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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling.

Daniel Boloc1, Natalia Rodríguez2, Patricia Gassó2,3

  • 1Dep. de Medicina, University of Barcelona, Barcelona, Spain.

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|October 3, 2017
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Summary
This summary is machine-generated.

SiNoPsis is a web portal that helps researchers screen single nucleotide polymorphisms (SNPs) by analyzing their genomic location and potential disruption of regulatory elements. This tool aids in prioritizing SNPs for genotyping and disease studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Bibliographic selection of single nucleotide polymorphisms (SNPs) is time-consuming and lacks genomic context visualization.
  • Standard methods hinder correlation of SNPs with other valuable genomic information.
  • A need exists for efficient SNP screening tools that consider genomic location and regulatory impact.

Purpose of the Study:

  • To develop a web-based tool, SiNoPsis, for efficient SNP-centered screening.
  • To assist researchers in prioritizing SNPs for genotyping and disease association studies.
  • To visualize SNP impact on genomic regulatory modules.

Main Methods:

  • Developed a web form utilizing Circos for SNP visualization and analysis.
  • Integrated data on gene expression structures, including transcription factor binding sites, histones, and promoter regions.
  • Incorporated eQTL and linkage disequilibrium (LD) data for associated SNP identification.

Main Results:

  • SiNoPsis provides a user-friendly web portal for SNP analysis.
  • The tool visualizes SNP effects on regulatory elements and identifies indirectly associated SNPs via eQTL and LD.
  • It offers textual and graphic outputs for SNP selection based on regulatory modules and functional variants.

Conclusions:

  • SiNoPsis facilitates SNP prioritization by integrating genomic location, regulatory impact, and association data.
  • The tool enhances SNP screening efficiency for genetic and disease research.
  • It is the sole portal offering SNP selection based on regulatory modules and LD in both text and graphical formats.