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NextGen Sequencing data intro.

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Avatar for David Rio Deiros David Rio Deiros
March 26, 2012
Research
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NextGen Sequencing data intro.

Brief introduction to nextgen sequencing data.

Avatar for David Rio Deiros

David Rio Deiros

March 26, 2012
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Transcript

  1. Next-Gen Sequencing Data

  2. @shiondev

  3. @drio

  4. None

  5. Σ Bases DNA == “The Genome”

  6. Σ Bases DNA == “The Genome” 3Gbp

  7. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG…

  8. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G  

  9. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G  

  10. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T  

  11. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐  

  12. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐   A  

  13. …ACAGTTTTCAAGAGCCGGTTTTACTAGGATTATTACTG… G   T   -­‐   A  

  14. SEQUENCING

  15. None

  16. # of Bases per day per machine

  17. 200kbp 2000

  18. 1Mbp 2003

  19. 200 Mbp 2005

  20. 3Gbp 2009

  21. 60Gbp 2012

  22. what can we do with NGS data?

  23. Re-sequencing

  24. Re-sequencing Looking for changes in a Genome

  25. Re-sequencing Looking for changes in a Genome (Given that we

    have a HIGH quality reference)

  26. Re-sequencing Looking for changes in a Genome (Given that we

    have a HIGH quality reference) Consequences?

  27. Reliably finding those changes is not easy

  28. (1%-3%) of your bases may be errors.

  29. 30x

  30. What’s the typical workflow in a re-sequencing project ?

  31. Library preparation

  32. Library preparation Sequencing

  33. Library preparation Sequencing Analysis I (images -> reads)

  34. .fastq ... >HWI-ST821_0129:5:1101:1927:2089#GATCAG/1 TGGACAACGGCCAGGTTAATGATGGGCAGGTAGAAGATGATCACT +HWI-ST821_0129:5:1101:1927:2089#GATCAG/1 ___ccccccYc[eff`]X`a^ef][RHP^_cXIYSXcXcfSWXcd ...

  35. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments)
  36. None

  37. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling)

  38. .vcf

  39. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling) Annotation

  40. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (Variant calling) Annotation Science starts here …
  41. None

  42. Library preparation Sequencing Analysis I (images -> reads) Analysis II

    (alignments) Analysis III (SNP calling) Annotation 5/15 Tb 150Gb 80G 16 8G 1G 1 400Mb 1

  43. 1 Genome (3-6 days) ~ 230Gb

  44. 1 Genome

  45. Let’s do it again for N genomes

  46. Let’s do it again for N genomes

  47. None
  48. None
  49. None
  50. None
  51. None
  52. None
  53. None

  54. personalize medicine

  55. personalize medicine Tailor physician decisions and practices to individual patients

  56. Let’s do it again for N genomes

  57. None
  58. None

  59. Thanks!