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Bes meeting spain 2015_alfredo garcia fernandez

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Bes meeting spain 2015_alfredo garcia fernandez

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Bes meeting spain 2015_alfredo garcia fernandez

  1. 1. Aplicaciones y limitaciones de las tecnologías Next Generation Sequencing a nuestros estudios
  2. 2. Sanger sequencing
  3. 3. Sanger sequencing Number of sequences 96 Sequences/run Length 0,5-2 KiloBases Accuracy 99% Cost 200.000 $ GigaBase
  4. 4. Sanger sequencing
  5. 5. Sanger sequencing • Published in 2003. • Free access. • 3 Billons $ and 15 years of work. • Starting point for future projects (Encode, 1000 Genomes…). • Economic impact until 2011: 796 Billons $.
  6. 6. Sanger sequencing • However: 1. The cost of a new genome still high, 10.000 – 100.000 $. 2. Hard lab work. 3. Development of new technologies are essentials.
  7. 7. Next Sequencing Technologies
  8. 8. Next Sequencing Technologies
  9. 9. Next Sequencing Technologies Sanger NGS Number of sequences 96 Seqs/run 8 Human Genomes/run Length 0.5-2 KiloBases Up to 40 KiloBases Accuracy 99% 85% to 99% Cost 200.000 $ GigaBase 2.000 $ GigaBase
  10. 10. Next Next Sequencing Technologies
  11. 11. New challenges • Bioinformatic approach, how work with Gbytes of sequences?? Linux
  12. 12. New challenges • Bioinformatic approach, how work with Gbytes of sequences?? Linux • Quality controls. • Decision in sequencing platform and software. • Constant change. First NGS technologies (e.g. Roche 454) are obsolete.
  13. 13. New challenges • Number of samples. • Necessity of replicates? Biological – Technical? • Type of reads. • Number of reads / Coverage. • Library construction and complexity. • Reference genome. Gene annotation.
  14. 14. Some applications: Assembly de novo
  15. 15. Some applications: Metagenomics • Characterize species (bacteria/virus) present in an environment • Soil, water, fecal… • Associate metagenomics results with the origin of the sample (e.g. host, environment etc.). • Sequence of specific region (e.g. 16S), not whole genome. • Binning with described species. • Specific software: Phymm, MetaPhlAn…
  16. 16. Some applications: Metagenomics • Binning with described species.
  17. 17. Some applications: Metagenomics • Increase bacterial genome sequences. • 4.100 species. 17.000 bacterial genomes.
  18. 18. Some applications: Population genomics • Whole genome not necessary for all cases. • Identify neutral and adaptive regions. • Not necessary reference genome. • Different approaches, based in restriction enzymes: • Genotyping By Sequencing (GBS). • Restriction site Associated DNA (RAD).
  19. 19. Some applications: Population genomics
  20. 20. Some applications: Population genomics
  21. 21. Some applications: Transcriptomics • Real expression of the DNA. • Not necessary reference genome. • Annotation with described genes. • Quantify genome expression.
  22. 22. Some applications: Transcriptomics • Read mapping (alignment): place the “shorts” reads in the genome • Quantification: • Assigning to genes • Determining whether a gene is expressed • Normalization • Compare between samples
  23. 23. Some applications: Transcriptomics
  24. 24. Some applications: Transcriptomics
  25. 25. Some applications: Transcriptomics
  26. 26. Some applications: Transcriptomics
  27. 27. Gracias…

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