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A. Novelletto, F. De Rango
Dept. Cell Biology, University of Calabria
GENOTYPING CONCORDANT / DISCORDANT
COUSIN PAIRS
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SUMMARY OF STUDY DESIGN
CONCORDANT DISCORDANT
IBD 25% 25%
IBD > 25% < 25%
Parametric Non parametric
I-1 I-1
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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)
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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
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EXPLORING THE PERFORMANCE OF THE DESIGN
DATA SIMULATION
EVALUATION WITH AVAILABLE SOFTWARE
Parametric LOD score NPL score QTL mapping
concordant
disc.
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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
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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
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-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)
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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
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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
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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
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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
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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
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CONCLUSION SET 1 - CONCORDANT
• NPL more appropriate
• Dramatic effect of allele frequencies at marker loci
• Minor advantage in typing I-1 in CONCORDANT
pairs
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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