scholarly journals Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions

2004 ◽  
Vol 14 (8) ◽  
pp. 1664-1668 ◽  
Author(s):  
M. R. Nelson
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Scale Validation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals DNA Melting Analysis for Detection of Single Nucleotide Polymorphisms

2001 ◽  
Vol 47 (4) ◽  
pp. 635-644 ◽  
Author(s):  
Robert H Lipsky ◽  
Chiara M Mazzanti ◽  
Joseph G Rudolph ◽  
Ke Xu ◽  
Gopal Vyas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dna Melting ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Efficient System ◽  
Gradient Gel Electrophoresis ◽  
Melting Analysis ◽  
Scale Detection

Abstract Background: Several methods for detection of single nucleotide polymorphisms (SNPs; e.g., denaturing gradient gel electrophoresis and denaturing HPLC) are indirectly based on the principle of differential melting of heteroduplex DNA. We present a method for detecting SNPs that is directly based on this principle. Methods: We used a double-stranded DNA-specific fluorescent dye, SYBR Green I (SYBR) in an efficient system (PE 7700 Sequence Detector) in which DNA melting was controlled and monitored in a 96-well plate format. We measured the decrease in fluorescence intensity that accompanied DNA duplex denaturation, evaluating the effects of fragment length, dye concentration, DNA concentration, and sequence context using four naturally occurring polymorphisms (three SNPs and a single-base deletion/insertion). Results: DNA melting analysis (DM) was used successfully for variant detection, and we also discovered two previously unknown SNPs by this approach. Concentrations of DNA amplicons were readily monitored by SYBR fluorescence, and DNA amplicon concentrations were highly reproducible, with a CV of 2.6%. We readily detected differences in the melting temperature between homoduplex and heteroduplex fragments 15–167 bp in length and differing by only a single nucleotide substitution. Conclusions: The efficiency and sensitivity of DMA make it highly suitable for the large-scale detection of sequence variants.

scholarly journals Association between a Variant in MicroRNA-646 and the Susceptibility to Hepatocellular Carcinoma in a Large-Scale Population

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Rui Wang ◽  
Jun Zhang ◽  
Weiru Jiang ◽  
Yanyun Ma ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Single Nucleotide Polymorphisms ◽  
Protective Effect ◽  
Large Scale ◽  
Cancer Development ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Scale Population

Background. Single-nucleotide polymorphisms in microRNAs play important roles in oncogenesis and cancer development.Objective. We aim to explore whether miR-646 rs6513497 is associated with the risk of hepatocellular carcinoma.Methods. Total 997 HCC patients and 993 cancer-free controls were enrolled in this study. Genotyping was performed using MassARRAY method.Results. Compared with the T allele of rs6513497, the G allele was associated with a significantly decreased risk of HCC (OR = 0.788, 95% CI = 0.631–0.985,P= 0.037); moreover, a more protective effect of the G allele was shown in males (OR = 0.695, 95% CI = 0.539–0.897,P= 0.005 in HCC and OR = 0.739, 95% CI = 0.562–0.972,P= 0.030 in HBV-related HCC), basically in a dominant manner (HCC: OR = 0.681, 95% CI = 0.162–0.896,P= 0.006; HBV-related HCC: OR = 0.715, 95% CI = 0.532–0.962,P= 0.027).Conclusions. Our findings support the view that the miR-646 SNP rs6513497 may contribute to the susceptibility of HCC.

A validation of parentage-based tagging using hatchery steelhead in the Snake River basin

2013 ◽  
Vol 70 (7) ◽  
pp. 1046-1054 ◽  
Author(s):  
Craig A. Steele ◽  
Eric C. Anderson ◽  
Michael W. Ackerman ◽  
Maureen A. Hess ◽  
Nathan R. Campbell ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
River Basin ◽  
Large Scale ◽  
Snake River ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Promising Alternative

Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs. We also demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of parentage-based research and management questions.

scholarly journals Single Nucleotide Polymorphisms, Indels, and Simple Sequence Repeats for Onion Cultivar Identification

