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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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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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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation.

Maxim Barenboim1, Thomas Manke

  • 1Bioinformatics and Deep-Sequencing Unit, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany. barenboim@ie-freiburg.mpg.de

Bioinformatics (Oxford, England)
|June 21, 2013
PubMed
Summary

This study introduces ChroMoS, a web server that integrates genetic and epigenetic data to help researchers understand the function of non-coding single nucleotide polymorphisms (SNPs) linked to diseases. It aids in classifying, prioritizing, and predicting the functional impact of these disease-associated SNPs.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) identify numerous disease-associated single nucleotide polymorphisms (SNPs).
  • A significant proportion of these SNPs are non-coding, hindering functional assessment due to limited knowledge of regulatory regions.
  • Understanding the functional consequences of non-coding SNPs is crucial for disease susceptibility and progression research.

Purpose of the Study:

  • To present ChroMoS, a novel web server designed to facilitate the classification, prioritization, and functional prediction of disease-associated SNPs.
  • To integrate genetic and epigenetic data for a comprehensive analysis of SNPs.
  • To provide tools for predicting the functional impact of SNPs on regulatory elements.

Main Methods:

  • Development of the ChroMoS (Chromatin Modified SNPs) web server.
  • Utilization of a comprehensive database of SNPs and chromatin states.
  • Inclusion of user-provided genetic information.
  • Implementation of prediction tools: sTRAP for transcription factor binding and MicroSNiPer for microRNA binding.

Main Results:

  • ChroMoS enables interactive classification and prioritization of SNPs.
  • The server allows computation of the functional impact of multiple SNPs.
  • Prediction tools assess potential effects on transcription factor and microRNA binding.

Conclusions:

  • ChroMoS provides a valuable resource for researchers studying the functional role of non-coding SNPs in disease.
  • The integrated approach aids in prioritizing SNPs for further investigation.
  • The prediction tools offer insights into the molecular mechanisms underlying SNP-associated diseases.