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Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
Omixon   accurate variant detection slideshare version 2011 aug 17
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Omixon accurate variant detection slideshare version 2011 aug 17

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This presentation describes some of our results in genomic variant detection. Using Omixon software we find variants not found by other software. We introduce a new short read mapping for Illumina, …

This presentation describes some of our results in genomic variant detection. Using Omixon software we find variants not found by other software. We introduce a new short read mapping for Illumina, Ion Torrent and 454 for highly sensitive mapping and alignment especially for repeats. This is an excellent way to correct for homopolymer errors in 454 and Ion Torrent data. For a free download visit http://www.omixon.com/omixon/abouttoolkit2.htm .

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  • (double, triple substitutions, indels next to SNPs,10-30 bpindels, homopolymerindels, indels in palindromes, variants within GA repeats or TATA box)
  • Transcript

    • 1. Finding Novel Variants with Omixon Variant Toolkit
      Attila Berces, PhD
      CEO, Omixon
    • 2. Omixon
      Bioinformatics
      Accurate variant analysis
      Cloud computing
      Usability
      • software products
      • 3. cloud computing service
      • 4. consultancy
    • Omixon – key people
      Science/technology
      Miklos Csuros, -
      professor University of Montreal, PhD from Yale University
      Tim Hague, BS Genetics, MSc System Design
      IBM, Lufthansa system
      Management
      Attila Bérces, PhD CEO,
      formerexecutive at AstraZeneca
      Lab head, Novartis
      S. George Simon,
      formerexecutivedirectoratMyriadGenetics
    • 5. Late breaking development
      Omixon Read Mapper
      for Illumina, Ion Torrent and Roche
    • 6. Omixon read mapper
      Scientific advances
      Sensitive handling of indels, especially tandem repeats
      Match/mismatch w/ local base composition
      Variable indexing density
      Letter space (Illumina, SOLiD5500, Roche, Ion Torrent)
      homopolymer error correction
    • 7. Omixon read mapper
      User benefits
      Identify variants with more confidence
      higher coverage
      Identify difficult-to-find variants
      Save on consumables lower coverage
      Accurate read mapping at fast computational speed
    • 8. Re-mapping validation
      Synthetic, 51 bpIllumina reads, experimental QVs
    • 9. Sensitive handling of short repeats
    • 10. Homo/hetero zygos double substitution
    • 11. Four times exon coverage
      [0-96]
      BWA
      [0-432]
      Omixon
    • 12. Higherexomecoverage
      [0-10]
      BWA
      [0-24]
      Omixon
    • 13. Identify more valid variants
      BWA
      Omixon
    • 14. Find homopolymerindels
      BWA
      Omixon
    • 15. Why focus on variant analysis accuracy?
    • 16.
    • 17. With scalable throughput and up to 99.99% accuracy, the SOLiD™ System enables you ……
    • 18.
    • 19. Illumina sequencing systems, powered by TruSeq technology, deliver
      the most accurate data across a broad range of applications.
    • 20. What is limiting the accuracy of variant analysis?
    • 21. DNP example
      100 % accurate synthetic SOLiD v.4 reads reproducing naturally occurring DNPs
    • 22. Found DNPs
      Bioscope: bioscope-v1.3-rBS131_55029_20101119113500; 
      BFAST 0.6.4f (2011-03-11); parameters: Clark MJ, Homer N, O'Connor BD, Chen Z,
      Eskin A, et al. PLoS Genet 6(1)
      SHRiMP 2.1.1b ( February 8, 2011) parameters: gmapper-cs -L database reads.csfasta
      -V -w 150% -n 1 -r 50% -v 55% -l 40% -Z -h 60% -a -1 (mapping in overly sensitive mode)
    • 23. BFAST
      SHRiMP
    • 24. … and with real data
    • 25. Omixon
      Omixon
      Bioscope
      BFAST
      SHRiMP
    • 26. Omixon
      Omixon
      Bioscope
      BFAST
      SHRiMP
    • 27. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 28. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 29. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 30. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 31. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 32. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 33. First conclusion
      Read accuracy is not the limiting factor in accurate variant analysis
    • 34. Sanger validation
    • 35. Visual inspection of short reads and variant calls
    • 36. Sanger validation of inferred variants
      Omixon
      Omixon
      Omixon
      Omixon
      Omixon
    • 37. Sanger validation of inferred variants
      Omixon
      Omixon
      Omixon
      Omixon
      Omixon
    • 38. Second conclusion
      As variant density increases the performance of most tools go down
    • 39. What types are the variants were only found by Omixon?
      DNPs
      TNPs
      Small indels, especially next to SNPs
      9-12 bpindels
      Homopolymerindels
      Homopolymerindel and SNP together
      Indels in palindromes
      Variants within GA repeats
      Pairwise substitution in TATA box
    • 40.
    • 41. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 42. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 43. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 44. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 45. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 46. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 47. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 48. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 49. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 50. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 51. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 52. Omixon
      Bioscope
      BFAST
      SHRiMP
    • 53. Benefits of the Omixon plug-in for CLC bio workbench/server
    • 54. Benefits of CLC bio plug-in
      Omixon
      CLC bio
    • 55. Benefits of CLC bio plug-in
      Omixon
      CLC bio
    • 56. Benefits of CLC bio plug-in
      Omixon
      CLC bio
    • 57. Benefits of CLC bio plug-in
      Omixon
      CLC bio
    • 58. Benefits of CLC bio plug-in
      Omixon
      CLC bio
    • 59. Outstanding challenges
    • 60. The sensitivity specificity challenge
    • 61. How is Omixon different?
    • 62. Sequencer-specific algorithms
      SOLiD
      Illumina
      SOLiD 5500
      Application-specific algorithms
      Exome-sequencing
      RNA-seq
      No sensitivity vs.specificitytrade-off
      Alignment based on DNA mutation model
    • 63. Codon-based alignment
    • 64.
    • 65. Please view our poster.
    • 66. No Smith-Waterman
      No artifacts to correct downstream
      Quality values used in alignment
      Quality recalibration is the result not the input of the process
    • 67. Our SOLiD Alignment Tools
      Csuros, Juhos, Berces "Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA" Springer Lecture Notes in Bioinformatics6293:176-188, 2010.
    • 68. Computational Challenge
    • 69.
    • 70.
    • 71.
    • 72.
    • 73. Conclusions
      There is no perfect method today for variant analysis but significant differences exist in accuracy
      OmixonVariant Toolkit provides highly sensitive and accurate analysis

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