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Bioinformatics Group Meeting HO, Dun 21 st March, 2013

SNPnexus : a web server for functional annotation of novel and publicly known genetic variants (2012 update). Bioinformatics Group Meeting HO, Dun 21 st March, 2013. Contents. Background SNP Today's paper: SNPnexus Motivation System workflow Query option Annotation category

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Bioinformatics Group Meeting HO, Dun 21 st March, 2013

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  1. SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update) Bioinformatics Group Meeting HO, Dun 21st March, 2013

  2. SNPnexus Contents • Background • SNP • Today's paper: SNPnexus • Motivation • System workflow • Query option • Annotation category • Demonstration

  3. SNPnexus Background

  4. SNPnexus Single Nucleotide Polymorphism (SNP) • A single nucleotide change in DNA sequence • Possible change • Substitution • Insertion/Deletion • May develop disease, change the response on pathogen, drugs… • Position of SNP • Coding regions, like gene • Some directly change the protein production • Non-coding / intergenic regions, like introns • May control the expression level of protein

  5. SNPnexus Today's Paper

  6. SNPnexus Motivation • SNP can identify disease in genetic basis • There are different types of SNP, some are important • For a doctor get a list of SNP/variants • Need to narrow down the variants list • But they don't know which SNP are "important" • To prioritize the SNP, doctors considers with • Gene/protein structure • Regulatory effect…

  7. SNPnexus SNPnexus • A web-based functional annotation tool to assess potential significance of variation

  8. SNPnexus System workflow • Three components • Query options • Annotation categories • Output • Back-end language • Perl annotation pipeline • MySQL database

  9. SNPnexus Query option • Query type • Single query • Batch query • Up to 100K entries • Support standard variant file (vcf format) • Query format • By SNP identifier (e.g. rs9910) • By genomic position (e.g. chr1:1100) • By chromosomal region (e.g. chr1:1100-5500) • Genome assembly • NCBI36/hg18 and GRCh37/hg19

  10. SNPnexus Annotation category • Different data are used to give a broader view on the variants • Genomic/Protein consequence • Give the basic information of the variation, like coding region • Data from public genome browser, like UCSC, Ensembl • Effect on protein function • As variation can introduce a change in amino acid • Give the prediction on the effect of non-synonymous single amino acid substitution • HapMap populations • Give the variation data in different population, defined by region

  11. SNPnexus Annotation category (2) • Regulatory effect • Give the data about regulatory elements • Like TFBS, promoter, enhancer, … • Conservation • Give the probability score that variant belongs to conserved region • Others • Disease association • Structural variant

  12. SNPnexus Annotation summary • Total 7 categories, 35 datasets

  13. SNPnexus Output • Provide different file formats for user • HTML • Excel • Graphics • Tab delimited text • Notification with email (optional) • Data are kept for 72 hours

  14. SNPnexus Demonstration

  15. SNPnexus Summary on SNPnexus • Developed a SNP annotation system to help users identifying "important" SNP • Provided various query formats and modes to facilitate user's submission • Combined with many datasets • Output in different formats helps user handling annotation result

  16. SNPnexus Q&A

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