Picking SNPs

1
Picking SNPs Application to Association Studies
Dana Crawford, PhD SeattleSNPs PGA University of
Washington March 20, 2006
2
Outline of Tutorial

• Concepts of tagSNPs
• LD and haplotype definitions
• Haplotype blocks and definitions
• Tools to identify tagSNPs

3
Why Do We Need tagSNPs?
Too Many SNPs to Genotype!

• Whole Genome
• 15,000,000 SNPs
• 6,000,000 SNPs gt 5 MAF

4
SNPs Are Correlated (aka linkage disequilibrium)
the nonindependence of alleles at different
sites. Pritchard and Przeworski 2001
5
Measuring Pair-wise SNP Correlations

• SNP correlation described by linkage
  disequilibrium (LD)
• Pair-wise measures of LD D and r2
• D pAB - pApB D D/Dmax
  Recombination
• r2 D2
• f(A1)f(A2)f(B1)f(B2) Power

6
LD Statistics Practical Uses

• r2 is inversely related to power
• 1/r2
• 1,000 cases 1,250 cases
• 1,000 controls r21.0 1,250 controls r2 0.80
• D is related to recombination history
• D 1 no recombination
• D lt 1 historical recombination

7
Where to Find Population LD Statistics
For your gene or region of interest, search

• HapMap www.hapmap.org
• Perlegen genome.perlegen.com
• Environmental Genome Project egp.gs.washington.ed
  u
• SeattleSNPs PGA pga.gs.washington.edu

8
Where to Find Population LD Statistics
For your gene or region of interest, search

• HapMap www.hapmap.org
• Perlegen genome.perlegen.com
• Environmental Genome Project egp.gs.washington.ed
  u
• SeattleSNPs PGA pga.gs.washington.edu

9
Visualizing Pair-wise LD
10
Visualizing Pair-wise LD
11
Visualizing Pair-wise LD
USF1
12
(No Transcript)
13
(No Transcript)
14
Visualizing Pair-wise LD
15
(No Transcript)
16
(No Transcript)
17
SeattleSNPs
SeattleSNPs Perlegen
18
Visualizing Pair-wise LD Beyond the Gene
19
Visualizing Pair-wise LD Beyond the Gene
20
(No Transcript)
21
(No Transcript)
22
Visualizing Pair-wise LD Beyond the Gene
23
Multi-SNP Correlations (aka Haplotypes)
a unique combination of genetic markers present
in a chromosome. pg 57 in Hartl Clark, 1997
24
Constructing Haplotypes
25
Constructing Haplotypes
Examples of Haplotype Inference Software EM
Algorithm Haploview http//www.broad.mit.edu/mpg/
haploview/index.php Arlequin http//lgb.unige.ch/
arlequin/ PHASE v2.1 http//www.stat.washington.e
du/stephens/software.html HAPLOTYPER http//www.p
eople.fas.harvard.edu/junliu/Haplo/docMain.htm
26
Haplotypes in SeattleSNPs

• gt250 genes re-sequenced in inflammation
  response
• 2 populations European- and African-descent
• PHASEv2.0 results posted on website
• Interactive tool (VH1) to visualize and sort
  haplotypes

http//pga.gs.washington.edu
27
Haplotypes in SeattleSNPs
28
Haplotypes in SeattleSNPs
29
Haplotypes in SeattleSNPs
30
Haplotypes in SeattleSNPs
31
Haplotypes in SeattleSNPs
32
Haplotypes in SeattleSNPs
33
Haplotypes in SeattleSNPs
34
Haplotypes in SeattleSNPs
35
Haplotypes in SeattleSNPs
36
Haplotypes in SeattleSNPs
37
Haplotypes in SeattleSNPs
38
Using LD and Haplotypes to Pick tagSNPs

• r2 is inversely related to power
• 1/r2
• 1,000 cases 1,250 cases
• 1,000 controls r21.0 1,250 controls r2 0.80
• D is related to recombination history
• D 1 no recombination
• D lt 1 historical recombination

Example LDSelect in GVS
Example Haplotype blocks
39
Using LD and Haplotypes to Pick tagSNPs

