SNPenomics

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Definition

  SNP
   -A Single Nucleotide Polymorphism is a small genetic variation very similar to point mutations. By definition, SNPs differ from the reference sequence of a species. SNPs are more stable than microsatellites since they differ by single nucloetides and do not induce additional errors by the DNA polymerase.

  Haplotypes
   -Haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. It is thought that these associations, and the identification of a few alleles of a haplotype block, can unambiguously identify all other polymorphic sites in its region. Such information is very valuable for investigating the genetics behind common diseases and is collected by the International HapMap Project.

SNP, Haplotypes


Why is it important?


  Most SNPs are found in non-coding sequences. SNPs in coding sequence can change amino acid sequence which they are more likely to alter the biological properties-giving individual polymorphism. 


    SNPs for Disease Diagnosis
   -Although most SNPs are not responsible for a disease, they can be biological markers for detecting probability of disease. Because they are usually close to a certain disease gene location. And they are accasionally responsible for a disease directly.

  
    SNPs for Drug Development
   -SNPs may be associated with sensibility of therapeutic molecules. There is difficult way to search about reaction to a particular drug to individual, but it's clear that SNPs can be different effect among them. In the future, person could be serviced "personalized medicine" which is treatment by analyzing a patient's SNP profile.


   
    
     
Current SNP Project


  International HapMap project-The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors. 

  Korean HapMap project-The goal of the Korean Hapmap project is to develop a resource to facilitate future studies that relate human genetic variation to health and disease in Korean population.

  PanAsia SNP project-The goal is to discover genetic differences among Asian to know trace evlutionary history by study SNP frequency distribution in Pan-Asia population.  




                                                   
Tools

  Recent

     -Bioinformatics, 2007, SNPTools: A software tool for visualization and analysis of microarray data
     SNPTools: The software can analyse and find differences in intensity-levels between groups of arrays and identify segments of SNPs(genes, clones) where the intensity-levels differ significantly between the groups.
    



     
     -Nucleic Acids Research, 2007, Vol. 35, SNPSTR: a database of  compound microsatellite-SNP markers
     SNPSTR: A new type of marker. SNPSTR provide a relatively new type of compound genetic marker calld SNPSTR which combines a microsatellite marker(STR) with one or more tightly linked SNPs.


    





     -Nucleic Acids Research, 2007, Vol. 35, Influenza virus datebase(IVDB): an integrated information resource and analysis platform for influenza virus research
     IVDB: IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships.
    



     


  SNP database

-International HapMap

-dbSNP

-HGVbase : The objective of HGVbase (the Human Genome Variation Database) is to provide an accurate, high utility and ultimately fully comprehensive catalog of normal human gene and genome variation, useful as a research tool to help define the genetic component of human phenotypic variation.

-SeatleSNPs : The Seattle SNPs PGA is focused on identifying, genotyping, and modeling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.

-SNP500 Cancer : The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer. SNP500Cancer provides a central resource for sequence verification of SNPs.


  SNP selection

-UCSC 

-Ensembl with biomart : Extract information from the Ensembl database and export sequences or tables in text, html, or Excel format with BioMart

-FESD : The Functional Element SNPs Database (FESD) categorizes regulatory element in human gene and provides a set of SNPs located within each area. The FESD divided the human genome into 10 different regulatory elements; promoter regions, CpG islands, 5'UTRs, translation start sites, splice sites, exons, introns, translation stop sites, poly adenylation signals (PASes), and 3'UTRs and then, assigned all known SNPs to each regulatory elements by their position. Using the FESD web interface, users can select a set of SNPs in the specific regulatory element and get their flanking sequences for genotyping experiments.

-SNPPine 

-SNPper


  SNP effect

-SIFT : SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids.

-MutDB : The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information.

-SNPNB : SNPNB is a user-friendly application for analyzing Single Nucleotide Polymorphism NeighBoring compositions.

-SNPeffect : database mapping molecular phenotypic effects of human nsSNPs


 

 

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