A1260212413IMKad

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Future Genomics
Nadav Ahituv UCSF
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In the midst of revolutionary times
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OUTLINE
1. The human genome
2. Novel sequencing technologies
3. New genomic terrains to be uncovered
4. Advantages of individual genomes
5. Challenges risks of individual genomes
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Why do we need more DNA?
1. Splicing
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Introns, exons splicing in eukaryotic genes
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Why do we need more DNA?
1. Splicing
2. Regulation
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Regulatory Elements Promoter, Enhancer,
Silencer, Insulator
Insulator
Promoter
Gene A
Enhancers
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Why do we need more DNA?
1. Splicing
2. Gene Regulation
3. We have a lot of viruses repeats in our
genome
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Genes make up ONLY 2 of our genome
2 Coding
45 Viruses Repeats
98 Noncoding
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Why do we need more DNA?
1. Splicing
2. Gene Regulation
3. We have a lot of viruses repeats in our
genome
4. We are more complex
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Pine Tree 12
60,000 18 billion
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OUTLINE
1. The human genome 3.1 billion 3.1 Giga base
(Gb)
2. Novel sequencing technologies
3. New genomic terrains to be uncovered
4. Advantages of individual genomes
5. Challenges Risks of individual genomes
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How Genomes are Sequenced

1. Fractionate the DNA into RANDOM small pieces and
   sequence all of them.

7-13 X coverage
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Sanger Sequencing
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Pyrosequencing
READ
WASH
ADD NEW NUCLEOTIDE
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Illumina Genome Analyzer (Solexa)
Total sequence 10Gb
Run time 5 days Average read length
30bp Price per run 3,000
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454 (Roche)
Total sequence 1Gb
Run time 5hr Average read length
500bp Price per run 5,000
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In the midst of revolutionary times
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3rd generation sequencing platforms
Complete Genomics
Pacific Biosciences
Oxford Nanopore Technologies
Helicos Biosciences
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OUTLINE
1. The human genome
2. Novel sequencing technologies
3. New genomic terrains to be uncovered
4. Advantages of individual genomes
5. Challenges risks of individual genomes
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1. Gene regulation
2. Histone code
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The Human Genome Status
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Genes make up ONLY 2 of our genome
2 Coding
98 Noncoding
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AGGAAGGGAAAGCGCAAGAGAGAGCGCACACGCACACACCCGCCGCGCGC
ACTCGCGCACGGACCCGCACGGGGACAGCTCGGAAGTCATCAGTTCCATG
