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The effect of Next - Generation Sequencing technology on complex trait research

The effect of Next - Generation Sequencing technology on complex trait research. Challenge analysis. Presented by December 10, 2013. Ladang Auxane Mombaerts Laurent Uyttendaele Vincent. TABLE OF CONTENTS. Introduction Challenge analysis

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The effect of Next - Generation Sequencing technology on complex trait research

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  1. The effect of Next-GenerationSequencingtechnology on complex trait research Challenge analysis Presentedby December 10, 2013 Ladang Auxane Mombaerts Laurent UyttendaeleVincent University of Liège GBIO0009-1 : Krystel Van Steen, Kyrill Bessonov

  2. TABLE OF CONTENTS • Introduction • Challenge analysis • Optimizingparameters for study design • Storing and handling data • Mapping and aligning • Variant calling • Analyzinglowfrequency and rare variants • Applications • Discussion • Conclusion University of Liège GBIO0009-1 : Krystel Van Steen, Kyrill Bessonov

  3. INTRODUCTION WhatisNext-GenerationSequencing (NGS) ? High throughput Low-cost Applications From 1970 untilnow 3 F. Sanger University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  4. Three mains parameters: High cost-to-data. Only parts of thegenome? Power based on depth of coverage. Sample selection. CHALLENGE ANALYSIS 4 • 1. Optimizing parameters for study design University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  5. CHALLENGE ANALYSIS • Storing and handling data University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  6. CHALLENGE ANALYSIS University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  7. CHALLENGE ANALYSIS • 3. Mapping and aligningalgorithms University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  8. CHALLENGE ANALYSIS University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  9. CHALLENGE ANALYSIS • 4. Variant calling Distinguish true variant from sequencing or mapping errors → Decrease the number of false positive SNP-calls University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  10. CHALLENGE ANALYSIS University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  11. CHALLENGE ANALYSIS • 5. Analyzinglowfrequency and rare variants May be a painfulstep ! University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  12. APPLICATIONS The number of scientific publications has exploded ! University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  13. DISCUSSION Development of new study design • Development of more effective methods to distinguish errors from low frequency & rare variants • Development of the most appropriate strategy to identify one disease. University of Liège University of Liège GBIO0009-1 : Krystel Van Steen, Kyrill Bessonov

  14. DISCUSSION Cost-benefit analysis Whole genome sequencing is unlikely to be cost effective as it still presents huge challenges. → coupling a reduction of the costs with an increase of the efficiency and the accuracy. → make NGS platforms marketable, competitive and usable for clinical applications. University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  15. DISCUSSION Validation analysis Standards for NGS clinical genomics are required, for instance to validate the test accuracy. → important downstream impact on the patient diagnostic and management. University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  16. DISCUSSION Currentknowledge and research • Lack of knowledge • in what a SNP implies • in how we detect interaction between genes • in which influence gene expression has • in which interpretation must be given to the genome variance … The more we make tests,the more knowledge we get,the more associations between phenotype and genome we can do. University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  17. Conclusion University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

  18. REFERENCES A G Day-Williams, E Zeggini, The effect of Next-Generation Sequencing technology on complex trait research, Eur J Clin Invest 2011, Vol 41 : 561-567. http://videos.rennes.inria.fr/genopole/GenOuest-2010/, [online on 7th December 2013] http://www.qiagen.com/products/applications/next-generation-sequencing/#Dataanalysis, [online on 9th December 2013] Figures http://www.labtimes.org/labtimes/method/methods/2010_01.lasso http://nextgenseek.com/2012/01/illumina-launches-a-new-faster-sequencer-hiseq-2500/ http://www.nucleics.com/DNA_sequencing_support/DNA-sequencing-dye-blobs.html http://videos.rennes.inria.fr/genopole/GenOuest-2010/peterlongo_plateforme_2010_10_26.pdf http://www.genomicslawreport.com/index.php/tag/illumina/ http://www.cancer.gov/cancertopics/understandingcancer/geneticvariation/page40 University of Liège GBIO0009-1 : Krystel Van Steen, KyrillBessonov

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