bioinformatics bioinformatics next-generation sequencing vs. microarray in epigenetic bosch vincent...
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![Page 1: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/1.jpg)
BIOINFORMATICS
NEXT-GENERATION SEQUENCING
VS. MICROARRAY IN EPIGENETIC
Bosch VincentKlecker SophieStraat Julien© Copyright 2013
![Page 2: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/2.jpg)
Talk Outline
Summary
Microarray
NGS
Discussion
Conclusion
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 3: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/3.jpg)
Summary
« Advantages of next-generation sequencing versus the microarray in epigenetic research »Pau l J . Hurd and Chr i s topher J . Ne l son25 June 2009
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 4: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/4.jpg)
Microarray
h t t p : / / w w w. w i s s e n s s c h a u . d e / g e n o m / g e n t e s t _ m i c ro a r r a y _ g e n c h i p . p h p
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 5: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/5.jpg)
Solexa/Illumina
http://seqanswers.com/forums/showthread.php?t=21
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 6: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/6.jpg)
Solexa/Illumina
http://seqanswers.com/forums/showthread.php?t=21
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
Go further:http://www.dnatube.com/video/27892/What-is-Illumina-Solexa-sequencing-
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SOLiD
http://pingjie.wordpress.com/2009/03/05/
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 8: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/8.jpg)
SOLiD
http://www.clinchem.org/content/55/4/641/F3.expansion
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
Go further:http://www.youtube.com/watch?v=nlvyF8bFDwM
![Page 9: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/9.jpg)
454 Pyrosequencing
http://www.medscape.com/viewarticle/738786_6
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & AGo further: http://www.youtube.com/watch?v=nFfgWGFe0aA
![Page 10: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/10.jpg)
Comparison Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 11: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/11.jpg)
Microarrays :
Used by most of the researchers and
available informatic tools
Cheaper (small genome)
Dominate certain application
Future of Microarrays and NGS Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 12: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/12.jpg)
NGS technologies:
Read longer sequences
Faster reading
Become more affordable
Future of Microarrays and NGS Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 13: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/13.jpg)
Example: Human genome
sequencing
2003
~2.7 billon dollars
13 years
2008 (with NGS)
~30 million dollars (1%)
2 months
Future of Microarrays and NGS Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 14: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/14.jpg)
NGS technologies & microarrays :
work together
Microarrays : survey of a genome
NGS tech.: more accurate data
Examples:
Microarrays, 454 and Solexa/Illumina
Bisulphite-treatment and MeDIP
Future of Microarrays and NGS Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 15: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/15.jpg)
Single Molecule Real Time sequencing
Single Molecule Real Time
sequencing
How does it work?
A single molecule of DNA polymerase
Real-time analyses
Advantages
Extremely high-throughput
Decreasing sequencing time
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 16: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/16.jpg)
Conclusion
Microarrays
NGS technologies
New generation:
Third generation: SMRT
Fourth generation: still in development
Data analysis, management,
storage?
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 17: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/17.jpg)
Advantages of next-generat ion sequencing versus the microarray in epigenet ic research. Paul J . Hurd and Chr istopher J . Ne lson, 25 June 2009
http: / /seqanswers.com/forums/showthread.php?t=21 http: / /p ingj ie .wordpress.com/2009/03/05/ http: / /www.cl inchem.org/content/55/4/641/F3.expansion http: / /www.medscape.com/viewart ic le/738786_6
Bibliography Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A
![Page 18: BIOINFORMATICS BIOINFORMATICS NEXT-GENERATION SEQUENCING VS. MICROARRAY IN EPIGENETIC Bosch Vincent Klecker Sophie Straat Julien © Copyright 2013](https://reader035.vdocuments.net/reader035/viewer/2022062222/56649f145503460f94c28255/html5/thumbnails/18.jpg)
Q & A
Introduction• Talk
Outline
• Summary
Microarray
NGS• S./Illumina
• SOLiD
• 454
• Compariso
n
Discussion• Future
• SMRT
Conclusion
Bibliography
Q & A