DNASequencing
GenomicScienceandLeadershipWorkshopMay25,2017
AgnesChan
(1)WhySequencingDNA?
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What is DNA (Deoxyribonucleic acid)?A biomolecule containing genetic information.DNA sequencing: Determine the order of nucleotides of a DNA fragment
https://www.genome.gov/18016863/a-brief-guide-to-genomics/ 3https://www.genome.gov/images/content/dna_factsheet.j
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WhystudyingDNAsequence?Studymicrobeslivinginnatureandourbodies(microbiome)
http://learn.genetics.utah.edu/content/gsl/diversity/ 4
Environments
Human skin microbiome
WhystudyingDNAsequence?Decodethehumangenome:Firsthumangenomesequenced(1990-2003),1000humangenomes
By Jthiele at English Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=5413
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WhystudyingDNAsequence?Decodethehumangenome:identifygenes,healthordisease
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SequenceandStructuralVariants
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WhystudyingDNAsequence?Decodethehumangenome:Geneticdiversitywithinandacrosspopulations
By Jthiele at English Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=54137526
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(2)SequencingTechnology
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GrowthofDNASequencing
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.100219510
TheCostofSequencingperHumanGenome
https://www.genome.gov/sequencingcosts/11
SangerSequencing– ChainTermination
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http://www.cegat.de/web/wp-content/uploads/2015/10/sequencing-1.png 13
IlluminaSequencing– Sequencing-by-synthesis
IlluminaSequencing– BridgeAmplification
http://www.3402bioinformaticsgroup.com/wp-content/uploads/2016/07/NGS.png 14
IlluminaTechnologyVideo
• https://www.youtube.com/watch?v=HMyCqWhwB8E• ClusterGeneration• Sequencing-by-synthesis(0to3:09)
NanoporeSequencinghttps://nanoporetech.com/how-it-works
http://www.nature.com/nrg/journal/v17/n6/fig_tab/nrg.2016.49_F5.html16
• 5-10Gb of DNA sequence data
• Ultra-long reads• Real time data• PC laptop
OxfordNanoporeTechnology
https://nanoporetech.com/products/smidgion 17
• Field-based sequencing not confined to labs
• Pathogen outbreaks• Environmental extremes
SmidgIONMinION
(3)DNALabfromTuesday
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WaterMicrobiomeStudyWorkflow
Collect samples
Isolate DNA Collect microbes on filter membrane
PCR amplification of 16S rRNA gene
Agarose gel analysis of PCR products
Run 16S analysis
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Interpret DNA Sequence
DNA Sequencing (Illumina MiSeq)
Day 1
Day 3
Who’sthere?
http://learn.genetics.utah.edu/content/microbiome/study/
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Review16SPCRresultsfromDay1
Foreachgroup:1. DNAsizemarker(100bp ladder)2. Positivecontrol3. Negativecontrol4. Skateparkrunoff
100 bp
• WhatisthesizeofthePCRproduct?• Whatdeterminesitssize?