The past, present, and future of DNA sequencing
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Transcript of The past, present, and future of DNA sequencing
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The past, present, and future of DNA sequencingDan Russell
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Overview• Prologue: Assembly and Finishing• The Past: Sanger• The Present: Next-Gen (454, Illumina, …)• The Future: ? (Nanopore, MinION, Single-molecule)
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Overview• Prologue: Assembly and Finishing• The Past: Sanger• The Present: Next-Gen (454, Illumina, …)• The Future: ? (Nanopore, MinION, Single-molecule)
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Method Read Length
Sanger 600-1000 bp
454 300-500 bp
Illumina ~100 bp
Ion Torrent ~200 bp
But…• Phage Genome: 30,000 to 500,000 bp• Bacteria: Several million bp• Human: 3 billion bp
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Shotgun Genome Sequencing
Complete genome copiesFragmented genome chunks
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Shotgun Genome Sequencing
Fragmented genome chunks
NOT REALLY DONE BY DUCK HUNTERSHydroshearing, sonication, enzymatic
shearing
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All the King’s horses and all the King’s men…
ATTGTTCCCACAGACCGCGGCGAAGCATTGTTCC ACCGTGTTTTCCGACCG
TTTCCGACCGAAATGGCTTGTTCCCACAGACCGTGAGCTCGATGCCGGCGAAGATGCCGGCGAAGCATTGT
TAATGCGACCTCGATGCCACAGACCGTGTTTCCCGA
AAGCATTGTTCCCACAG TGTTTTCCGACCGAAATCCGACCGAAATGGCTCCTGCCGGCGAAGCCTTGT
Assembly, aka
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Dan’s recommended assemblers
Your Sequencing Technology Recommended Assembler
Sanger phredPhrap
Ion Torrent/454 Newbler
Illumina velvet
REGARDLESS OF ASSEMBLY PROGRAM, I’D RECOMMEND USING CONSED FOR FINISHING!
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Some words have special meanings in scientific context
THEORY
FINISH
Special use of the word “finish”
Before annotation, phage genomes should be sequenced AND finished.
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What is finishing?
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When we put all the reads back together this time:
GAP!
But now we at least know the sequence on each side, so we can design primers to run a sequencing reaction towards the gap, and hopefully connect our contigs.
What is finishing?
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What is finishing?
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What is finishing?A combination of computer and wet-bench work to ensure that the entire genome sequence is present and that all bases are high quality.
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1. Shotgun sequencing to generate reads2. Assembly of reads3. Identification of weak areas4. Targeted sequencing runs to fix5. Verification of finished sequence6. Generation of final fasta file
Done for all phages sequenced at Pitt
Done by most independent seq facilities
NOT DONE by most seq facilities
From DNA to Annotatable Sequence
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1. Shotgun sequencing to generate reads2. Assembly of reads3. Identification of weak areas4. Targeted sequencing runs to fix5. Verification of finished sequence6. Generation of final fasta file
Done for all phages sequenced at Pitt
Done by most independent seq facilities
NOT DONE by most seq facilities = “FINISHING”
From DNA to Annotatable Sequence
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Overview• Prologue: Assembly and Finishing• The Past: Sanger• The Present: Next-Gen (454, Illumina, …)• The Future: ? (Nanopore, MinION, Single-molecule)
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Fragments were cloned:
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Sanger Sequencing ReactionsFor given template DNA, it’s like PCR except:
Uses only a single primer and polymerase to make new ssDNA pieces.
Includes regular nucleotides (A, C, G, T) for extension, but also includes dideoxy nucleotides.
