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SNP Resources: Finding SNPs, Databases and Data Extraction

SNP Resources: Finding SNPs, Databases and Data Extraction. Debbie Nickerson NIEHS SNPs Workshop. Genotype - Phenotype Studies. You have candidate gene/region/pathway of interest and samples ready to study:. What SNPs are available? How do I find the common SNPs?

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SNP Resources: Finding SNPs, Databases and Data Extraction

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  1. SNP Resources: Finding SNPs, Databases and Data Extraction Debbie Nickerson NIEHS SNPs Workshop

  2. Genotype - Phenotype Studies You have candidate gene/region/pathway of interest and samples ready to study: What SNPs are available? How do I find the common SNPs? What is the validation/quality of the SNPs? Are these SNPs informative in my population/samples? What can I download information? How do I pick the “best” SNPs? - Dana Crawford

  3. Minimal SNP information for genotyping/characterization • What is the SNP? Flanking sequence and alleles. • FASTA format • >snp_name • ACCGAGTAGCCAG • [A/G] • ACTGGGATAGAAC • dbSNP reference SNP # (rs #) • Where is the SNP mapped? Exon, promoter, UTR, etc • How was it discovered? Method • What assurances do you have that it is real? Validated how? • What population – African, European, etc? • What is the allele frequency of each SNP? Common (>5%), rare • Are other SNPs associated - redundant? • Is genotyping data for control populations available?

  4. 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. 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

  6. Finding SNPs: NIEHS SNPs Candidate Genes egp.gs.washington.edu

  7. Finding SNPs: NIEHS SNPs Candidate Genes

  8. Finding SNPs: NIEHS SNPs Candidate Genes

  9. Finding SNPs: NIEHS SNPs Candidate Genes

  10. African American African YRI European CEU Hispanic Asian CHB JPT

  11. SNP_pos <tab> Ind_ID <tab> allele1 <tab> allele2 Repeat for all individuals Repeat for next SNP

  12. PolyPhen - Polymorphism Phenotyping Structural protein characteristics and evolutionary comparison SIFT = Sorting Intolerant From Tolerant Evolutionary comparison of non-synonymous SNPs

  13. Finding SNPs: NIEHS SNPs Candidate Genes

  14. Finding SNPs: NIEHS SNPs Candidate Genes egp.gs.washington.edu

  15. Finding SNPs: NIEHS SNPs Candidate Genes

  16. 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

  17. 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)

  18. Gene SNPs -http://www.genome.utah.edu/genesnps/

  19. GeneSNPs navigation

  20. GeneSNPs links to other resouces

  21. GeneSNPs: multiple views of SNPS in context of gene elements

  22. 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/

  23. Polydoms - http://polydoms.cchmc.org/polydoms/

  24. Polydoms - http://polydoms.cchmc.org/polydoms/ Scroll Down

  25. PolyPhen: Polymorphism Phenotyping- 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/

  26. PolyPhen: Polymorphism Phenotyping- prediction of functional effect of human nsSNPs

  27. GVS: Genome Variation Server http://gvs.gs.washington.edu/GVS/ • Provides rapid analysis of 4.5 million genotyped SNPs from dbSNP and the HapMap • 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

  28. GVS: Genome Variation Server ADH4 http://gvs.gs.washington.edu/GVS/

  29. GVS: Genome Variation Server

  30. GVS: Genome Variation Server • Table of genotypes • Image of visual genotypes

  31. GVS: Genome Variation Server Genotypes displayed in prettybase table and visual genotype graphic

  32. GVS: Genome Variation Server

  33. 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 Dense genotypes around a candidate gene can be integrated with broader HapMap genotypes

  34. GVS: Genome Variation Server Dense genotypes around a candidate gene can be integrated with lower-density HapMap genotypes

  35. GVS: Genome Variation Server Common samples-combined variations B. Combined samples- common variations Combined samples- combined variations Common Combined

  36. GVS: Genome Variation Server Common samples- combined variations -Common samples- Combined variations

  37. GVS: Genome Variation Server B. Combined samples- common variations EGP -Combined samples- HapMap

  38. GVS: Genome Variation Server C. Combined samples- combined variations Combined variations -Combined samples-

  39. 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

  40. www.hapmap.org

  41. Finding SNPs: HapMap Browser

  42. Finding SNPs: HapMap Browser

  43. Finding SNPs: HapMap Genotypes

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