Incorporating Physiological Genomics into the Medical Student Curriculum

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Incorporating Physiological Genomics into the
Medical Student Curriculum

• IUPS Refresher Course
• Integrating Genomics into Physiology Courses A
  New Paradigm or Just More Information?
• Anne Kwitek, Ph.D.
• Human and Molecular Genetics Center
• Medical College of Wisconsin

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Integration of Physiological Genomics

• Separate Course
• Incorporate within Medical Physiology Course
• Independent genetics series
• Information integrated throughout the Course

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Challenges

• Teaching both introductory genetics AND how it
  fits with basic physiology
• Seemingly disparate information how to make
  physiological genomics fit a basic physiology
  course

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What to Cover

• Introduction to genomics and genetics
• Basic tools and technology
• Linkage
• Monogenic disease
• Complex disease
• Expression
• Examples using topics covered in class

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Goals of Genetics Lectures

• Introduction
• Become familiar with the concepts and
  technologies behind genomics and genetics
• Applications
• Applications of genetics and genomics toward the
  understanding of human monogenic disease
• Applications of genetics and genomics toward the
  understanding of human complex disease

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Introduction to Genomic Tools and Technology
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Genomics vs. Genetics

• Genomics Structural aspects of the genome
• Genetics The use of transmission of genetic
  material

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Genetic Markers to Locate Disease

• Simple Sequence Repeat (SSR) microsatellite
• CA repeat
• Short Tandem Repeat Polymorphism (STRP)
• Simple Sequence Length Polymorphism (SSLP)
• Single Nucleotide Polymorphism (SNP)

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Simple Sequence Repeat (SSR)
Mom tctttgggactg cacacacacaca
tcagaatccggag tctttgggactg cacacacacacaca
tcagaatccggag
Dad tctttgggactg cacacacacacacaca
tcagaatccggag tctttgggactg cacacacacacacacaca
tcagaatccggag
Child
Child
Child
Child
1 2 3 4
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Single Nucleotide Polymorphisms (SNPs)

• We are 99.9 identical at the genome level
• (1/1000 bp differences)
• Will use sequence variants (SNPs) as a form of
  diagnosis
• Different outcomes of variation
• Coding
• Synonymous changes
• Non-synonymous changes
• Non-coding
• Changes in gene expression/protein levels

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Expression Profiling

• Compare expression in tissues between disease and
  normal states
• Compare expression in tissues before/after drug
  treatment
• Evaluate many thousands of genes at the same time
• Genes turned up or down in disease state may lead
  to understanding of mechanism
• Lead to a diagnostic fingerprint

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See Figure 3.9 from A Primer of Genome Science,
Second Edition Greg Gibson and Spencer V.
Muse Sunderland, MA Sinauer Associates, 2004
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Linkage and Association
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Disease Traits

• Qualitative
• Trait that is either present or absent
• e.g. Cystic fibrosis
• Quantitative
• Trait with a continuous distribution of
  measurement
• e.g. height, weight
• Clinical definition of disease
• E.g. Hypertension

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Monogenic (Mendelian) Disease

• Simple inheritance patterns within families
• Autosomal Dominant
• Autosomal Recessive
• X-linked
• Caused by a mutation in a single gene
• Relatively rare
• Powerful for identifying genes by linkage
  analysis and positional cloning

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Complex (Common) Disease

• No clear pattern of Mendelian inheritance
• A mix of genetic and environmental factors
• Incomplete penetrance
• Phenocopies
• Heterogeneity
• High frequency of disease-causing allele

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Gene Mapping Strategies

• Linkage Analysis within Pedigrees
• Allele Sharing within Relative (Sib) Pairs
• Association Study

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Linkage Analysis Within Pedigrees

• Tests for the likelihood of recombination between
  assumed disease and marker alleles.
• Great for single gene disorders
• Limitation for common/multifactorial diseases
• frequency of disease
• locus heterogeneity
• penetrance of the disease

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Example of Linked Marker
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2
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3
2
2
2
2
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Association Study

• Correlation of different SNPs in this region with
  disease.
• Family-based and case-control based

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Association Studies

• Advantages
• Ease of collecting subjects to study, i.e. cases
  and controls
• More powerful to detect genes
• Analysis methodology similar to standard
  case-control methods
• Disadvantages
• Most assumption-laden
• Spurious Associations far exceed true
  associations
• Ascertainment Bias/Allele frequencies