• r2 is inversely related to power
• 1/r2
• 1,000 cases 1,250 cases
• 1,000 controls r21.0 1,250 controls r2 0.80

Example LDSelect
40
LDSelect Using LD to Pick tagSNPs

• LDSelect
• Uses SNP discovery data (not haplotypes)
• Finds all correlated SNPs to minimize the total
  number
• Maintains genetic diversity of locus

Carlson et al. AJHG (2004)
41
TagSNPs Are Population Specific
African-Americans CRP
European-Americans CRP
42
SNP Selection Using GVS
43
SNP Selection Using GVS
22 SNPs (gt5 MAF) 7 tagSNPs
44
(No Transcript)
45
SNP Selection tagSNP Data
46
Side Note Categorizing tagSNPs

• SNP context
• Nonrepetitive gt repetitive
• Location of SNP
• Coding gt noncoding
• Function
• Nonsynonymous gt synonymous

47
Categorizing tagSNPs
48
Haplotypes in Genetic Association Studies
Two main approaches with haplotypes
49
Haplotypes in Genetic Association Studies
Two main approaches with haplotypes
Haplotypes Pick tagSNPs Genotype
samples
Pick tagSNPs Infer haplotypes Test for
association
50
Haplotype Blocks
Daly et al 2001
Daly et al Nat. Genet. (2001)
51
Block Definitions
Daly et al 2001
Daly et al Nat. Genet. (2001)
D Gabriel et al Science (2002)
52
Block Definitions
53
Haplotype Blocks and tagSNPs

• Identifying blocks and tagSNPs
• Manually
• Algorithms
• Haploview

54
Haplotype Blocks and tagSNPs
IL1B 19 SNPs (MAF gt5) 4 common haplotypes
55
Haplotype Blocks and tagSNPs

• Identifying blocks and tagSNPs
• Manually
• Algorithms
• HaploView

56
HapMap Data and Haploview
57
(No Transcript)
58
(No Transcript)
59
(No Transcript)
60
HapMap Data and Haploview
61
(No Transcript)
62
(No Transcript)
63
(No Transcript)
64
Import HapMap Data into Haploview
65
(No Transcript)
66
(No Transcript)
67
(No Transcript)
68
(No Transcript)
69
May not be minimal set
70
Minimal set of tagSNPs based on r2
71
Note HapMap is not complete variation data
72
Variation data, LD, and tagSNPs for ABCE1 in
European-Americans
HapMap
7 SNPs
4 tagSNPs
4 tagSNPs
73
Where to Find Tagging Software
HaploBlockFinder
http//cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.
cgi
http//www.broad.mit.edu/personal/jcbarret/haplo/
Haploview
http//pga.gs.washington.edu
LDSelect
http//www.well.ox.ac.uk/xiayi/haplotype/index.ht
ml
SNPtagger
TagIT
http//popgen.biol.ucl.ac.uk/software.html
http//www-rcf.usc.edu/stram/tagSNPs.html
tagSNPs
74
Haplotypes, TagSNPs, and Caveats

• Haplotypes are inferred
• Block-like structure assumed for some software
• Different block definitions
• Block boundaries sensitive to marker density
• Genotype savings may not be great (recombination)

75
Common Errors in Association Studies Bell and
Cardon (2001)

• Small sample size
• Subgroup analysis and multiple testing
• Random error
• Poorly matched control group
• Failure to attempt study replication
• Failure to detect LD with adjacent loci
• Overinterpreting results and positive
  publication bias
• Unwarranted candidate gene declaration after
  identifying
• association in arbitrary genetic region

76
Picking SNPs Application to Association
Studies Summary

• Resources available for pair-wise LD and
  haplotypes
• Software for tagSNP selection available
• Be aware the limitations of the approach you
  choose
• Replication required by several journals

77
SeattleSNPs Genotyping Service

• Free genotyping (BeadArray)
• Emphasis on young investigators
• Research related to heart, lung, blood, or sleep
  disorders
• Moderate to large population samples
• Apply at pga.gs.washington.edu
• Due date TBA