Mutations de novo. Introduction to genetics. Department of Medical Genetics Medical University of Warsaw

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1 Mutations de novo Introduction to genetics Department of Medical Genetics Medical University of Warsaw

2 De novo mutations - importance so far omitted from our course to make things simpler very rare indeed, BUT... historical necessity (population size vs allele heterogeneity vs consequences of homozygosity) suprising frequency in diseases with genetic background (today s topic) causes of mutations?

3 Mutations vs allele frequency (mutation-retromutation equilibrium) p q with frequency µ (mutation rate) p q with frequency ν (retromutation rate) Generation 0: p 0 =1; q 0 =0 Generation 1: q 1 = µp 0 =µ; p 1 =(1-µ) Generation 2: q 2 = q 1 +µp p 2 =(1-µ) 2 1 ; Generation n: q n =q n-1 +µp n-1 ; p n =(1-µ) n q n =q n-1 +µp n-1 -νq n-1 equilibrium: q n =q n-1 µp n-1 νq n-1 = 0 µp n-1 = νq n-1 since p+q=1 p=(1-q) µ(1-q)=vq µ-µq=νq µ=νq+µq=q(µ+ν) q = µ / (µ+ν) p = ν / (µ+ν)

4 Selection & allele frequency (selection in medical genetics) For a mutation with a strong phenotypic effect the frequency of a mutated allele is determined by selection rather than retromutation selection coefficient (S) denotes a degree of reproductive deficiency of a given genotype in relation to a genotype with the highest reproductive rate in a population S jest dopełnieniem wartości przystosowawczej (W) genotypu do jedności (S = 1 W).

5 Selection & allele frequency (selection in medical genetics) S=1/3 N=9 N=4 (50%->31%) N=9 3=27 N=4 2=8 (50%->23%) N=27 3=81 N=8 2=16 (50%->16%) N=81 3=243 N=16 2=32 (50%->12%)

6 Selection & allele frequency (selection in medical genetics) S=1/3 Genetically lethal disease either kills before puberty or causes sterility S=1

7 Disease frequency vs allele frequency Disease frequency F Mutated allele frequency q Hardy & Weinberg principle p 2 +2pq+q 2 =1 p+q=1 Autosomal dominant inheritance F F = 2pq q= p 1 2p q F 2 Autosomal recesive inheritance F = q 2 q= F X-linked recessive inheritance males: F m = q q = F m

8 Autosomal dominant diseases (genetically lethal) All defective alleles are being lost in each generation and must be replaced via mutations q = µ de novo mutation p wild-type allele frequency q mutated allele frequency µ mutation frequency selection All cases of disease are due to new mutations!!! Very low recurrence risk apart from germline mosaicism

9 Autosomal dominant diseases (all) Some defective alleles are being lost in each generation and must be replaced via mutations de novo mutation S q = µ p wild-type allele frequency q mutated allele frequency S selection coefficient µ mutation frequency selection

10 Autosomal recessive diseases (genetically lethal) All homozygotes are sterile, their alleles are lost in each generation and must be replaced via mutations population: N disease frequency: q 2 N o of individuals not passing their alleles: q 2 N (only q are lost) N o of alleles lost: 2 q 2 N N o of all alleles: 2 N frequency of alleles being lost: 2 q 2 N / 2 N = q 2 only q are lost lost alleles replaced due to de novo mutations: µ=q 2 de novo mutation selection

11 Autosomal recessive diseases (genetically lethal) All homozygotes are sterile, their alleles are lost in each generation and must be replaced via mutations q 2 = µ de novo mutation p wild-type allele frequency q mutated allele frequency µ mutation frequency example: q=0.01 => µ= (µ is very small, 0) Practically in autosomal recessive diseases mutations de novo need not be considered! selection

12 Autosomal recessive diseases (all) All homozygotes are less fertile, some of their alleles are lost in each generation and must be replaced via mutations population: N disease frequency: q 2 N o of individuals not passing their alleles: q 2 N (only q are lost) N o of alleles lost: 2 S q 2 N N o of all alleles: 2 N frequency of alleles being lost: 2 S q 2 N / 2 N = S q 2 only q are lost lost alleles replaced due to de novo mutations: µ=s q 2 de novo mutation selection

13 Autosomal recessive diseases (all) All homozygotes are less fertile, some of their alleles are lost in each generation and must be replaced via mutations de novo mutation µ = S q 2 p wild-type allele frequency q mutated allele frequency S selection coefficient µ mutation frequency example: q=0.01 & S=0.25 => µ= = selection If an autosomal recessive disease is not genetically lethal, de novo mutations play even lesser role!

