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SNP Resources: Finding Snps, Databases and Data Extraction

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SNP Resources: Finding Snps, Databases and Data Extraction Genotype - Phenotype Studies You have candidate gene/region/pathway of interest and samples ready to study: SNP Resources: Finding SNPs, What SNPs are available? Databases and Data Extraction How do I find the common SNPs? What is the validation/quality of the SNPs? Are these SNPs informative in my population/samples? Debbie Nickerson What can I download information? How do I pick the “best” SNPs? - Dana Crawford NIEHS SNPs Workshop How do I pick the “best” SNPs? - Dana Crawford Minimal SNP information for genotyping/characterization Finding SNPs: Databases and Extraction • What is the SNP? Flanking sequence and alleles. FASTA format How do I find and download SNP data for analysis/genotyping? >snp_name 1. NIEHS Environmental Genome Project (EGP) ACCGAGTAGCCAG Candidate gene website [A/G] ACTGGGATAGAAC 2. NIEHS web applications and other tools GeneSNPS, PolyDoms, PolyPhen, GVS • dbSNP reference SNP # (rs #) • Where is the SNP mapped? Exon, promoter, UTR, etc 3. HapMap Genome Browser • How was it discovered? Method • What assurances do you have that it is real? Validated how? 4. Entrez Gene • What population – African, European, etc? - dbSNP • What is the allele frequency of each SNP? Common (>5%), rare - Entrez SNP • Are other SNPs associated - redundant? • Is genotyping data for control populations available? 1 Finding SNPs: Databases and Extraction Finding SNPs: NIEHS SNPs Candidate Genes How do I find and download SNP data for analysis/genotyping? 1. NIEHS Environmental Genome Project (EGP) Candidate gene website 2. NIEHS web applications and other tools GeneSNPS, PolyDoms, PolyPhen, GVS 3. HapMap Genome Browser 4. Entrez Gene - dbSNP - Entrez SNP egp.gs.washington.edu Finding SNPs: NIEHS SNPs Candidate Genes Finding SNPs: NIEHS SNPs Candidate Genes 2 Finding SNPs: NIEHS SNPs Candidate Genes 3 African American African YRI European CEU Hispanic Asian CHB JPT SNP_pos <tab> Ind_ID <tab> allele1 <tab> allele2 Repeat for all individuals Repeat for next SNP PolyPhen - Polymorphism Phenotyping Structural protein characteristics and evolutionary comparison SIFT = Sorting Intolerant From Tolerant Evolutionary comparison of non-synonymous SNPs 4 Finding SNPs: NIEHS SNPs Candidate Genes Finding SNPs: NIEHS SNPs Candidate Genes egp.gs.washington.edu Finding SNPs: NIEHS SNPs Candidate Genes Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? 1. NIEHS Environmental Genome Project (EGP) Candidate gene website 2. NIEHS web applications and other tools GeneSNPS, PolyDoms, PolyPhen, GVS 3. HapMap Genome Browser 4. Entrez Gene - dbSNP - Entrez SNP 5 Gene SNPs - http://www.genome.utah.edu/genesnps/ GeneSNPs http://www.genome.utah.edu/genesnps/ Graphic view of SNPs in context of gene elements All NIEHS genes presented - organized by pathway/function SNPs from dbSNP - organized by submitter handle Link-outs to EntrezSNP pages and other resources Multiple views of SNPs in contexts of gene elements, protein domains, linkage disequilibrium Tutorial available from OpenHelix (http://www.openhelix.com) GeneSNPs navigation GeneSNPs links to other resouces 6 GeneSNPs: multiple views of SNPS in context of gene elements Polydoms A web-based application that maps synonymous and non-synonymous SNPs onto known functional protein domains • SNPs are from dbSNP and GeneSNPs • Domain structures from NCBI's Conserved Domain Database • Functional predictions based on SIFT and PolyPhen • 3 dimensional mapping of SNPs on protein structure using Chime viewer http://polydoms.cchmc.org/polydoms/ Polydoms - Polydoms - http://polydoms.cchmc.org/polydoms/ http://polydoms.cchmc.org/polydoms/ Scroll Down 7 PolyPhen: Polymorphism Phenotyping- PolyPhen: Polymorphism Phenotyping- prediction of functional effect of human nsSNPs prediction of functional effect of human nsSNPs Physical and comparative analyses used to make predictions Uses SwissProt annotations to identify known domains Calculates a substitution probability from BLAST alignments