What Is Genomics? Genomics is the study of how the entire genome of a species functions as a unit...
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What Is Genomics?Genomics is the study of how the entire genome of a species functions as a unit and evolves over time.
It is the study of life’s blueprint, life’s diversity, and life’s history.Bioinformatics: Analyses the information content of genomes.
Comparative Genomics: Compares genome sequences with each other to infer evolutionary relationships and mechanisms of evolution.
Functional Genomics: Probes how genomes function, as a whole, to give rise to organisms.
Ecological Genomics: Understands how genomes, and the organisms they encode, fill specific environmental niches.
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>500 complete microbial genomes 730 in progress
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Why Sequence Whole Genomes?
• To speed characterization of genes mapped by linkage
• To obtain a "parts list" for what makes up an organism.
• To discover what sets of genes make organisms (and each of us) similar to and different from one another.
• To understand our evolutionary heritage. Our genomes are a reflection of our recent and ancient origins.
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Dideoxy “chain termination” DNA sequencing-Sanger v1, continued
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Dideoxy “chain termination” DNA sequencing-
Sanger v2 !!
Fred Sanger, SECOND Nobel Prize in 1980 (Chemistry; his first was in1958 for methods for determining amino acid sequences in proteins).
Made easily robot friendly.
High throughput DNA sequencing hasallowed the sequencing of whole Genomes.
This has driven the Genomics revolution.
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Sheared and ssDNA Oil emulsion: 1 template/bead
Polony: clonal amplification
Polony + enzyme beads
Picoliter plate
The Next Gen Technologies: Pyrosequencing (454, Roche)
First of the ‘parallel’ sequencing platforms.
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Sequencing-by-synthesisPyrosequencing
3’ATCGTTGCACGTCGACGTA5’TAGCAACG
dGTP PPi
ATP
ATP sulfurylase
Luciferase
400K reads X 400 bases = 16-20 Mb in 4 hrs!
So, 125 Mb is only 6 runs for 1X coverage!
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Sequence by synthesis – one base at a time
Each base has a different color
Each base has a reversible terminator
The Next Gen Technologies: Illumina (Solexa)
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DNA Single molecule array
Sample preparation Cluster growth
5’
5’3’
G
T
C
A
G
T
C
A
G
T
C
A
C
A
G
TC
A
T
C
A
C
C
TAG
CG
TA
GT
1 2 3 7 8 94 5 6
Image acquisition Base calling
T G C T A C G A T …
Sequencing
5 million clusters / channel; 8 channels / flow cell = 40 million reads times ~35 cycles (bases) = 120 billion bases in 3 days (1.2Gb)
The Next Gen Technologies: Illumina (Solexa)
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Sanger Shotgun
454 Solexa
Cloning Yes No No
Chemistry Sanger pyrosequencing reversible terminators
DNA bases per $
Human (1X!!) $
1000
3,000,000
50,000
60,000
500,000
6,000
Time A really long time
4 hours 4 days
Accuracy Consensus 99.99%
Worst of the 3; not good with homopolymer repeats
1-3% errors
Assembly
Computational
tools
Best OK Horrible
Gap Closure and Finishing
Pain Pain in the rear ROYAL Pain in the rear
Technology Development drives Biology
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First, we've learned that we have a lot to learn
Over 35% of genes in ANY organism (including Human) have no deducible function!
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feynman.html
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