Frequency of mosaicism points towards mutation prone early cleavage cell divisions. Chad Harland, Wouter Coppieters, Latifa Karim, Carole Charlier, Michel Georges
Germ-line de novo mutations Definition: Sequence variants absent in incoming gametes, present in outgoing gamete.
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)
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
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
Adaptation vs adaptability Rec = 0 Rec > 0 Rec + cost of fidelity Ne1 < Ne2 Constant Env Mutator gene Fitness gene Changing Env
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
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
Estimated mutation rate Ségurel, Wyman & Przeworksi, 2014
Damona partim I 800 lanes 20 & 2-fold depth M: sperm F: blood 150 sperm cells 150 oocytes 11 / 01 /2015 3/4 completed
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
Mosaïcism in the proband 1. Allelic imbalance 2. Incomplete linkage P M P M P
Unique pedigrees PGS PGD MGS MGD SIRE DAM Pr1 Pr2 Pr3 Pr4 5 5 Offspring 5 11 All individuals sequenced at 20-fold depth
Pr4 40 11 30 20 10 0 FOETUS (MOSAIC) SPERM OOCYTE
Pr4 40 11 30 20 7F/6M 10 0 FOETUS (MOSAIC) SPERM OOCYTE
Proportion of variants Allelic ratio de novo mutations 0.4 0.35 0.3 0.25 Pr-M (M) PR-M (O) S+D-NM 0.33 0.49 0.46 0.2 0.15 0.1 0.05 0 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Alt / Tot
30% of de novo mutations detected (standard) in sperm are Pr-M Pr4 40 11 30 20 7F/6M 10 0 FOETUS (MOSAIC) SPERM OOCYTE
PGS PGD MGS MGD SIRE DAM Pr1 Pr2 Pr3 5 5 Offspring 5 40 30 20 10 0
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! 40 30 20 10 0
Germ-line de novo mutations Definition: Sequence variants absent in incoming gametes, present in outgoing gamete.
Mosaïcism in the parents 1. Allelic imbalance 2. - P M P M P
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! 40 30 20 10 0
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 5 40 30 20 10 0
Estimated mutation rate Male: 1.6 x 10-8 Average: 1.16 x 10-8 2.4-fold difference Female: 6.9 x 10-9 Ségurel, Wyman & Przeworksi, 2014
23 cell divisions per year 20 cell divisions Detectable mosaïcism 40 PGC 2 (M) 5 (F) x 10 6 spermatagonia / oogonia MALES AFTER PUBERTY
Allelic balance Mosaicism in male proband 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 Mutations ranked by allelic balance Simulation 95% Simulation Mean NL288
Allelic Balance Mosaicism in female probands 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 De novo mutations ranked by allelic balance Simulation 95% Simulation Mean NL267 NL286 NL368
Mosaicism in male parent 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 Simulation 95% Simulation mean NL286 NL267
Mosaicism in female parents 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 Simulation 95% Simulation Mean NL368 NL267 NL286
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
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...
Funding
Types of de novo mutations 0.4 0.35 0.3 Ti/Tv 1.3 8-oxoguanine dependent G to T? 0.25 0.2 0.15 0.1 0.05 0 A->C A->G A->T C->A C->G C->T Other Males Females
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 90 80 70 60 50 40 30 20 10 0 CpG ->GpG CpG -> TpG M>F Replication dependent? Tri-nucleotide context
Serial translocation via circular intermediates underlies bovine color-sidedness Michel Georges University of Liège Belgium
Colorsidedness, lineback or witrik => dominant Cs allele
Polar overdominance at the calipyge locus
Texel Sheep