of homologous and orthologous sequences Ranks substitutions on scale of predicted functional effects from “benign” to “probably damaging” http://genetics.bwh.harvard.edu/pph/ GVS: Genome Variation Server GVS: Genome Variation Server http://gvs.gs.washington.edu/GVS/ Provides rapid analysis of 4.5 million genotyped SNPs from dbSNP and the HapMap ADH4 Mapped to human genome build 36 (hg18) Displays genotype data in text and image formats Displays tagSNPs or clusters of informative SNPs in text and image formats Displays linkage disequilibrium (LD) in text and image formats Online tutorial provided at OpenHelix.com http://gvs.gs.washington.edu/GVS/ 8 GVS: Genome Variation Server GVS: Genome Variation Server GVS: Genome Variation Server •Table of genotypes Genotypes displayed in prettybase table and visual genotype graphic •Image of visual genotypes 9 GVS: Genome Variation Server GVS: Genome Variation Server Dense genotypes around a candidate gene can be integrated with broader HapMap genotypes High Density Genic Coverage (EGP) Low Density Genome Coverage (HapMap) = EGP SNP discovery (1/200 bp) = HapMap SNPs (~1/1000 bp) GVS: Genome Variation Server GVS: Genome Variation Server Dense genotypes around a candidate gene can be integrated with lower-density HapMap genotypes A. Common samples- combined variations B. Combined samples- common variations C. Combined samples- combined variations Common Combined 10 GVS: Genome Variation Server GVS: Genome Variation Server B. Combined samples- common variations A. Common samples- combined variations EGP EGP samples- samples- -Common samples- -Common samples- -Combined Combined variations -Combined HapMap HapMap GVS: Genome Variation Server C. Combined samples- combined variations Combined variations samples- samples- -Combined -Combined 11 Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? 1. NIEHS Environmental Genome Project (EGP) Candidate gene website 2. NIEHS web applications and other tools GeneSNPS, PolyDoms, PolyPhen, GVS 3. HapMap Genome Browser 4. Entrez Gene - dbSNP - Entrez SNP Finding SNPs: HapMap Browser www.hapmap.org 12 Finding SNPs: HapMap Browser Finding SNPs: HapMap Genotypes Finding SNPs: HapMap Browser Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? 1. HapMap data sets are useful because individual genotype 1. NIEHS Environmental Genome Project (EGP) data in deeply sampled populations can be used to Candidate gene website determine optimal genotyping strategies (tagSNPs) or perform population genetic analyses (linkage 2. NIEHS web applications and other tools disequilbrium) GeneSNPS, PolyDoms, PolyPhen, GVS 2. Data are specific to the HapMap project (not all dbSNP) 3. HapMap Genome Browser HapMap data is available in dbSNP 4. Entrez Gene 3. Visualization of data and direct access to - dbSNP SNP data, individual genotypes, and LD analysis - Entrez SNP possible in the browser and formats can be saved for Haploview 13 NCBI - Database Resource Finding SNPs using NCBI databases http://www.ncbi.nlm.nih.gov/ NOS2A www.ncbi.nlm.nih.gov Default View cSNPs 14 Finding SNPs using NCBI databases http://www.ncbi.nlm.nih.gov/ 15 Entrez SNP - Query Term Capabilities 16 Finding SNPs - Entrez SNP Summary Summary 1. dbSNP is useful for investigating detailed information on a Finding SNPs: Databases and Extraction small number SNPs - and it’s good for a picture of the gene Reviewing candidate genes using views and resources in - NIEHS SNPs 2. Entrez SNP is a direct, fast database for querying SNP data - GeneSNPs 3. Data from Entrez SNP can be retrieved in batches for many SNPs Prediction of functional variations - Polydoms and PolyPhen 4. Entrez SNP data can be “limited” to specific subsets of SNPs 4. Entrez SNP data can be “limited” to specific subsets of SNPs Integration of dense, gene-centric SNP maps with genomic and formatted in plain text for easy parsing and manipulation HapMap SNPs - GVS 5. More detailed queries can be formed using specific “field tags” for retrieving SNP data HapMap viewer NCBI databases through Entrez portal -Entrez Gene, dbSNP, Entrez SNP -many ways to retrieve and format data 17.
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