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Applications of Physiological Genomics
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Why Study Monogenic Disease

• Advantages
• Clear genetic inheritance
• Single gene mutation
• Hopefully lead to better understanding of
  mechanism of more common forms of disease
• Disadvantages
• Rare
• Not causing most common disease

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Linkage Studies of Hypertrophic Cardiomyopathy
(HCM)

• One of the most common inherited cardiac
  disorders
• Prevalence in young adults of 1 in 500
• Autosomal dominant
• Variable expressivity
• Etiological heterogeneity
• Environmental and genetic modifiers

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Linkage Studies on Monogenic HCM
1/2
3/4
1/4
1/3
1/4
1/4
2/3
1/1
1/2
1/3
1/3
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Linkage Results to Gene Mutation

• Linkage of a marker to a disease does not mean a
  gene is found!
• Fine-mapping
• Positional Candidate Genes
• Look for obvious biological candidates within the
  region of linkage
• Screen for mutations in this gene in disease
  families SEQUENCING
• Successful for HCM!

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Mutations in Monogenic Disease

• Mutations are often causal
• Mutations are often severe, i.e. destroy
  protein function
• Non-sense mutations
• Missense mutations
• Insertions/deletions

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Understanding Pathways through Monogenic Disease

• Other mutations related to common disease?
• Not complete loss of function mutations
• Interactions with other genes/environment
• May not be gene involved in common forms, but
  part of the pathway

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Hypertension and the Kidney

• Linkage in monogenic forms of severe hypertension
  and hypotension
• Gitelman Syndrome
• GRA
• Aldosterone Synthase Deficiency
• Liddle Syndrome
• PHA1
• Bartter syndrome
• AME
• Hydroxylase deficiency
• Hypertension exacerbated by pregnancy

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Hypertension and the Kidney

• 17 genes cloned
• 8 for hypertension
• 9 for hypotension
• All genes involving sodium handling in the
  nephron
• All Monogenic forms of hypertension/hypotension

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See Figure 1 from Lifton et al. Cell 104545-556,
2001 http//www.cell.com/content/issue?volume104
issue4 Free access
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Genes in Complex Disease

• Multiple genes, each with additive effect
• Genes interacting with one another
• Genes interacting with environment

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Hypertension

• Complex
• Many different subtypes
• Animal models offer advantages for finding genes
  for complex disease
• Inbred
• Controlled breeding
• Controlled environment

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Comparative Genomics

• Tying Phenotype and Genotype Across Species

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Comparative Genomics and Gene Identification
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Human and Rat ARPKDWard, et al, Nature Genetics,
30259-269 http//www.nature.com/ng/journal/v30/n
3/full/ng833.html (free access)
PKD
Linkage Human 6
Linkage Rat 9
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PKDH1 Gene in Human and Rat
PKD
Gene Mutation
Gene Mutation
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Subdividing Cancer through Gene Expression
Profiling

• Classify cancers based on their gene expression
  profiles
• Compare different cancer types to identify
  fingerprint gene expression
• Provide diagnostic tool

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See Figure on gene expression profiles of
mesenchymal, leukemia, epithelial, and melanoma
cells along with 3 probability graphs comparing
overall survival of patients with GC B-like vs.
activated B-like from A Primer of Genome
Science, Second Edition by Greg Gibson and
Spencer V. Muse. Sunderland, MA Sinauer
Associates, 2004
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Genomics to Proteomics
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Finding Genes for Disease

• We know the blueprint
• Technology makes possible large-scale testing
  that will likely become the norm in your practice
• Diagnostics
• Therapy

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The Basics About Genetic Testing

• To find out if a person is a carrier for a
  certain disease
• To learn if a person has an inherited
  predisposition to a certain disease, like breast
  or ovarian cancer (also known as susceptibility
  testing)
• To help expecting parents know whether their
  unborn child will have a genetic disease or
  disorder (prenatal testing)
• To confirm diagnosis of certain diseases or
  disorders (for example, Alzheimer's disease)

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Goals of Personalized Medicine

• Match the right drug/treatment with the right
  patient
• Predisposition testing
• Preventative medicine