Frequency of mosaicism points towards mutation prone early cleavage cell divisions.
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1 Frequency of mosaicism points towards mutation prone early cleavage cell divisions. Chad Harland, Wouter Coppieters, Latifa Karim, Carole Charlier, Michel Georges
2 Germ-line de novo mutations Definition: Sequence variants absent in incoming gametes, present in outgoing gamete.
3 Germ-line de novo mutations Importance: Source of genetic polymorphism Origin: Substrate for natural and artificial selection Cause of genetic diseases Replication errors (cell-cycle-number dependent) DNA breakdown (time dependent)
4 Germ-line de novo mutations Variation: Quantitative & qualitative Sex (M>F), age (old > young) Adaptation vs adaptability Measure: Indirect (disease frequency, sequence divergence) => average Direct (NGS) => individual
5
6
7 Germ-line de novo mutations Variation: Quantitative & qualitative Sex (M>F), age (old > young) Adaptation vs adaptability Measure: Indirect (disease frequency, sequence divergence) => average Direct (NGS) => individual
8 Adaptation vs adaptability Rec = 0 Rec > 0 Rec + cost of fidelity Ne1 < Ne2 Constant Env Mutator gene Fitness gene Changing Env
9 Germ-line de novo mutations Variation: Quantitative & qualitative Sex (M>F), age (old > young) Adaptation vs adaptability Measure: Indirect (disease frequency, sequence divergence) => average Direct (NGS) => individual
10 Standard direct measure SOMA GL 1. Present in soma of offspring, absent in soma of parents (2. Transmitted) 3. Never seen before P M P M P
11 Estimated mutation rate Ségurel, Wyman & Przeworksi, 2014
12 Damona partim I 800 lanes 20 & 2-fold depth M: sperm F: blood 150 sperm cells 150 oocytes 11 / 01 /2015 3/4 completed
13 Standard direct measure SOMA GL 1. Present in soma of offspring, absent in soma of parents (2. Transmitted) 3. Never seen before P M P M P
14 Mosaïcism in the proband 1. Allelic imbalance 2. Incomplete linkage P M P M P
15 Unique pedigrees PGS PGD MGS MGD SIRE DAM Pr1 Pr2 Pr3 Pr4 5 5 Offspring 5 11 All individuals sequenced at 20-fold depth
16 Pr FOETUS (MOSAIC) SPERM OOCYTE
17 Pr F/6M 10 0 FOETUS (MOSAIC) SPERM OOCYTE
18 Proportion of variants Allelic ratio de novo mutations Pr-M (M) PR-M (O) S+D-NM Alt / Tot
19 30% of de novo mutations detected (standard) in sperm are Pr-M Pr F/6M 10 0 FOETUS (MOSAIC) SPERM OOCYTE
20 PGS PGD MGS MGD SIRE DAM Pr1 Pr2 Pr3 5 5 Offspring
21 PGS PGD MGS MGD SIRE Pr1 5 5 Offspring DAM Pr2 Pr3 5 20% of de novo mutations detected (standard) in somatic DNA (F) are PR-M!
22 Germ-line de novo mutations Definition: Sequence variants absent in incoming gametes, present in outgoing gamete.
23 Mosaïcism in the parents 1. Allelic imbalance 2. - P M P M P
24 PGS PGD MGS MGD SIRE Pr1 5 5 Offspring DAM Pr2 Pr3 5 20% of de novo mutations detected (standard) in somatic DNA (F) are PR-M!
25 PGS PGD MGS MGD SIRE DAM Pr1 Pr2 Pr3 34% (sperm) & 52% (oocyte) of de novo mutations detectable in parental sperm & somatic DNA!! 5 5 Offspring
26 Estimated mutation rate Male: 1.6 x 10-8 Average: 1.16 x fold difference Female: 6.9 x 10-9 Ségurel, Wyman & Przeworksi, 2014
27 23 cell divisions per year 20 cell divisions Detectable mosaïcism 40 PGC 2 (M) 5 (F) x 10 6 spermatagonia / oogonia MALES AFTER PUBERTY
28 Allelic balance Mosaicism in male proband Mutations ranked by allelic balance Simulation 95% Simulation Mean NL288
29 Allelic Balance Mosaicism in female probands De novo mutations ranked by allelic balance Simulation 95% Simulation Mean NL267 NL286 NL368
30 Mosaicism in male parent Simulation 95% Simulation mean NL286 NL267
31 Mosaicism in female parents Simulation 95% Simulation Mean NL368 NL267 NL286
32 23 cell divisions per year 20 cell divisions Selection? Mutation prone? Detectable mosaïcism 40 PGC 2 (M) 5 (F) x 10 6 spermatagonia / oogonia MALES AFTER PUBERTY
33 Conclusions Germline and somatic mosaïcism of de novo mutations is pervasive... This should be taken into account to accurately estimate mutation rates in the male and female germ-line... It suggests that early cell divisions are particularly prone to mutation events...
34 Funding
35 Types of de novo mutations Ti/Tv oxoguanine dependent G to T? A->C A->G A->T C->A C->G C->T Other Males Females
36 aaa caa gaa taa aac cac gac tac aag cag gag tag aat cat gat tat aca cca gca tca acc ccc gcc tcc acg ccg gcg tcg act cct gct tct Fold enrichment Types of de novo mutations CpG ->GpG CpG -> TpG M>F Replication dependent? Tri-nucleotide context
37 Serial translocation via circular intermediates underlies bovine color-sidedness Michel Georges University of Liège Belgium
38 Colorsidedness, lineback or witrik => dominant Cs allele
39
40 Polar overdominance at the calipyge locus
41 Texel Sheep
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