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Genetic Variations Resources May 15, 2013

Genetic Variations Resources May 15, 2013. Ansuman Chattopadhyay , PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics. Objective. Human genetic variations

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Genetic Variations Resources May 15, 2013

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  1. Genetic Variations ResourcesMay 15, 2013 AnsumanChattopadhyay, PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

  2. Objective • Human genetic variations • Genetic variations databases • Functional analysis of mutations/SNPs

  3. Topics • Databases: • dbSNP • db GAP • GenPheni • DGV • Decipher • OMIM • HGMD • Regulome db • Tools • HugeNavigator • FastSNP • SPOT • GenomeTrax

  4. Human Genetic Variations 0.4-0.6 % Population 100 % Population 100 % Population Deletions / Inversions / Translocations Duplications Deletions Insertions Chromosomal rearrangements Copy Number Variations (CNVs) In/Del Micro- and Mini- satellites SNPs 1Mb >5Mb 1kb 1bp

  5. Human Genome Variations Scherer, S.W. (2009), "Copy number variation", in Scherer, S. (ed.), Copy Number Variation: , The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London 321,340,1 bp (0.11 % of the genome) : SNPs 40,568,593 bp (1.35% of the genome) : CNVs

  6. Single Nucleotide Polymorphisms SNPs

  7. SNP Facts

  8. Life Cycle of SNPs and Mutations Mutation/ Private SNP SNPs

  9. Classifications of SNPs • Genomic location based

  10. Classifications of SNPs • Nucleotide substitution based

  11. Polymorphisms and Disease Markers

  12. International Hap Map Project http://www.hapmap.org/ • Whole-genome genotyping of 10 million SNPs • Technologically daunting • Prohibitively expensive • Researchers tried to downsize the problem of genome-wide genotyping • by studying haplotypes. • A haplotype is a contiguous, linear set of SNP alleles along a • genome that is inherited as a block.

  13. The Origin of Haplotype

  14. Haplotype Blocks

  15. Haplotype and Tag SNPs

  16. Hap Map Population

  17. http://www.1000genomes.org/about

  18. Bioinformatics Institutions http://www.ebi.ac.uk/ http://www.ncbi.nlm.nih.gov/

  19. dbSNP

  20. dbSNP Stats http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi as of January 25, 2010

  21. Current Status of dbSNP http://goo.gl/TwltA MassGenomics blog by Dan Koboldt

  22. dbSNP Data Types

  23. Ref SNP : rs4244285

  24. Ref SNP : rs4244285

  25. Genetic Terminologies

  26. Ref SNP : rs4244285

  27. Submitted SNP: ss5586415

  28. SNPedia and NextBio • http://goo.gl/aOsoX http://goo.gl/Lqqd4

  29. Searching dbSNP • Identify • SNPs present in a gene sequence • SNPs reported to be present in a genomic region

  30. Searching dbSNP • UCSC Genome Browser • UCSC Table Browser • NCBI dbSNP page http://www.ncbi.nlm.nih.gov/snp

  31. Searching dbSNP

  32. Searching dbSNP

  33. dbSNP Search result Display

  34. GWAS

  35. GWAS Plot Each SNP is assessed for ‘‘genome-wide’’ significance, after Bonferroni correction.

  36. Publications on HapMap Hap map GWAS

  37. Genome Wide Association Studies http://www.genome.gov/gwastudies/

  38. Find SNPs for a Disease/Trait CDC developed HuGENavigator : http://hugenavigator.net/

  39. GWAS Integrator

  40. GWAS Integrator What SNPs are associated • with “asthma”?

  41. GWAS Integrator : rs7216389

  42. GWAS Integrator What SNPs are associated • with “asthma”?

  43. GWAS Integrator

  44. GWAS Integrator : rs7216389 Ref: Moffatt Mf etal. childhood asthma. Nature. 2007 Jul 26;448(7152):470-3. Epub 2007 Jul 4. PubMed PMID: 17611496.

  45. GWAS Integrator : rs7216389

  46. Find associated Genes for a Disease/Trait

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