GGCGAATGCTGCTGCTGGCGAGATGTCTGCTGCTAGTCCTCGTCTCCTCG
CTGCGGTATGCTCGGGACTGGCGTGCGGACCGGGCAGGGGGTTCGGGAAG
AGGAGGCACCCCAAAAAGCTGACCCCTTTAGCCTACAAGCAGTTTATCCC
CAATGTGGCCGAGAAGACCCTAGGCGCCAGCGGAAGGTATGAAGGGAAGA
TCTCCAGAAACTCCGAGCGATTTAAGGAACTCACCCCCAATTACAACCCC
GACATCATATTTAAGGATGAAGAAAACACCGGAGCGGACAGGCTGATGAC
TCAGTAGGAACCCAGCGCCGGGGCGTGGAATGTGTGGCTTTCCAGGGGGT
TACGAGAAGCCGAACACTTCCAGACTTAACTCTGTTTGCTCTTCGGGCAG
ATGAAGGTGATTTCACCCGCTCCTTCCCCACCCACCTGCCCGCCCCCCAT
TCTTCCTCTTCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGT
TAGGGTGTGGTGGGGGTGAGGACGGTAACAGACGTGGTTCATTATGGCCT
GATTTGATGAGTCTTGCTACAATGGCCTTCCCCATCCTACCTCTGCCTGG
CTTGTAACTTGGGGAGACCTTCACTTTGGGGGCGTCGGCCCTTTCCAGTC
AGGAGTGGAAATGGAAGGAGAGGCTGGGAATCCCCCTCCCACAAACATGA
AGTGGTCTCCTGGTACTGTACGAACGAACGAACGTAGCCTTGGGCTTGGA
GCTCAGAGCCCCCACGTTTCCCGTTGCCTCTGTGGTTTTCTTTCCACCAC
TACCCCCACCCTGCACCTCCCCACCAAAGAATTCTCAACTGGAAAAGCCA
GGAGGCGGTTCTGACAAAAGGCAGGGGCTCCAGGGGAGACTCCCCCGTCC
CTGGGTGGCTGGCTGTATCGCAGAGCTGGCTTTGCGATTGCGTGTCCGCA
ATTGTGCCCATCAGAGTGTGAATGTATTGATATTTCTTTAAGGATGCTCT
TTCGTTCTTCCAAGCCCGAGGTACCTTAGGGGAGGGACTTAGAACTTATT
GGCATTGCATCACTTTAGTTTTCAACCTGCTTGCATAAGAATTAAGAGCG
AATAAATATTAGTGTGGGGGGAGGGGAAGCTAAGCAAAATATGAATTCCT
CTCTCTCTCCCCACCTCCTTTGAGATTTCTGAGCTGCCAATCTCCCAGCC
AATTCTAGACTTTCTGAAACTCCATGCACGTATAACTGAAGCCAGAAATG
GGTTTCCTTGCAAATATAGGTCAACATCCTTTTTATTGCCCTATTAAAAT
ATTCAAGTCCTACCTTTAGGGCTAGGTGCGTACAGCGGCTGATGGAGTGG
CGCTGGTGGGGCGCAAGTGCAGGGGGAGGGTACTGACGGCAGAGAGAGAG
GAGCTACCTCCGTGCCGCCCTGCTTCCCGACCCGATTCCCAGGCTTGCTT
GAGGCCGAGAAAGGCGAGGGGCAGGCAAGGTAGCCTGCTCCAGCTGTCGG
AAGGGAGAGGAATGGGAAATGGTCCTGATTTCCTTGCTCTCCCTCATCTG
CTCCCGACCACCTTAAATCTGGACCGCGAGTGTGGACGCGCGCGCCAGTG
CCAGACAGCAGCGCGATCCACAATTAACTCTGCACGGGCCATGGGGTGCC
CGTTGCGTGCAGCTGGCTGGAGGGAGTTCTCCGGCTAGCCCGAGGCGCCC
ATCCTCTCGTCACCCTCACTCCCCGCGGAGGAGGGGCCTTGCCAGGGTCC
CTCGGAACCCGAGAGGAGGGAGGCACTGCGGAGAGAGCGGCGGGGGCGTG
GATACCCGAGGTCCCAGAGCCAGAGTGGGTCAGCTTCTGACCTGCTCTGC
GGGAGGCCAATACCGCAGAAGGGGTCCTGGGCTCGCACACCTTCCCAGGG
CTTGAGCCTTGCAGCCCTGCTGCAATAACTACCCGTGA
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AGGAAGGGAAAGCGCAAGAGAGAGCGCACACGCACACACCCGCCGCGCGC
ACTCGCGCACGGACCCGCACGGGGACAGCTCGGAAGTCATCAGTTCCATG
GGCGAATGCTGCTGCTGGCGAGATGTCTGCTGCTAGTCCTCGTCTCCTCG
CTGCGGTATGCTCGGGACTGGCGTGCGGACCGGGCAGGGGGTTCGGGAAG
AGGAGGCACCCCAAAAAGCTGACCCCTTTAGCCTACAAGCAGTTTATCCC
CAATGTGGCCGAGAAGACCCTAGGCGCCAGCGGAAGGTATGAAGGGAAGA
TCTCCAGAAACTCCGAGCGATTTAAGGAACTCACCCCCAATTACAACCCC
GACATCATATTTAAGGATGAAGAAAACACCGGAGCGGACAGGCTGATGAC
TCAGTAGGAACCCAGCGCCGGGGCGTGGAATGTGTGGCTTTCCAGGGGGT
TACGAGAAGCCGAACACTTCCAGACTTAACTCTGTTTGCTCTTCGGGCAG
ATGAAGGTGATTTCACCCGCTCCTTCCCCACCCACCTGCCCGCCCCCCAT
TCTTCCTCTTCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGT
TAGGGTGTGGTGGGGGTGAGGACGGTAACAGACGTGGTTCATTATGGCCT
GATTTGATGAGTCTTGCTACAATGGCCTTCCCCATCCTACCTCTGCCTGG
CTTGTAACTTGGGGAGACCTTCACTTTGGGGGCGTCGGCCCTTTCCAGTC
AGGAGTGGAAATGGAAGGAGAGGCTGGGAATCCCCCTCCCACAAACATGA
AGTGGTCTCCTGGTACTGTACGAACGAACGAACGTAGCCTTGGGCTTGGA
GCTCAGAGCCCCCACGTTTCCCGTTGCCTCTGTGGTTTTCTTTCCACCAC
TACCCCCACCCTGCACCTCCCCACCAAAGAATTCTCAACTGGAAAAGCCA
GGAGGCGGTTCTGACAAAAGGCAGGGGCTCCAGGGGAGACTCCCCCGTCC
CTGGGTGGCTGGCTGTATCGCAGAGCTGGCTTTGCGATTGCGTGTCCGCA
ATTGTGCCCATCAGAGTGTGAATGTATTGATATTTCTTTAAGGATGCTCT
TTCGTTCTTCCAAGCCCGAGGTACCTTAGGGGAGGGACTTAGAACTTATT
GGCATTGCATCACTTTAGTTTTCAACCTGCTTGCATAAGAATTAAGAGCG
