Variome Browser

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Human Variation Database

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Variome Browser

  1. 1. Variome Browser v0.1 Cheng-Yang (Louis) Tang BioIT at NGC 2008/11/28 http://vb.ngc.sinica.edu.tw
  2. 2. Variome Browser <ul><li>The first Rich Internet Application on the planet to let you navigate into the human variome world. </li></ul>
  3. 3. Variome Browser <ul><li>The first Rich Internet Application on the planet to let you navigate into the human variome world. </li></ul><ul><li>Evaluates the Impact of every single base swapping variation on every transcript. </li></ul>
  4. 4. Variome Browser <ul><li>The first Rich Internet Application on the planet to let you navigate into the human variome world. </li></ul><ul><li>Evaluates the Impact of every single base swapping variation on every transcript. </li></ul><ul><li>Integrates 3 kinds of variation impact data : </li></ul><ul><ul><li>Disease </li></ul></ul><ul><ul><li>SNP </li></ul></ul><ul><ul><li>Risk Evaluation </li></ul></ul>
  5. 5. Data
  6. 6. Target Bases 3' Intron Exon 5' Promoter Gene Structure 5’ UTR 3’ UTR CDS
  7. 7. Target Bases 3' Intron Exon 5' Promoter Gene Structure 5’ UTR 3’ UTR CDS A
  8. 8. Target Variations 3' 5' A
  9. 9. Target Variations 3' 5' T G C A
  10. 10. Target Variations 3' 5' Transcript 001 Transcript 002 Transcript 003 T G C A A A A
  11. 11. Target Variations 3' 5' Transcript 001 Transcript 002 Transcript 003 Possible base-change ( 3 ) x transcript number ( 3 ) = variation number ( 9 ) T G C A A A A
  12. 12. Variation Impact Variation
  13. 13. Variation Impact Variation Disease db
  14. 14. Variation Impact Variation SNP Disease db
  15. 15. Variation Impact Variation SNP Risk evaluation Rescue-ESE FAS-ESS Disease db
  16. 16. Risk Evaluation Tabor HK, Risch NJ, Myers RM: Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Reviews Genetics 2002, 3 (5):391-397 . 5 Risk types (8 subtypes) 5 Risk levels (1) Non-sense (2) Mis-sense (Non-conservative change) (3) Mis-sense (Protein domain abolition) (4) Mis-sense (splicing regulation) (5) Mis-sense (conservative change) (6) Splicing regulation (Protein domain abolition) (7) Splicing regulation (8) Sense <ul><li>Very High </li></ul><ul><li>High </li></ul><ul><li>Medium </li></ul><ul><li>Low </li></ul><ul><li>Very Low </li></ul>
  17. 17. Risk Evaluation Tabor HK, Risch NJ, Myers RM: Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Reviews Genetics 2002, 3(5):391-397 .
  18. 18. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  19. 19. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  20. 20. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  21. 21. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  22. 22. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  23. 23. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  24. 24. Risk Evaluation <ul><li>Coding Region? </li></ul><ul><li>Synonymous? </li></ul><ul><li>Non-sense? </li></ul><ul><li>ESE or ESS motif abolition? </li></ul><ul><li>Protein Function Affected? </li></ul><ul><li>Protein Domain abolition? </li></ul>Rescue-ESE FAS-ESS
  25. 25. Risk Evaluation 5 Risk types (8 subtypes) 5 Risk levels (1) Non-sense (2) Mis-sense (Non-conservative change) (3) Mis-sense (Protein domain abolition) (4) Mis-sense (splicing regulation) (5) Mis-sense (conservative change) (6) Splicing regulation (Protein domain abolition) (7) Splicing regulation (8) Sense <ul><li>Very High </li></ul><ul><li>High </li></ul><ul><li>Medium </li></ul><ul><li>Low </li></ul><ul><li>Very Low </li></ul>
  26. 26. Risk Evaluation Workflow
  27. 27. Data Summery <ul><li>Target Bases: Those on CDS </li></ul><ul><li>Target Variations: Single base swapping on every transcript </li></ul><ul><li>Variation Impact: </li></ul><ul><ul><li>Disease db: OMIM, HGVS </li></ul></ul><ul><ul><li>SNP: dbSNP </li></ul></ul><ul><ul><li>Risk Evaluation </li></ul></ul>
