lecture 14: dna sequencing - rhodes collegecs.rhodes.edu/welshc/comp465_f13/lecture14a.pdf10/18/2013...
TRANSCRIPT
10182013 COMP 465 Fall 2013 1
Lecture 14 DNA Sequencing
Study Chapter 89
10182013 COMP 465 Fall 2013 2
DNA Sequencing
bull Shear DNA into
millions of small
fragments
bull Read 500 ndash 700
nucleotides at a time
from the small
fragments
(Sanger method)
10182013 COMP 465 Fall 2013 3
Fragment Assembly
bull Assembles the individual overlapping short fragments (reads) into a genomic sequence
bull Shortest Superstring problem from last time is an overly simplified abstraction
bull Problems
ndash DNA read error rate of 1 to 3
ndash Canrsquot separate coding and template strands
ndash DNA is full of repeats
bull Letrsquos take a closer look
10182013 COMP 465 Fall 2013 4
Construction of Repeat Graph
bull Construction of repeat graph from k ndash mers
emulates an SBH experiment with a huge
(virtual) DNA chip
bull Breaking reads into k ndash mers Transform
sequencing data into virtual DNA chip data
10182013 COMP 465 Fall 2013 5
Construction of Repeat Graph (contrsquod)
bull Error correction in reads ldquoconsensus firstrdquo
approach to fragment assembly Makes reads
(almost) error-free BEFORE the assembly even
starts
bull Using reads and mate-pairs to simplify the
repeat graph (Eulerian Superpath Problem)
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 2
DNA Sequencing
bull Shear DNA into
millions of small
fragments
bull Read 500 ndash 700
nucleotides at a time
from the small
fragments
(Sanger method)
10182013 COMP 465 Fall 2013 3
Fragment Assembly
bull Assembles the individual overlapping short fragments (reads) into a genomic sequence
bull Shortest Superstring problem from last time is an overly simplified abstraction
bull Problems
ndash DNA read error rate of 1 to 3
ndash Canrsquot separate coding and template strands
ndash DNA is full of repeats
bull Letrsquos take a closer look
10182013 COMP 465 Fall 2013 4
Construction of Repeat Graph
bull Construction of repeat graph from k ndash mers
emulates an SBH experiment with a huge
(virtual) DNA chip
bull Breaking reads into k ndash mers Transform
sequencing data into virtual DNA chip data
10182013 COMP 465 Fall 2013 5
Construction of Repeat Graph (contrsquod)
bull Error correction in reads ldquoconsensus firstrdquo
approach to fragment assembly Makes reads
(almost) error-free BEFORE the assembly even
starts
bull Using reads and mate-pairs to simplify the
repeat graph (Eulerian Superpath Problem)
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 3
Fragment Assembly
bull Assembles the individual overlapping short fragments (reads) into a genomic sequence
bull Shortest Superstring problem from last time is an overly simplified abstraction
bull Problems
ndash DNA read error rate of 1 to 3
ndash Canrsquot separate coding and template strands
ndash DNA is full of repeats
bull Letrsquos take a closer look
10182013 COMP 465 Fall 2013 4
Construction of Repeat Graph
bull Construction of repeat graph from k ndash mers
emulates an SBH experiment with a huge
(virtual) DNA chip
bull Breaking reads into k ndash mers Transform
sequencing data into virtual DNA chip data
10182013 COMP 465 Fall 2013 5
Construction of Repeat Graph (contrsquod)
bull Error correction in reads ldquoconsensus firstrdquo
approach to fragment assembly Makes reads
(almost) error-free BEFORE the assembly even
starts
bull Using reads and mate-pairs to simplify the
repeat graph (Eulerian Superpath Problem)
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 4
Construction of Repeat Graph
bull Construction of repeat graph from k ndash mers
emulates an SBH experiment with a huge
(virtual) DNA chip
bull Breaking reads into k ndash mers Transform
sequencing data into virtual DNA chip data
10182013 COMP 465 Fall 2013 5
Construction of Repeat Graph (contrsquod)
bull Error correction in reads ldquoconsensus firstrdquo
approach to fragment assembly Makes reads
(almost) error-free BEFORE the assembly even
starts
bull Using reads and mate-pairs to simplify the
repeat graph (Eulerian Superpath Problem)
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 5
Construction of Repeat Graph (contrsquod)
bull Error correction in reads ldquoconsensus firstrdquo
approach to fragment assembly Makes reads
(almost) error-free BEFORE the assembly even
starts
bull Using reads and mate-pairs to simplify the
repeat graph (Eulerian Superpath Problem)
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 6
Approaches to Fragment Assembly
Find a path visiting every VERTEX exactly
once in the OVERLAP graph
Hamiltonian path problem
NP-complete algorithms unknown
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 7
Approaches to Fragment Assembly (contrsquod)
Find a path visiting every EDGE exactly once
in the REPEAT graph
Eulerian path problem
Linear time algorithms are known
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 8
Making Repeat Graph Without DNA
bull Problem Construct the repeat graph from a collection of reads
bull Solution Break the reads into smaller pieces
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 9
Repeat Sequences Emulating a DNA Chip
bull Virtual DNA chip allows the biological problem to be solved within the technological constraints
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 10
Repeat Sequences Emulating a DNA Chip (contrsquod)
bull Reads are constructed from an original sequence in lengths that allow biologists a high level of certainty