AATAAATATTAGTGTGGGGGGAGGGGAAGCTAAGCAAAATATGAATTCCT
CTCTCTCTCCCCACCTCCTTTGAGATTTCTGAGCTGCCAATCTCCCAGCC
AATTCTAGACTTTCTGAAACTCCATGCACGTATAACTGAAGCCAGAAATG
GGTTTCCTTGCAAATATAGGTCAACATCCTTTTTATTGCCCTATTAAAAT
ATTCAAGTCCTACCTTTAGGGCTAGGTGCGTACAGCGGCTGATGGAGTGG
CGCTGGTGGGGCGCAAGTGCAGGGGGAGGGTACTGACGGCAGAGAGAGAG
GAGCTACCTCCGTGCCGCCCTGCTTCCCGACCCGATTCCCAGGCTTGCTT
GAGGCCGAGAAAGGCGAGGGGCAGGCAAGGTAGCCTGCTCCAGCTGTCGG
AAGGGAGAGGAATGGGAAATGGTCCTGATTTCCTTGCTCTCCCTCATCTG
CTCCCGACCACCTTAAATCTGGACCGCGAGTGTGGACGCGCGCGCCAGTG
CCAGACAGCAGCGCGATCCACAATTAACTCTGCACGGGCCATGGGGTGCC
CGTTGCGTGCAGCTGGCTGGAGGGAGTTCTCCGGCTAGCCCGAGGCGCCC
ATCCTCTCGTCACCCTCACTCCCCGCGGAGGAGGGGCCTTGCCAGGGTCC
CTCGGAACCCGAGAGGAGGGAGGCACTGCGGAGAGAGCGGCGGGGGCGTG
GATACCCGAGGTCCCAGAGCCAGAGTGGGTCAGCTTCTGACCTGCTCTGC
GGGAGGCCAATACCGCAGAAGGGGTCCTGGGCTCGCACACCTTCCCAGGG
CTTGAGCCTTGCAGCCCTGCTGCAAAAAAAAAAAAAAA
98
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Noncoding regulatory sequences
nucleotide changes
Differences in gene expression
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98 of the genome
AGGAAGGGAAAGCGCAAGAGAGAGCGCACACGCACACACCCGCCGCGCGC
ACTCGCGCACGGACCCGCACGGGGACAGCTCGGAAGTCATCAGTTCCATG
GGCGAATGCTGCTGCTGGCGAGATGTCTGCTGCTAGTCCTCGTCTCCTCG
CTG
Comparative Genomics
NO CODE
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Evolutionary conservation can find regulatory
elements
Non-Coding Sequence
Last common ancestor
Evolutionarily Conserved Sequences are
Functionally Important.
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98 of the genome
AGGAAGGGAAAGCGCAAGAGAGAGCGCACACGCACACACCCGCCGCGCGC
ACTCGCGCACGGACCCGCACGGGGACAGCTCGGAAGTCATCAGTTCCATG
GGCGAATGCTGCTGCTGGCGAGATGTCTGCTGCTAGTCCTCGTCTCCTCG
CTG
Comparative Genomics
NO CODE
High-Throughput Characterization
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Regulatory Elements Promoter, Enhancer,
Silencer, Insulator
Insulator
Promoter
Gene A
Enhancers
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Enhancer Assay
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Zebrafish Enhancers
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Bins of Enhancer Activities
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http//enhancer.lbl.gov
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Applications
1. Gene/Genome annotation 2. Reagent to drive
tissue specific expression 3. EvoDevo 4.
Exploring the regulatory code 5. Role of
regulatory sequences in human disease
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3. EvoDevo The bat Prx1 limb enhancer leads to
longer limbs in the mouse
Mouse limb en.
Prx1
/
Cretekos Genes Dev. 2008, 22141-51
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4. Exploring the regulatory code
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Applications
1. Gene/Genome annotation 2. Reagent to drive
tissue specific expression 3. EvoDevo 4.
Exploring the regulatory code 5. Role of
regulatory sequences in human disease
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Limb enhancer with substantial evidence for
involvement in human disease
Mutations
Holoprosencephaly Limb Other
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gt100 limb enhancers discovered
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Limb malformations outline

