Selecting%20TagSNPs%20in%20Candidate%20Genes%20for%20Genetic%20Association%20Studies

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Selecting TagSNPs in Candidate Genes for Genetic
Association Studies

• Shehnaz K. Hussain, PhD, ScM
• Assistant Professor
• Department of Epidemiology, UCLA
• skhussain_at_ucla.edu
• Epidemiology 244 Cancer Epidemiology Methods

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Objectives

• Molecular genetics primer
• Databases and tools to conduct in silico analyses
  for tagSNP selection/prioritization

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Central dogma
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What are SNPs?

• More than 99 of all nucleotides are the same in
  all humans
• 1 of nucleotides are polymorphic
• SNPsgtgt insertions-deletions
• Bi-nucleotide T (80) A (20)
• Where do SNPs occur?
• Exons
• Introns
• Flanking regions

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What are haplotypes?

• A haplotype is the pattern of nucleotides on a
  single chromosome
• Two copies of each chromosome
• The haplotype inference problem

? T ? G ? A
T T C G T A
TA TT CG GG TA AA
? T ? G ? A
A T G G A A
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What is linkage disequilibrium?

• Linkage disequilibrium (LD) describes the
  non-random association of nucleotides on the same
  chromosome in a population
• One nucleotide at one position (locus) predicts
  the occurrence of another nucleotide at another
  locus

LD
No LD
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What are markers?
Disease Phenotype
Test for genetic association between the
phenotype and the DSL
Test for association between phenotype and
marker loci
LD
Candidate gene
Marker loci (SNPs)
Disease Susceptibility Locus
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What are tagSNPs?

• TagSNPs are a subset of all SNPs in a gene that
  mark groups of SNPs in LD
• Avoids redundant genotyping

LD
LD
Marker loci (SNPs)
Disease Susceptibility Locus
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The joint effect of tagSNPs in cytokine genes and
cigarette smoking in cervical cancer risk
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T-cell proliferation

IL
-
2
IL
-
2
IL
-
2
gene
IL
-
2
gene
Activated T
-
cell
Activated T
-
cell
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Background

• Cigarette smoking ? 1.5- to 3-fold cancer risk
• Cigarette smoking ? levels of IL-2 and IFN?
  (cervical and circulating)
• ? levels of IL-2 and IFN?
• HPV persistence in the cervix
• Cervical neoplasia
• Decreased survival from invasive cervical cancer

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Model
Cigarette smoking
HPV-associated squamous cell cervical cancer
SNPs in IL-2, IL-2R, and IFNG
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Methods

• Study design
• Population-based case-only study
• Subjects
• 308 Caucasian squamous cell cervical cancer cases
  diagnosed 1986-2004
• Residing in 3 western Washington counties
• Data collection
• Structured inperson interviews
• DNA isolated from buffy coats

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Multi-stage tagSNP design
Select reference panel
Re-sequence panel, identify SNPs (many markers,
few subjects)
Choose tagSNPs
Genotype tagSNPs in main study(few markers, many
subjects)
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1. Select reference panel

• A sample of your study population
• Most representative
• Samples from the Coriell Repository
• Ability to integrate your data with other
  resources

Candidate gene SNPs
HapMap SNPs
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2. Re-sequence reference panel
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Alternatives to re-sequencing

• Program for Genomic Applications (PGA)
• SeattleSNPs inflammation
• NIEHS SNPs environmental response
• Innate Immunity
• International HapMap Project
• 5 million SNPs in four ethnically distinct
  populations

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3. Choose tagSNPs
Option LDSelect (Carlson, 2002) Tagger (de Bakker, 2005)
r2 threshold Yes Yes
SNP exclusions/inclusions No Yes
SNP design score No Yes
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LDSelect output for IL-2SeattleSNPs, r20.80,
MAF 0.05, Caucasian
Bin Total Number of Sites TagSNPs
1 2 rs2069763 rs2069772
2 2 rs2069776 rs2069778
3 2 rs2069777 rs2069779
4 1 rs2069762
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Genomic context

• Exons (cSNPs)
• SIFT (Ng, 2002)
• PolyPhen (Ramensky, 2002)
• Upstream flanking region
• Intron-exon junctions

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Sequence conservation

• UCSC Genome Browser, PhasCons (Siepel, 2005)

Score
Repeat region
Unique region
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(No Transcript)
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TagSNP summary

• Efficient yet comprehensive coverage of the
  genetic variation in our candidate genes
• Reduce costs
• Preference should be given to putatively
  functional variants
• Literature, gene context, sequence conservation

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• Thanks for your attention!
• Questions?