  28. 28. User Interface
  29. 29. User Interface
  30. 30. User Interface
  31. 31. User Interface 1. Search
  32. 32. User Interface 1. Search 2. Image
  33. 33. User Interface 1. Search 2. Image 3. Table
  34. 34. User Interface 1. Search 4. History 2. Image 3. Table
  35. 35. User Interface 1. Search 4. History 2. Image 3. Table 5. Filter
  36. 36. Search
  37. 37. Search <ul><li>Chromosome range </li></ul><ul><ul><li>chr12:100000-20000 </li></ul></ul><ul><li>Gene symbols </li></ul><ul><ul><li>APOE, BRCA1, VKORC1, etc. </li></ul></ul><ul><li>More formats are being supported in the next version </li></ul>
  38. 38. Search
  39. 39. Advanced Search
  40. 40. Advanced Search
  41. 41. Advanced Search
  42. 42. Advanced Search
  43. 43. Advanced Search
  44. 44. Advanced Search
  45. 45. Image
  46. 46. Image
  47. 47. Image
  48. 48. Image 1. Genome View
  49. 49. Image 1. Genome View 2. Chromosome View
  50. 50. Image 1. Genome View 2. Chromosome View 3. Transcript View
  51. 51. Image
  52. 52. Image
  53. 53. Image
  54. 54. Image
  55. 55. Table
  56. 56. Table <ul><li>Disease </li></ul>
  57. 57. Table <ul><li>SNP </li></ul>
  58. 58. Table <ul><li>Variant coordinate </li></ul>
  59. 59. Table <ul><li>Prediction </li></ul>
  60. 60. Details
  61. 61. Variant Details
  62. 62. Impact
  63. 63. Risk Evaluation
  64. 64. SNP
  65. 65. Disease
  66. 66. Risk Evaluation Flow
  67. 67. History
  68. 68. History
  69. 69. Filter
  70. 70. Filter
  71. 71. Filter
  72. 72. Live Demo http://vb.ngc.sinica.edu.tw/
  73. 73. Future
  74. 74. Future <ul><li>IE Support </li></ul>
  75. 75. Future <ul><li>IE Support </li></ul><ul><li>More Keyword formats </li></ul><ul><ul><li>mRNA accession (e.g. NM_000014) </li></ul></ul><ul><ul><li>Point-based keywords (e.g. chr1:20000, flanking region, etc.) </li></ul></ul><ul><ul><li>Raw Sequence </li></ul></ul>
  76. 76. Future <ul><li>IE Support </li></ul><ul><li>More Keyword formats </li></ul><ul><ul><li>mRNA accession (e.g. NM_000014) </li></ul></ul><ul><ul><li>Point-based keywords (e.g. chr1:20000, flanking region, etc.) </li></ul></ul><ul><ul><li>Raw Sequence </li></ul></ul><ul><li>Sortable table </li></ul>
  77. 77. Future <ul><li>IE Support </li></ul><ul><li>More Keyword formats </li></ul><ul><ul><li>mRNA accession (e.g. NM_000014) </li></ul></ul><ul><ul><li>Point-based keywords (e.g. chr1:20000, flanking region, etc.) </li></ul></ul><ul><ul><li>Raw Sequence </li></ul></ul><ul><li>Sortable table </li></ul><ul><li>Export table data </li></ul>
  78. 78. Future <ul><li>IE Support </li></ul><ul><li>More Keyword formats </li></ul><ul><ul><li>mRNA accession (e.g. NM_000014) </li></ul></ul><ul><ul><li>Point-based keywords (e.g. chr1:20000, flanking region, etc.) </li></ul></ul><ul><ul><li>Raw Sequence </li></ul></ul><ul><li>Sortable table </li></ul><ul><li>Export table data </li></ul><ul><li>Resizable Border </li></ul>
  79. 79. Future <ul><li>IE Support </li></ul><ul><li>More Keyword formats </li></ul><ul><ul><li>mRNA accession (e.g. NM_000014) </li></ul></ul><ul><ul><li>Point-based keywords (e.g. chr1:20000, flanking region, etc.) </li></ul></ul><ul><ul><li>Raw Sequence </li></ul></ul><ul><li>Sortable table </li></ul><ul><li>Export table data </li></ul><ul><li>Resizable Border </li></ul><ul><li>Includes variations locating outside CDS? </li></ul><ul><li>Mouse variome? </li></ul>
  80. 80. Conclusion <ul><li>Innovative Browser of the human variome data. </li></ul><ul><li>Comprehensive evaluation of single-based swapping variations on CDS </li></ul><ul><li>Integrates variation impact data including disease, SNP and Risk Evaluation results. </li></ul><ul><li>http://vb.ngc.sinica.edu.tw </li></ul>
  81. 81. Acknowledgement 緣起:陳志成老師、所長實驗室 指導:姚文萱老師 支援: NGC, Biomedical IT 經費: NRPGM
  82. 82. Thanks for your attention! http://vb.ngc.sinica.edu.tw

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