bull They are then broken again to allow the technology to sequence each within a reasonable array
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 11
Minimizing Errors
bull If an error exists in one of the 20-mer reads the error will be perpetuated among all of the smaller pieces broken from that read
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 12
Minimizing Errors (contrsquod)
bull However that error will not be present in the other instances of the 20-mer read
bull So it is possible to eliminate most point mutation errors before reconstructing the original sequence
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10182013 COMP 465 Fall 2013 13
Conclusion from Previous Lecture
bull Graph theory is a vital tool for solving biological problems
bull Wide range of applications including sequencing motif finding protein networks and many more
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
DNA Sequencing Timeline
10212013 COMP 465 Fall 2013 14
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 15
Generations of Sequences
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
High-Throughput Sequencing
bull Also referred to as Next-Generation Sequencing
bull Parallelize the sequencing process producing thousands or millions of sequences concurrently
bull Lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods
bull In ultra-high-throughput sequencing as many as 500000 sequencing-by-synthesis operations may be run in parallel
10212013 COMP 465 Fall 2013 16
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10212013 COMP 465 Fall 2013 17
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 18
Next Generation Sequencing Amplified Single Molecule Sequencing
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Next Generation Sequencing Amplified Single Molecule Sequencing
10222013 COMP 465 Fall 2013 19
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
454 Sequencing
10222013 COMP 465 Fall 2013 20
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
454 Sequencing
10222013 COMP 465 Fall 2013 21
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 22
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 23
454 Sequencing Pyrosequencing
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 24
454 Sequencing Pyrosequencing
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
SOLiD
10222013 COMP 465 Fall 2013 25
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 26
SOLiD
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Sequencing By Ligation
10222013 COMP 465 Fall 2013 27
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 28
Sequencing By Ligation
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 29
Sequencing By Ligation
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 30
Sequencing By Ligation
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 31
Sequencing By Ligation
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 32
Sequencing By Ligation
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 33
Sequencing By Ligation
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 34
Sequencing By Ligation
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Sequencing By Ligation
10222013 COMP 465 Fall 2013 35
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Illumina
10222013 COMP 465 Fall 2013 36
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Illumina
10222013 COMP 465 Fall 2013 37
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Illumina
10222013 COMP 465 Fall 2013 38
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Which Next-Gen Sequencer to Choose for your Project
10222013 COMP 465 Fall 2013 39
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Mouse Genomes Project
bull httpwwwsangeracukcgi-binmodelorgsmousegenomeslookseqindexplshow=8101738730-101738871paired_pileupamplane=C3H_HeJbamampwidth=900ampwin=141ampdisplay=|perfect|single|inversions|pairlinks|potsnps|uniqueness|gc|coverage|orientation|annotation|gc|coverage|ampmaxdist=1000
10222013 COMP 465 Fall 2013 40
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Sequence Comparisons
10222013 COMP 465 Fall 2013 41
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Human Genome Project
bull In Dec 1 1999 researchers in the Human Genome Project announced the complete sequencing of the DNA making up human chromosome 22
bull In 2000 the completion of a ldquoworking draftrdquo DNA sequence of the human genome was announced
bull Special issues of Nature and Science came out in February of 2001 with the complete working draft human genome
10222013 COMP 465 Fall 2013 42
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Human Genome Project
10222013 COMP 465 Fall 2013 43
bull International HapMap Project began in 2002
bull Special issue of Nature Human Genome Collection (2006)
bull On June 13 2013 The US Supreme Court ruled that naturally occurring DNA cannot be patented but that synthetically created cDNA is patent-eligible
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
10222013 COMP 465 Fall 2013 44
References
bull Simons Robert W Advanced Molecular Genetics Course UCLA (2002)
bull Batzoglou S Computational Genomics Course Stanford University (2006) httpaistanfordedu~serafimCS262_2006
bull Vierstraete Andy Next Generation Sequencing University of Ghent httpusersugentbe~avierstrnextgennextgenhtml
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45
Next Time
bull Protein Sequencing
bull Sections 810-815
10212013 COMP 465 Fall 2013 45