1 / 128

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

deacon
Télécharger la présentation

Genetic Variations Resources May 15, 2013

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related