Bioinformatics

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Bioinformatics
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DNA Sequencer

• Perkin Elmer ABI 3770 Automated Sequencer

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Human Genetic Variation

• Disease risk
• Drug response
• Correlations between biological variation and DNA
  sequence variation

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Genetics inherited contribution to phenotypic
variation

• Genetic Diversity
• Genetic Identity

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Inherited contribution to risk of type II Diabetes

• Your neighbor (unrelated) 5-10
• Your sibling 30-40
• Your identical twin gt90

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• Virtually all medical conditions (other than
  trauma) have a genetic component
• So does ability to react to treatments
• Increasingly, genetic information is being used
  to diagnose and treat disease
• Gene therapy
• Individualized drugs

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Traditional Approach

• Linkage or recombinatorial mapping
• Successful for single gene disorders
• Little success for common complex traits, such as
  heart disease, diabetes, asthma, mental disorders

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• The human genome sequence 3.2 billion bp

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• Human Genetic Variation
• SNPs-Single Nucleotide Polymorphisms

GATTTAGATCGCGATAGAG GATTTAGATCTCGATAGAG
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Pharmacogenomics

• The use of DNA sequence information to measure
  and predict the reaction of individuals to drugs.

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Pharmacogenomics

• Personalized drugs
• Faster clinical trials through selected trial
  populations
• Less drug side effects

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Drug Responses

• Absorption
• Distribution
• Activation
• Metabolism
• Excretion

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• Genetic Factors
• Environmental Factors

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Patients

• Responders
• Non-responders
• Toxic responders

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Goals

• Right Drug
• Right Dose
• Right Patient

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Procedure

• Scanning
• vs.
• Scoring

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Types of SNPs

• Causative SNPs (synonymous)
• coding SNPS
• non-coding SNPs
• Linked SNPs (non-synonymous)
• non-coding SNPs

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To find SNPs in raw sequence ...
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Single Nucleotide Polymorphisms

• How many?
• What kind?
• How do we find them?

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• 99.9 identity - how many differences?
• O.1 of 3.200 Mb 3.2 Mb
• 3.200.000 SNPs
• One SNP every 1,300 bases.

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GATTTAGATCGCGATAGAGGATTTAGATCTCGATAGAG

• Rare Alleles
• ---o--------------------
• -----o------------------
• -------o----------------
• -----------o------------
• ---------------o--------
• -------------------o----
• Many

• Common Alleles
• ----o-------------------
• ----o-------------------
• ----o-------------------
• --------------------o---
• --------------------o---
• --------------------o---
• Few

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Raw Genome Data
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Database mining

• Discover new SNPs
• Contig overlaps
• Comparison along entire sequence
• Comparing redundant EST sequences
• Validate SNPs
• Sequencing
• Microchips

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SNPs in Overlapping Genomic Sequences
Overlapping BACs from library
50 of overlaps contain polymorphisms
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• gtgbBE588357.1BE588357 194087 BARC 5BOV Bos
  taurus cDNA Length369
• Score 272 bits (137), Expect 4e-71
• Identities 258/297 (86), Gaps 1/297 (0)
• Strand Plus / Plus
• Query 17 aggatccaacgtcgctccagctgctcttgacgactccac
  agataccccgaagccatggca
  
  
• Sbjct 1 aggatccaacgtcgctgcggctacccttaaccact-c
  gcagaccccccgcagccatggcc
• Query 77 agcaagggcttgcaggacctgaagcaacaggtggagggg
  accgcccaggaagccgtgtca
• 
  
• Sbjct 60 agcaagggcttgcaggacctgaagaagcaagtggaggg
  ggcggcccaggaagcggtgaca
• Query137 gcggccggagcggcagctcagcaagtggtggaccaggcca
  cagaggcggggcagaaagcc
• 
  
• Sbjct 120 tcggccggaacagcggttcagcaagtggtggatcaggcc
  acagaagcagggcagaaagcc
• 
  
• Query 197 atggaccagctggccaagaccacccaggaaaccatcgac
  aagactgctaaccaggcctct
• 
  
• Sbjct 180 atggaccaggttgccaagactacccaggaaaccatcga
  ccagactgctaaccaggcctct

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Validation

• Correlation between phenotype and SNP
• Recombinatorial linkage vs. SNP linkage

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GATTTAGATCGCGATAGAGGATTTAGATCTCGATAGAG

• Common Alleles
• ----o-------------------
• ----o-------------------
• ----o-------------------
• --------------------o---
• --------------------o---
• --------------------o---
• Few

• Rare Alleles
• ---o--------------------
• -----o------------------
• -------o----------------
• -----------o------------
• ---------------o--------
• -------------------o----
• Many

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Data from 24 individuals for the marker S gene
1118
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GATTTAGATCGCGATAGAGGATTTAGATCTCGATAGAG

• Responders
• ---o----o--------o----o------o----o--o-
• ---o----o--------o----o-----------o--o-
• ---o-o--o--------o----o-----------o--o-
• Non-responders
• --------o--------------------o----o--o-
• ----o---o--------------------o----o--o-
• --------o--------------------o----o--o-

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Microarrays and Genechips

• Expression Studies
• measure RNA levels
• allow study of genes under different conditions,
  from different tissues, and/or different
  developmental stages
• Human Genetic Variation
• Single nucleotide polymorphisms (SNPs)

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cDNA spotted microarrays
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5'
Cleavage site
C
5'
C
5'
Release of Probe Arm
G
Probe arm becomes invader in secondary reaction
Cleavage site
F
5'
C
Release of fluorescent molecule
F
Invader Reaction
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Cleavage site
5-CGCGCCGAGG
ATTCCAGCCAGTGGGGA-3 Downstream primary probe
5-CGGCAGCTTCCT CGG CCATTGCT Upstream invader
3-GCCGTCGAAGGAGCCGGTAACGTAAGGTCGGTCACCCCT-5
Target
Cleavage site
5-F-T
CTCGTCTCGG
T
T
Signal Probe
5-CGCGCCGAGGA
T
T
GCGCGGCTCCAGAGCAGAGCC
5-F-T
Invader Reaction for marker S gene 1118
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Data from 24 individuals for the marker S
gene 1118