Your SlideShare is downloading. ×
0
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
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Omixon accurate variant detection slideshare version 2011 aug 17

337

Published on

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 .

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
337
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
0
Comments
0
Likes
0
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

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

    ×