Download presentation

Presentation is loading. Please wait.

Published bySara Bain Modified over 3 years ago

1
A. Novelletto, F. De Rango Dept. Cell Biology, University of Calabria GENOTYPING CONCORDANT / DISCORDANT COUSIN PAIRS

2
SUMMARY OF STUDY DESIGN CONCORDANT DISCORDANT IBD25% IBD> 25% < 25% Parametric Non parametric I-1

3
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)

4
Response to selection design Marker gene diversity n. of pairs n. of typings for centenarians Param. vs. non param. analysis RELEVANT VARIABLES

5
EXPLORING THE PERFORMANCE OF THE DESIGN DATA SIMULATION EVALUATION WITH AVAILABLE SOFTWARE Parametric LOD score NPL scoreQTL mapping concordant disc.

6
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

7
PART 1 - effect of:n. of pairs marker allele freq. CONCORDANT – all pairs alike 1/2 2/3 1/23/4 2 sharing 1 sharing 0 sharing I-1

8
-14 -12 -10 -8 -6 -4 -2 0 12448 0 sharing 1 sharing 2 sharing n. of pairs Log 10 (p) NPL score CONCORDANT, rare marker allele (q =.05)

9
CONCORDANT, medium marker allele (q =.12) Log 10 (p) NPL score 0 sharing 1 sharing 2 sharing 12448 -14 -12 -10 -8 -6 -4 -2 0 n. of pairs

10
Log 10 (p) NPL score 0 sharing 2 sharing 12448 -14 -12 -10 -8 -6 -4 -2 0 n. of pairs CONCORDANT, common marker allele (q =.20) 1 sharing

11
CONCORDANT, common marker allele (q =.20), dominant model LOD score 0 sharing 1 sharing 2 sharing n. of pairs -1.00E-02 -6.00E-03 -2.00E-03 2.00E-03 6.00E-03 1.00E-02 12448

12
CONCORDANT, common marker allele (q =.20), dominant model, I-1 typed LOD score 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 12448

13
CONCORDANT, common marker allele (q =.20), recessive model LOD score 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 12448

14
CONCLUSION SET 1 - CONCORDANT NPL more appropriate Dramatic effect of allele frequencies at marker loci Minor advantage in typing I-1 in CONCORDANT pairs

15
PART 2 - effect of response to selection design CONCORDANT – different proportions of 0, 1, 2 sharing 1/2 2/3 1/23/4 2 sharing 1 sharing 0 sharing I-1

16
0 0.2 0.4 0.6 0.8 1 3:12:11.4:11:1 96 pairs 48 pairs (p) NPL score rare allelecommon CONCORDANT, 0:1 sharing ratios

17
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

18
PART 3 - effect of: n. of pairs marker allele freq. DISCORDANT – all pairs alike 1/2 2/3 1/23/4 2 sharing 1 sharing 0 sharing Very different liabilities for genotypes at the longevity locus I-1

19
LOD score 0 sharing 1 sharing 2 sharing DISCORDANT, recessive model rare marker allele (q =.05) n. of pairs -6 -5 -4 -3 -2 0 1 2 3 12448

20
LOD score 0 sharing 1 sharing 2 sharing DISCORDANT, dominant model rare marker allele (q =.05) -6 -5 -4 -3 -2 0 1 2 3 12448 n. of pairs

21
LOD score 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 12448 I-1 typed

22
LOD score 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 12448

23
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

24
PART 4 - effect of response to selection design DISCORDANT – different proportions of 0, 1, 2 sharing 1/2 2/3 1/23/4 2 sharing 1 sharing 0 sharing I-1

25
LOD score DISCORDANT, recessive model, 0:1 sharing ratios common allelerare 0 0,5 1 1,5 2 2,5 3 3,5 4 1:12:13:15:1 96 pairs 48 pairs

26
LOD score DISCORDANT, dominant model, 0:1 sharing ratios common allelerare 1:12:13:15:1 0 0,5 1 1,5 2 2,5 3 3,5 4 4,5 5 96 pairs 48 pairs

27
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

28
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 -0,5 0 0,5 1 1,5 2 1234567 map position

29
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

Similar presentations

OK

Practical With Merlin Gonçalo Abecasis. MERLIN Website www.sph.umich.edu/csg/abecasis/Merlin www.sph.umich.edu/csg/abecasis/Merlin Reference FAQ Source.

Practical With Merlin Gonçalo Abecasis. MERLIN Website www.sph.umich.edu/csg/abecasis/Merlin www.sph.umich.edu/csg/abecasis/Merlin Reference FAQ Source.

© 2017 SlidePlayer.com Inc.

All rights reserved.

Ads by Google

Ppt on asymptotic notation of algorithms definition Ppt on corporate etiquettes meaning Ppt on solid dielectrics glass Lockout tagout ppt online Ppt on pricing policy document Training ppt on email etiquettes Ppt on indian railway system Ppt on how to use powerpoint 2013 Ppt on question tags examples Ppt on distance displacement speed velocity acceleration and equations of motion