A
A
AAA A
A GA
TCC
C
C
CC
C TT
T
T
TG
G
G
G
G
G
Regular Nucleotides
Dideoxy Nucleotides
A AAA AT
C CC T
TT
TG
GG
G
G
1. Labeled2. Terminators
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer G T C T T G G G C T
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Sanger SequencingG T C T T G G G C T A G C G C
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A
Primer G T C T T G G G C T A
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
5’T G C G C G G C C C A
Primer G
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
5’T G C G C G G C C C A G 12 bp
5’T G C G C G G C C C A
Primer G T C T T G G G C
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
5’T G C G C G G C C C A G 12 bp
5’T G C G C G G C C C A G T C T T G G G C 20 bp
5’T G C G C G G C C C A
Primer G T C T T
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Sanger Sequencing
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
5’T G C G C G G C C C A G 12 bp
5’T G C G C G G C C C A G T C T T G G G C 20 bp
5’T G C G C G G C C C A G T C T T 16 bp
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Sanger Sequencing
A C G C G C C G G G T ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?5’3’
G T C T T G G G C T A G C G C5’
T G C G C G G C C C A
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp
26 bp
5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
5’T G C G C G G C C C A G 12 bp
5’T G C G C G G C C C A G T C T T G G G C 20 bp
5’T G C G C G G C C C A G T C T T 16 bp
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5’T G C G C G G C C C A G T C T T G G G 19 bp5’T G C G C G G C C C A G T C T T G G G C T A 22 bp
Sanger Sequencing
G T C T T G G G C T5’
T G C G C G G C C C A 21 bp5’T G C G C G G C C C A G T C T T G G G C 20 bp5’T G C G C G G C C C A G 12 bp5’T G C G C G G C C C A G T 13 bp5’T G C G C G G C C C A G T C T T 16 bp5’T G C G C G G C C C A G T C 14 bp5’T G C G C G G C C C A G T C T 15 bp5’T G C G C G G C C C A G T C T T G 17 bp5’T G C G C G G C C C A G T C T T G G 18 bpLa
ser
Read
er
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Sanger Sequencing OutputEach sequencing reaction gives us a chromatogram, usually ~600-1000 bp:
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Sanger Throughput Limitations• Must have 1 colony picked for every 2
reactions• Must have 1 PCR tube for each reaction• Must have 1 capillary for each reaction
from The Economist
Improvements in costfrom making Sangerhigher throughput
Improvements in costfrom Next-Gensequencing technologies
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Overview• Prologue: Assembly and Finishing• The Past: Sanger• The Present: Next-Gen (454, Illumina, …)• The Future: ? (Nanopore, MinION, Single-molecule)
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Shotgun sequencing by Ion Torrent Personal Genome Machine and 454
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GenomicFragment
Adapters
Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
GenomicFragment
Barcode
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
Bead/ISP
AdapterComplementSequences
The idea is that each bead should be amplified all over with a SINGLE library fragment.
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
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Shotgun sequencing by PGM/454
~3.5 µm for Ion Torrent, ~30 µm for 454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
T TTT T
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
C CCC C
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
A AAA A
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G GGG G
G
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
GT TT
T TT
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G TC CC
C CC
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T CA AA
A A
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T CG GG
G G
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T CT TT
T TT T
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T C T TC CC
C C
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T C T TA AA
A A
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T C T TG GG
G GG G G
The real power of this method is that it can take place in millions of tiny wells in a single plate at once.
Shotgun sequencing by PGM/454
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A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1
2
3 4
5
G T C T TG GG
G GG G G
The real power of this method is that it can take place in millions of tiny wells in a single plate at once.
Raw 454 data
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Ion Torrent Sequencing
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Illumina Sequencing
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Next-Gen SequencingTake home message: Massively Parallel
1,000 monkeys at 1,000 typewriters is nothing
We’re talking 100,000 to 100 million concurrent reads
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Overview• Prologue: Assembly and Finishing• The Past: Sanger• The Present: Next-Gen (454, Illumina, …)• The Future: ? (Nanopore, MinION, Single-molecule)
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Largely because of PHIRE and SEA-PHAGES…
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DNA Sequencing over Time
from The Economist
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Single Molecule Sequencing
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“The MinION has been used to successfully read the genome of a lambda bacteriophage, which has 48,500-ish base pairs, twice during one pass. That's impressive, because reading 100,000 base pairs during a single DNA capture has never been managed before using traditional sequencing techniques.
The operational life of the MinION is only about six hours, but during that time it can read more than 150 million base pairs. That's somewhat short of the larger human chromosomes (which contain up to 250 million base pairs), but Oxford Nanopore has also introduced GridION -- a platform where multiple cartridges can be clustered together. The company reckon that a 20-node GridION setup can sequence a complete human genome in just 15 minutes.”
—Wired
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Epilogue
So should we really still be sequencing more mycobacteriophage genomes? We have 250+…
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Chimps vs. Humans
Cluster A vs. Cluster B Mycobacteriophages
At the DNA level…
> 95% similar
< 50% similar
…but that’s just one pair of clusters, how many are there?
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DNA Sequencing over Time
from The Economist
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Comparing Different Technologies
Advantages Disadvantages
Lowest error rate
Long read length (~750 bp)
Can target a primer
High cost per base
Long time to generate data
Need for cloning
Amount of data per run
Sanger Sequencing
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Comparing Different Technologies
Advantages Disadvantages
Low error rate
Medium read length(~400-600 bp)
Relatively high cost per base
Must run at large scale
Medium/high startup costs
454 Sequencing
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Comparing Different Technologies
Advantages Disadvantages
Low startup costs
Scalable (10 – 1000 Mb of data per run)
Medium/low cost per base
Low error rate
Fast runs (<3 hours)
New, developing technology
Cost not as low as Illumina
Read lengths only ~100-200 bp so far
Ion Torrent Sequencing
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Comparing Different Technologies
Advantages Disadvantages
Low error rate
Lowest cost per base
Tons of data
Must run at very large scale
Short read length(50-75 bp)
Runs take multiple days
High startup costs
De Novo assembly difficult
Illumina Sequencing
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Comparing Different Technologies
Advantages Disadvantages
Can use single molecule as template
Potential for very long reads(several kb+)
High error rate (~10-15%)
Medium/high cost per base
High startup costs
PacBio Sequencing