• Mutation analysis in humans

Syndactyly
Polysyndactyly
Find Additional Limb Enhancers

• Computational approaches next generation
  sequencing

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1. Gene regulation
2. Histone code
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Histone Modifications more code to decipher
146bp
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Histones have tails
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Histone H3 Example
H3K18ac
H3K4me
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3
Cleavage
Acetylation
Methylation
Unknown
Unknown
Repression
Repression
Activation
Activation
KLysine Methylated or Acetylated
RArginine Methylated
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Munshi A. et al. Gen Genom 2009, 36 75-88
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OUTLINE
1. The human genome
2. Novel sequencing technologies
3. New genomic terrains to be uncovered
4. Advantages of individual genomes
5. Challenges risks of individual genomes
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1. Predicting disease risk.
2. Drug response.
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Finding specific nucleotide variants can predict
disease risk
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Most assoicated common variants of common
diseases do not give a high disease risk
Manollo T.A. et al. JCI 2008, 118 1590-1605
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Ancestry Tracing
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1. Predicting disease risk.
2. Drug response.
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Example of genetic variation drug response
Irinotecan
(TA)7TAA
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Reduced UGT1A1 expression
MORE SN-38 (active)
Diarrhea, Leucopaenia
Rapid testing kit for (TA)7 variant
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1. Predicting disease risk.
2. Drug response.
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OUTLINE
1. The human genome
2. Novel sequencing technologies
3. New genomic terrains to be uncovered
4. Advantages of individual genomes.
5. Challenges risks of individual genomes.
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Whole-genome matchmaking
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Challenges Risks

• Psychological and social effects of genetic
  testing for the individual tested.

• How will your genome be stored and accessed?

• How should health insurance companies treat
  genomic data?

-Companies might only insure people with
healthy genomes.
-Therapies could be reimbursed only for those
patients who are identified as likely to respond?

• How narrowly should clinical trials be designed
  to include or exclude people based on their
  genome.

• Genomic racism.

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Ahituv Lab
Ramon Y. Birnbaum Mee J. Kim Qiang Li Karl
Murphy Elaine Nitta Nir Oksenberg Julia E.
VanderMeer
UCSF
Deanna L. Kroetz Kathleen M. Giacomini Katherine
S. Pollard
Berkeley Lab JGI
Len A. Pennacchio Edward M. Rubin
Stanford
Gill Bejerano
Funding Sandler, NIGMS, NICHD, NHGRI
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