2005 ◽  
Vol 130 (6) ◽  
pp. 912-917 ◽  
Author(s):  
Jernej Jakse ◽  
William Martin ◽  
John McCallum ◽  
Michael J. Havey
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Simple Sequence Repeats ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Onion Seed ◽  
Onion Cultivar ◽  
Simple Sequence

The commercial production of onion (Allium cepa L.) inbreds, hybrids, and open-pollinated (OP) cultivars would benefit from a robust set of molecular markers that confidently distinguish among elite germplasms. Large-scale DNA sequencing has revealed that single nucleotide polymorphisms (SNPs), short insertion-deletion (indel) events, and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers. We identified 398 SNPs, indels, and SSRs among 35 elite onion ulations and observed that all populations could be distinguished. Phylogenetic analyses of simple-matching and Jaccard's coefficients for SSRs produced essentially identical trees and relationships were consistent with known pedigrees and previous marker evaluations. The SSRs revealed that elite germplasms from specific companies or breeding programs were often closely related. In contrast, phylogenetic analyses of SNPs and indels did not reveal clear relationships among elite onion populations and there was no agreement among trees generated using SNPs and indels vs. SSRs. This discrepancy was likely due to SNPs and indels occurring among amplicons from duplicated regions (paralogs) of the onion genome. Nevertheless, these PCR-based markers will be useful in the quality control of inbred, hybrid, and OP onion seed lots.

scholarly journals Single nucleotide polymorphisms associated with gastric cancer in Iranian patients

2021 ◽  
Vol 7 (2) ◽  
pp. e37-e37
Author(s):  
Arash Alghasi ◽  
Gholamreza Farnoosh ◽  
Ali Saeedi Boroujeni ◽  
Mohammad Bahadoram ◽  
Sima Tahmaseby Gandomkari ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Nucleotide Polymorphisms ◽  
Caspase 9 ◽  
Northern Iran ◽  
Single Nucleotide ◽  
C677t Mthfr ◽  
Increased Risk ◽  
Iranian Patients

Gastric cancer is one of the leading worldwide cancers formed in the lining of the stomach, and is the most prevalent cancer in northern Iran. Recent interventions for the early diagnosis of gastric cancer are based on genetic susceptibility parameters and the interactions between genes and the environment. Accordingly, this narrative review was designed to summarize the genetic markers involved in Iranian patients with gastric cancer, classified by cellular function. There was a significant relationship between single nucleotide polymorphisms (SNPs) in rs1051208 C allele (RAF1), rs531564 (pri-miR-124-1), rs1053023 (STAT3), rs8193 C allele (CD44), rs3130932G allele (OCT4), rs283821943, rs2032586 (ABCB1), codons 72,248 (p53), -137 G/C (IL-18), Pro12Ala (PPARγ), rs1053023 (STAT3), rs4647603 (caspase 3), -712C>T (caspase 9), -1263 A> (caspase 9) and gastric cancer. Increased risk was observed in C677T (MTHFR). Finally, decreased risk of gastric cancer was explored in -938 C>A (bcl2). Asp299Gly (TLR-4), rs1028181-513T/C (IL-19) Pro12Ala (PPARγ) may play a crucial role in susceptibility of Helicobacter pylori and gastric pathogenesis. According to the findings, the genetic polymorphisms in the immune-associated genes were related to the gastric cancer among the Iranian patients. Therefore, further large-scale functional investigations are needed to draw definite conclusions.

Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

10.1038/74215 ◽  
2000 ◽  
Vol 24 (4) ◽  
pp. 381-386 ◽  
Author(s):  
Kerstin Lindblad-Toh ◽  
Ellen Winchester ◽  
Mark J. Daly ◽  
David G. Wang ◽  
Joel N. Hirschhorn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Range-wide parallel climate-associated genomic clines in Atlantic salmon

2017 ◽  
Vol 4 (11) ◽  
pp. 171394 ◽  
Author(s):  
Nicholas W. Jeffery ◽  
Ryan R. E. Stanley ◽  
Brendan F. Wringe ◽  
Javier Guijarro-Sabaniel ◽  
Vincent Bourret ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Atlantic Salmon ◽  
North Atlantic ◽  
Large Scale ◽  
Intraspecific Diversity ◽  
Clinal Variation ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The North ◽  
The North Atlantic

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon ( Salmo salar ). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.

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