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BioJS Human Genetic Variation Viewer

BioJS Human Genetic Variation Viewer

BioJavascript Human Genetic Variation Viewer
presented at the USC/UCLA Joint Bioinformatics Meeting held at University Of Southern California.

Developed as part of Google Summer of Code 2014

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Saket Choudhary

October 30, 2014
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  1. human genetic variation viewer . Saket Choudhary 1, Leyla Garcia2

    and Andrew Nightingale2 October 30, 2014 . . C . G . C . A . T . C . G . A . G . C . T . . C . G . C . G . T . C . G . A . G . C . T 1University of Southern California and 2EMBL-EBI
  2. outline ∙ Motivation ∙ Solution ∙ Demo and Use-Cases ∙

    Implementation ∙ Future Work 1
  3. . .motivation

  4. visualizations are powerful! The power of the unaided mind is

    highly overrated. The real powers come from devising external aids that enhance cognitive abilities. – Donald Norman 3
  5. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... 4
  6. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... ∙ Different categories of mutations: Benign, Damaging, Intermediate 4
  7. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... ∙ Different categories of mutations: Benign, Damaging, Intermediate ∙ Lack of consensus amongst scoring mechanisms: SIFT ̸= Polyphen 4
  8. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... ∙ Different categories of mutations: Benign, Damaging, Intermediate ∙ Lack of consensus amongst scoring mechanisms: SIFT ̸= Polyphen ∙ Lots of mutations =⇒ Loads of differing predictions 4
  9. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... ∙ Different categories of mutations: Benign, Damaging, Intermediate ∙ Lack of consensus amongst scoring mechanisms: SIFT ̸= Polyphen ∙ Lots of mutations =⇒ Loads of differing predictions ∙ Exploratory visualization is the first step towards discovering patterns, comparing consensus, aggregating predictions 4
  10. motivation ∙ NGS has given rise to catalog of genetic

    variants: dbSNP, COSMIC... ∙ Different categories of mutations: Benign, Damaging, Intermediate ∙ Lack of consensus amongst scoring mechanisms: SIFT ̸= Polyphen ∙ Lots of mutations =⇒ Loads of differing predictions ∙ Exploratory visualization is the first step towards discovering patterns, comparing consensus, aggregating predictions ∙ Variation viewers are practically absent, those present provide limited flexibility 4
  11. solution ∙ A graphical hub to present annotated variants from

    different sources 5
  12. solution ∙ A graphical hub to present annotated variants from

    different sources ∙ Incremental levels of abstractions 5
  13. solution ∙ A graphical hub to present annotated variants from

    different sources ∙ Incremental levels of abstractions ∙ Scalable and Interactive exploration on the web browser 5
  14. overview Figure: Overview 6

  15. zoomed view Figure: Zoomed View 7

  16. Demo http://saketkc.github.io/biojs 8

  17. . .details

  18. implementation ∙ Written in javascript using the d3js library 10

  19. implementation ∙ Written in javascript using the d3js library ∙

    Deployed as a BioJS component 10
  20. implementation ∙ Written in javascript using the d3js library ∙

    Deployed as a BioJS component ∙ Flexible system with ability to capture and react to user-actions 10
  21. why biojs ∙ BioJS is a javascript library for developing

    visualization of the biological data 11
  22. why biojs ∙ BioJS is a javascript library for developing

    visualization of the biological data ∙ 11
  23. why biojs Reusable components that can talk to each other

    12
  24. data input ∙ Pre-generated JSON files ∙ Current version uses

    files generated by an unpublished webservice at EBI ∙ Protein variants only 13
  25. data input { ”id”:”P00533_variant226”, ”sourceIds”:[”COSM1090877”,”COSM1090879”], ”position”:541, ”wild_type”:”L”, ”mutation”:”I”, ”frequency”:0.0, ”polyphenPrediction”:”benign”,

    ”polyphenScore”:0.0, ”siftPrediction”:”tolerated”, ”siftScore”:0.86, ”somaticStatus”:1, ”consequenceTypes”:”missense variant”, ”cytogeneticBand”:”7p11.2”, ”genomicLocation”:”7:g.55229314C>A” } 14
  26. features ∙ User defined scoring criteria 15

  27. features ∙ User defined scoring criteria ∙ Different levels of

    abstractions, tooltips 15
  28. features ∙ User defined scoring criteria ∙ Different levels of

    abstractions, tooltips ∙ Overview: Condensed information 15
  29. features ∙ User defined scoring criteria ∙ Different levels of

    abstractions, tooltips ∙ Overview: Condensed information ∙ Zoomed View: All annotations 15
  30. features ∙ User defined scoring criteria ∙ Different levels of

    abstractions, tooltips ∙ Overview: Condensed information ∙ Zoomed View: All annotations ∙ SIFT, Polyphen, .... 15
  31. features ∙ User defined scoring criteria ∙ Different levels of

    abstractions, tooltips ∙ Overview: Condensed information ∙ Zoomed View: All annotations ∙ SIFT, Polyphen, .... ∙ Scalable, adaptable to new scores, mutation categories 15
  32. use cases ∙ Identifying most or least mutated sites on

    a protein 16
  33. use cases ∙ Identifying most or least mutated sites on

    a protein ∙ Discover differences between different scoring criteria 16
  34. use cases ∙ Identifying most or least mutated sites on

    a protein ∙ Discover differences between different scoring criteria ∙ Benchmarking predictions 16
  35. improvements ∙ VCF support(almost there!) 17

  36. improvements ∙ VCF support(almost there!) ∙ Integration with Galaxy, web

    based bioinformatics workflows 17
  37. improvements ∙ VCF support(almost there!) ∙ Integration with Galaxy, web

    based bioinformatics workflows ∙ Performance improvements 17
  38. improvements ∙ VCF support(almost there!) ∙ Integration with Galaxy, web

    based bioinformatics workflows ∙ Performance improvements ∙ Interaction with 3D Protein viewer to highlight domains 17
  39. . .conclusion

  40. summary ∙ A tool for visualizing genetic variants ∙ Limited

    applications as a standalone tool, more usable with Protein Features Viewer ∙ Supports visualization of different levels of information ∙ Cross component talks ∙ User defined and user controlled ∙ Open Sourced(MIT License): https://github.com/saketkc/ biojs-genetic-variation-viewer 19
  41. acknowledgements Google | Google Summer of Code 2014 BioJS Community

    Egor Dolzhenko USC MCB 20
  42. Questions? 21