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SNP Resources: Finding SNPs Databases and Data Extraction

SNP Resources: Finding SNPs Databases and Data Extraction. Mark J. Rieder, PhD Robert J. Livingston, PhD NIEHS Variation Workshop January 30-31, 2005. Genotype - Phenotype Studies. Typical Approach: “I have candidate gene/region and samples ready to study.

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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 Mark J. Rieder, PhD Robert J. Livingston, PhD NIEHS Variation Workshop January 30-31, 2005

  2. Genotype - Phenotype Studies Typical Approach: “I have candidate gene/region and samples ready to study. Tell me what SNPs to genotype.” Other questions: How do I know I have *all* the SNPs? What is the validation/quality of the SNPs that are known? Are these SNPs informative in my population/sample? What do I need to know for selecting the “best” SNPs? How do I pick the “best” SNPs? What information do I need to characterize a SNP for genotyping?

  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 • picture of gene with mapped to the gene structure. • 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 (>10%), rare • Are other SNPs associated - redundant? Genotyping data!

  4. Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? • 1. Entrez Gene • - dbSNP • - Entrez SNP • 2. HapMap Genome Browser • 3. NIEHS Environmental Genome Project (EGP) • Candidate gene website • 4. NIEHS web applications and other tools • GeneSNPS, PolyDoms, TraFac, PolyPhen, • ECR Browser, GVS

  5. NCBI - Database Resource NOS2A www.ncbi.nlm.nih.gov

  6. Finding SNPs: Where do I start? http://www.ncbi.nlm.nih.gov/gquery

  7. Finding SNPs: Where do I start? NCBI - Entrez Gene

  8. Finding SNPs: Entrez Gene

  9. dbSNP Geneview

  10. dbSNP Geneview

  11. (by 2hit-2allele) HapMap Verified Finding SNPs: dbSNP validation

  12. Finding SNPs: dbSNP database

  13. Entrez SNP - dbSNP genotype retrieval

  14. Finding SNPs - Gene Genotype Report

  15. Finding SNPs - Gene Genotype Report

  16. Finding SNPs - Gene Genotype Report

  17. 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 • picture of gene with mapped to the gene structure. • 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 (>10%), rare • Are other SNPs associated - redundant? Genotyping data! dbSNP - data is there

  18. Entrez Gene Entry - Entrez SNP

  19. Entrez SNP - direct dbSNP querying

  20. Entrez SNP - Parseable Multi-SNP reports

  21. Entrez SNP - Parseable Multi-SNP reports

  22. Entrez SNP - Search Limiting Capabilities NOS2A

  23. Entrez SNP - Search Limits

  24. Entrez SNP - Search Limiting Capabilities

  25. Entrez SNP - Query Term Capabilities

  26. Entrez SNP - Search Terms Fields

  27. Entrez SNP - Search Terms Fields More advanced queries: 2[CHR] AND "coding nonsynon"[FUNC]

  28. Entrez SNP - Search Terms Fields More advanced queries: 2[CHR] AND "coding nonsynon"[FUNC] AND ”EGP_SNPS"[HANDLE] Note: Can also use wildcard (*) characters, AND, OR, and NOT operators

  29. Entrez SNP - Advanced Queries

  30. 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 • picture of gene with mapped to the gene structure. • 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 (>10%), rare • Are other SNPs associated - redundant? Genotyping data! EntrezSNP - better!

  31. Finding SNPs - Entrez SNP Summary • dbSNP is useful for investigating detailed information on a small number SNPs - and its good for a picture of the gene • Entrez SNP is a direct, fast, database for querying SNP data. • Data from Entrez SNP can be retrieved in batches for many SNPs • Entrez SNP data can be “limited” to specific subsets of SNPs and formatted in plain text for easy parsing and manipulation • More detailed queries can be formed using specific “field tags” for retrieving SNP data

  32. Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? • 1. Entrez Gene • - dbSNP • - Entrez SNP • 2.HapMap Genome Browser • 3. NIEHS Environmental Genome Project (EGP) • Candidate gene website • 4. NIEHS web applications and other tools • GeneSNPS, PolyDoms, TraFac, PolyPhen, • ECR Browser, GVS

  33. www.hapmap.org

  34. Finding SNPs: HapMap Browser

  35. Finding SNPs: HapMap Browser

  36. Finding SNPs: HapMap Genotypes

  37. Finding SNPs: HapMap Browser

  38. 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 • picture of gene with mapped to the gene structure. • 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 (>10%), rare • Are other SNPs associated - redundant? Genotyping data!

  39. Finding SNPs: HapMap Browser • HapMap data sets are useful because individual genotype data can be used to determine optimal genotyping strategies (tagSNPs) or perform population genetic analyses (linkage disequilbrium) • Data are specific produced by those projects (not all dbSNP) • HapMap data is available in dbSNP • HapMap data (Phase II) can be accessed preleased prior to dbSNPs • Easier visualization of data and direct access to SNP data, individual genotypes, and LD analysis

  40. Finding SNPs: Databases and Extraction How do I find and download SNP data for analysis/genotyping? • 1. Entrez Gene • - dbSNP • - Entrez SNP • 2. HapMap Genome Browser • 3. NIEHS Environmental Genome Project (EGP) • Candidate gene website • 4. NIEHS web applications and other tools • GeneSNPS, PolyDoms, TraFac, PolyPhen, • ECR Browser, GVS

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

  42. Finding SNPs: NIEHS SNPs Candidate Genes

  43. Finding SNPs: NIEHS SNPs Candidate Genes

  44. Finding SNPs: NIEHS SNPs Candidate Genes

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