Linkage AnalysisLinkage Analysis

Eric Jorgenson

Epidemiology 217

2/21/12

Worldwide Distribution of Human Earwax SNP rs17822931

Yoshiura et al., Nature Genetics 2006

Geographic Distribution of PTC Phenotype

Wooding Genetics 2006, adapted from Cavalli-Sforza 1994

High

Low

Bimodal Distribution of PTCBimodal Distribution of PTC

PTC Distribution

0

5

10

15

20

25

30

35

40

45

1 2 3 4 5 6 7 8 9 10 11 12 13 14

Number of Subjects

Your Phenotypes and GenotypesTaste SNP Ear wax SNP

Sample Name taster ear wax rs10246939 rs1726866 rs17822931

BU10 Y D CT AG TT

BU12 N D None None None

BU14 N D? TT AA TT

BU15 Y W CT AG CC

BU17 Y W CT AG CC

BU19 Y D CC GG TT

BU20 N W TT AA CC

BU21 mild W TT AA CC

BU22 Y D? CC GG CC

BU23 Y W CC GG CT

BU24 Y W? CT AG CC

BU25 Y W CT AG CC

BU26 Y W? CT AG CT

BU27 N W TT AA CC

BU28 Y W CT AG CT

BU29 Y mild W CT AG CT

BU30 Y W CT AG CC

From Joe Wiemels

Types of Genetic StudiesTypes of Genetic Studies

• Family StudiesFamily Studies– Compare trait values across family membersCompare trait values across family members

• Linkage AnalysisLinkage Analysis– Compare trait values with inheritance patternsCompare trait values with inheritance patterns

• AssociationAssociation– Compare trait values against genetic variantsCompare trait values against genetic variants

Family StudiesFamily Studies

• Familial RelationshipsFamilial Relationships– TwinsTwins– SiblingsSiblings– Parents/offspringParents/offspring

• Phenotype informationPhenotype information– Affected/Unaffected (Prostate Cancer)Affected/Unaffected (Prostate Cancer)– Quantitative measure (Blood Pressure)Quantitative measure (Blood Pressure)

• No Genotype information requiredNo Genotype information required

Why do Family Studies?Why do Family Studies?

• Is the trait genetic?Is the trait genetic?

• What is the mode of transmission?What is the mode of transmission?– DominantDominant– RecessiveRecessive– AdditiveAdditive– Polygenic (Multiple genes involved)Polygenic (Multiple genes involved)

Mutation and MeiosisMutation and Meiosis

Recessive traitRecessive trait

First PTC Family StudyFirst PTC Family Study

Number of FamiliesCan taste Can not taste

Both parents can taste 40 90 16One parent can taste, the other can not 51 80 37Neither parent can taste 9 0 17

Children

L. H. Snyder Science 1931

Linkage Analysis

• Narrow down position of disease gene

• No biological knowledge needed

• Genetic markers (not disease gene)

• Recombination

Recombination

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aa

Recombination

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aaRR NRNRNRNR RR

Independent Assortment

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aa25% 25%25% 25%

No recombination

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aa0% 50%50% 0%

Recombination Fraction

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aa61 420442 77

Recombination Fraction

A a

bB

a a

b b

A

b

a

b B b

aa61 420442 77

Recombination Fraction =Recombinants / Total =

61 + 77 / 61 + 77 + 442 + 420 = 138 / 1000

= 13.8%

Linkage

• Recombination fraction < 50%

• Two traits: PTC and KELL blood group

• Two genetic markers

• One trait and one genetic marker

Linkage Analysis

Human Linkage Analysis

• RFLP Markers for Linkage (1980)• Huntington’s Disease Linkage (1983)• Cystic Fibrosis Linkage (1985)• Cystic Fibrosis Gene (1989)• Huntington’s Disease Gene (1993)

