A. Novelletto, F. De Rango

Dept. Cell Biology, University of Calabria

GENOTYPING CONCORDANT / DISCORDANT

COUSIN PAIRS

SUMMARY OF STUDY DESIGN

CONCORDANT DISCORDANT

IBD 25% 25%

IBD > 25% < 25%

Parametric Non parametric

I-1 I-1

QUESTIONS RAISED

• IBD ≠ IBS ; to what extent this difference affects the

feasibility

• Power of the experiment

• How can info on the age of I-2, II-1 and II-2 be

exploited

• Under which circumstances the typing of I-1

becomes informative

• Can the linkage analysis be extended to physical

variables (e.g. MMSE, handgrip)

Response to selection design

Mar

ker

gen

e d

iver

sity

n. of pairs

n. of typings for centenarians

Param. vs. non param. analysis

RELEVANT VARIABLES

EXPLORING THE PERFORMANCE OF THE DESIGN

DATA SIMULATION

EVALUATION WITH AVAILABLE SOFTWARE

Parametric LOD score NPL score QTL mapping

concordant

disc.

ftp://ftp-genome.wi.mit.edu/distribution/software/genehunter

• Very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size.

• This information is then used in exact computation of multipoint LOD scores, non-parametric linkage statistics, and now in a wide range of sibpair analyses and a new variance components analysis.

• The multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data.

GENEHUNTER

PART 1 - effect of: n. of pairsmarker allele freq.

CONCORDANT – all pairs alike

1/2 1/2

1/2 2/3

1/2 3/4

2 sharing

1 sharing

0 sharing

I-1

-14

-12

-10

-8

-6

-4

-2

0

1 24 48

0 sharing

1 sharing

2 sharing

n. of pairs

Lo

g1

0(p

) N

PL

sco

reCONCORDANT, rare marker allele (q = .05)

CONCORDANT, medium marker allele (q = .12)L

og

10(p

) N

PL

sco

re

0 sharing

1 sharing

2 sharing

1 24 48

-14

-12

-10

-8

-6

-4

-2

0

n. of pairs

Lo

g1

0(p

) N

PL

sco

re

0 sharing

2 sharing

1 24 48

-14

-12

-10

-8

-6

-4

-2

0

n. of pairs

CONCORDANT, common marker allele (q = .20)

1 sharing

CONCORDANT, common marker allele (q = .20),dominant model

LO

D s

core

0 sharing

1 sharing2 sharing

n. of pairs

-1.00E-02

-6.00E-03

-2.00E-03

2.00E-03

6.00E-03

1.00E-02

1 24 48

CONCORDANT, common marker allele (q = .20),dominant model, I-1 typed

LO

D s

core

0 sharing

1 & 2 sharing

n. of pairs

-1.00E-02

-6.00E-03

-2.00E-03

2.00E-03

6.00E-03

1.00E-02

1 24 48

CONCORDANT, common marker allele (q = .20),recessive model

LO

D s

core

0 sharing1& 2 sharing

n. of pairs

-1.00E-02

-6.00E-03

-2.00E-03

2.00E-03

6.00E-03

1.00E-02

1 24 48

CONCLUSION SET 1 - CONCORDANT

• NPL more appropriate

• Dramatic effect of allele frequencies at marker loci

• Minor advantage in typing I-1 in CONCORDANT

pairs

PART 2 - effect of response to selection design

CONCORDANT – different proportions of 0, 1, 2 sharing

1/2 1/2

1/2 2/3

1/2 3/4

2 sharing

1 sharing

0 sharing

I-1

0

0.2

0.4

0.6

0.8

1

3:1 2:1 1.4:1 1:1 1:1

96 pairs

48 pairs

(p)

NP

L s

core

rare allele common

CONCORDANT, 0:1 sharing ratios

CONCLUSION SET 2 - CONCORDANT

• Dramatic effect of allele frequencies at marker loci

confirmed

• Haplotyping (and perhaps search for private SNPs)

needed to increase marker diversity

• Ratio of non sharing/sharing cousin pairs

approaching 1:1 preferred

• Entire study needed to reach significance with

concordant pairs only

PART 3 - effect of: n. of pairsmarker allele freq.

DISCORDANT – all pairs alike

1/2 1/2

1/2 2/3

1/2 3/4

2 sharing

1 sharing

0 sharing

Very different liabilities for genotypes at the “longevity” locus

I-1

LO

D s

core

0 sharing

1 sharing

2 sharing

DISCORDANT, recessive model rare marker allele (q = .05)

n. of pairs

-6

-5

-4

-3

-2

-1

0

1

2

3

1 24 48

LO

D s

core

0 sharing

1 sharing2 sharing

DISCORDANT, dominant model rare marker allele (q = .05)

-6

-5

-4

-3

-2

-1

0

1

2

3

1 24 48

n. of pairs

LO

D s

core

I-1 untyped

DISCORDANT, recessive model

n. of pairs

0,0

1,0

2,0

3,0

4,0

5,0

6,0

7,0

8,0

9,0

1 24 48

I-1 typed

LO

D s

core

I-1 untyped

DISCORDANT, dominant model

n. of pairs

I-1 typed

0,0

1,0

2,0

3,0

4,0

5,0

6,0

7,0

8,0

9,0

1 24 48

CONCLUSION SET 3 - DISCORDANT

• Parametric LOD SCORE analysis obligate

• Minor effect of allele frequencies at marker loci

• Strong advantage in typing I-1 in DISCORDANT pairs

PART 4 - effect of response to selection design

DISCORDANT – different proportions of 0, 1, 2 sharing

1/2 1/2

1/2 2/3

1/2 3/4

2 sharing

1 sharing

0 sharing

I-1

LO

D s

core

DISCORDANT, recessive model,0:1 sharing ratios

common allele rare

0

0,5

1

1,5

2

2,5

3

3,5

4

1:1 2:1 3:1 5:1 5:1

96 pairs

48 pairs

LO

D s

core

DISCORDANT, dominant model,0:1 sharing ratios

common allele rare

1:1 2:1 3:1 5:1 5:1

0

0,5

1

1,5

2

2,5

3

3,5

4

4,5

5

96 pairs

48 pairs

CONCLUSION SET 4 - DISCORDANT

• Allele frequencies at marker loci not as crucial as in

CONCORDANT pairs

• Lack of informativeness can be compensated by

typing I-1

SHORT-TERM DEVELOPMENTS

• Approaching the CV/CD hypothesis by modulating

parameters of the “longevity” locus (allele

frequencies and GRR)

• Exploring the same data sets with different

algorithms (e.g. MCMC, Simwalk)

• Exploring multipoint data

-2,5

-2

-1,5

-1

-0,5

0

0,5

1

1,5

2

1 2 3 4 5 6 7

map position

APPROACHING THE REAL DATA

Typing of cousing pairs

• Haplotyping from family data

Collecting population data

• Determining allele frequencies• Haplotyping from population

data ( PHASE, Arlequin)

“Real time” monitoring of results