Genomewide Linkage Analysis

Genetic Markers

Genes

= 10% on average

Linkage Analysis

• LOD score based on recombination

• LOD () = log ()R (1 - )NR

____________________

( = 1/2) R + NR

Dominant Trait

D d

D dD d

d d

d d

1 2

1 3 2 3 2 3

3 3

Linkage Analysis

1 2

1 3 2 3 2 3

3 3

NR R NR

LOD score

LOD () = log ()1 (1 - )2

____________________

( = 1/2) 1 + 2 LOD Score

0.01 -1.11

0.05 -0.44

0.1 -0.19

0.2 0.01

0.3 0.07

0.4 0.06

0.5 0.00

IBD

• Identity by descent

• Allele Sharing methods

• Often used for affected sib pairs

Identity By Descent

a A a A

A aa AA A aa25% 25%25% 25%

Identity By Descent

a A

A aa AA A aa

Parent 1

1 1

1 1

Alleles shared IBD

Identity By Descent

a A

A aa AA A aa

Parent 1

1 1

1 1

Alleles IBD Frequency

2 0%

1 100%

0 0%

Identity By Descent

A A

A aa AA A aa

Sibling 1

2 1

1 0

Alleles shared IBD

Identity By Descent

A A

A aa AA A aa

Sibling 1

2 1

1 0

Alleles IBD Frequency

2 25%

1 50%

0 25%

Identity By Descent

• IBD can be used for linkage analysis

• Expect 50% alleles shared between siblings

• Look for IBD > 50% for concordant pairs

• Look for IBD < 50% for discordant pairs

PTC Linkage AnalysisPTC Linkage Analysis

0

1

2

3

4

5

6

7

8

9

Location in the Genome

LOD Score

Chromosome 7

0

1

2

3

4

5

6

7

8

9

0 15 30 45 60 75 90 105 120 135 150 165 180 195 210 225 240 255 270 285

Location (cM)

LOD Score

PTC Linkage AnalysisPTC Linkage Analysis

Human Chromosomes

TAS2R38

Fine MappingFine Mapping

Linkage markers

Genes

Kim et al. Science 2003

Linkage Disequilibrium

a

b

A

B b

a

b

a

A a

bB

a a

b b

A

b

a

b B b

aa

Linkage Disequilibrium

A a

bB

a a

b b

A

b

a

b B b

aa

Linkage Disequilibrium

A

b

a

b

Linkage Disequilibrium

A

b

a

b b

a

b

a

a a

bb

A a

b b

A

b

a

b b b

aa

Linkage Disequilibrium

A

B

A

b b

A

b

aa

b

a

bTime

Linkage Disequilibrium Mapping

Genetic Markers

Genes

PTC Linkage Disequilibrium Mapping

Kim et al. Science 2003

TAS2R38 Receptor Structure

Kim et al. J Dent Res 2004

rs713598

rs1726866

rs10246939

3 SNPs in the TAS2R38 Gene

P A V

A V I

P A I

A A V

P V I

P V V

A A I A VV

TAS2R38 Diplotype and PTC Score

0

2

4

6

8

10

12

14

16

1 2 3 4 5 6 7 8 9 10 11 12 13 14

Raw PTC Score

Number of Subjects

PAV/PAV

PAV/AVI

AAV/AVI

AVI/AVI

Kim et al. Science 2003

Confirm Mode of Inheritance

Number of FamiliesCan taste Can not taste

Both parents can taste 40 90 16One parent can taste, the other can not 51 80 37Neither parent can taste 9 0 17

Children

L. H. Snyder Science 1931

Chromosome 7

0

1

2

3

4

5

6

7

8

9

015 30 45 60 75 90 105 120 135 150 165 180 195 210 225 240 255 270 285

Location (cM)

LOD Score

Unadjusted

Adjusted

Explain Linkage Signal

Geographic Distribution of PTC Phenotype

Wooding Genetics 2006, adapted from Cavalli-Sforza 1994

Geographic Distribution of PTC Haplotypes

Table 4. Frequency of PTC haplotypes in populations worldwide

Haplotype European

(n = 200)

West Asian

(n = 22)

East Asian

(n = 54)

African

(n = 24)

S.W. Native American (n = 18)

A VI 0.47 0.67 0.31 0.25

A A V 0.03 0.04

A A I 0.17

PA V 0.49 0.33 0.69 0.50 1.00

PVI 0.04

Kim et al. Science 2003

Diplotype and PTC Score

0

2

4

6

8

10

12

14

16

1 2 3 4 5 6 7 8 9 10 11 12 13 14

Raw PTC Score

Number of Subjects

PAV/PAV

PAV/AVI

AAV/AVI

AVI/AVI

Kim et al. Science 2003

3 SNPs form 3 Haplotypes

P A V

A V I

A A V

Taster

Non-taster

Rare

Comparing Diplotypes

Diplotype Mean PTC ScorePAV/AVI 8.81AAV/AVI 7.00AVI/AVI 1.86

Predicted Effect of the 3 SNPs

Amino Acid Substitution PAM250P --> A 1A --> V 0V --> I 4

TAS2R38 Haplotype Function

0

0.2

0.4

0.6

0.8

1

1.2

0.1 1 10 100 1000

PTC concentration (μ )M

/Ratio PTC SST

PAV

PAI

PVV

PVI

AAV

AAI

AVV

AVI

PTC Diplotype and Taste

Sandell and Breslin Current Biology 2006

Next Week

• Next Generation Sequencing

Appendix: Phase Unknown Linkage

Phase Unknown

D d

D dD d

d d

d d

1 2

1 3 2 3 2 3

3 3

? ?

? ?

? ?

? ?? ?

Phase Unknown

1 2

1 3 2 3 2 3

3 3

? ? ?

What if we don’t know phase?

• We calculate the LOD score for each phase

• Divide by 2

Phase Unknown

LOD () = ½ log ()1 (1 - )2

____________________

( = 1/2) 1 + 2

+

½ log ()2 (1 – )1

____________________

( = 1/2) 2 + 1

= -0.02 for = 0.44