14 X-linked recessive diseases (genetically lethal) If the disease is genetically lethal, all mutated alleles carried by hemizygotic males are lost in each generation de novo mutation achieving equilibrium is more complex selection XY XX

15 X-linked recessive diseases Frequency of mutations (µ), sicked males (A) and female carriers (H) A H A H/2 A=½H+ µ A=½(4µ )+µ A=2µ+µ A=3µ µ H/2+µ A=3µ H/2+µ H/2+ H=4µ µ+µ H=½H+2µ H-½H=2µ ½H=2µ // 2 H=4µ Częstość: A chorych mężczyzn H kobiet nosicielek µ mutacji

16 X-linked recessive diseases Frequency of mutations (µ), sicked males (A) and female carriers (H) 3µ 4µ 3µ 2µ µ 2µ+µ 2µ+µ 3µ 2µ+ 4µ µ+µ Częstość: A chorych mężczyzn H kobiet nosicielek µ mutacji

17 X-linked recessive diseases Frequency of mutations (µ), sicked males (A) and female carriers (H) 3/1000 4/1000 N = 1000M+1000K µ= 1/1000 3/1000 1/1000 3/1000 2µ+µ 4/2000 (2/1000) 2/ /1000 2µ+ 4/1000 µ+µ

18 X-linked recessive diseases Frequency of mutations (µ), sicked males (A) and female carriers (H) The frequency of female carriers H=½H+µ+µ H=4 The frequency of sick males A=½H+ µ A=3µ µ-mutation rate µ

19 Sporadic case 1

20 Sex-linked recessive disease mutation de novo (µ f =µ m ) or inheritance? [Bayes theorem] Probability of I2 is a carrier I2 isn t a carrier initial 4µ 1 conditional (sick son) 1/2 µ odds 2 µ µ final risk 2/3 1/3 L1: I2 jest nosicielką L2: mutacja de novo

21 Sex-linked recessive disease mutation de novo (µ f =µ m ) or inheritance? [LR] ~4µ 1/2 L1 = 4µ 0,5 = 2µ µ ~1 L2 = 1 µ = µ L1: I2 is a carrier L2: mutation de novo LR=L1/L2=2 (2:1): Every third sporadic case is due to de novo mutation!!!

22 Duchenne muscular dystrophy myopathy due to DMD mutations (1/3500 M) Calves pseudohypertrophy muscles are replaced with fat and connective tissue in 8-years old boy with Duchenne muscular dystrophy Results of dystrophin gene mutation in DMD: a sample of a muscle of the healthy person (upper) and the affected one (lower) stained with HE (left) or immunostained with antibody against dystrophin (right) Gowers maneuver: boy with DMD rises from the ground

23 Duchenne muscular dystrophy myopathy due to DMD mutations A third of mothers who have a single son affected will not themselves be carriers of a mutation in the DMD gene!!! Thus they have very low risk (µ) of subsequent problems

24 De novo mutation rates of male & female origin in the diseases studied so far α - male/female ratio of mutations) Is evolution male-driven?

25 Meiosis in females and in males Nat Rev Gen 2001

26 X-linked recessive diseases Frequency of mutations (µ), sicked males (A) and female carriers (H) when µ F µ M A H A H/2 A=½H+µ F A=½(µ M + µ F )+µ F A=2µ F +µ M H=½H+µ M +µ F H/2 µ H-½H=µ M +µ F M +µ F ½H=µ M +µ F / 2 H=2µ M +2µ F A= H/2+µ 2µ F F M H= H/2+ 2µ µ F +µ F + 2µ M M Częstość: A chorych mężczyzn H kobiet nosicielek µ mutacji

27 X linked recessive inheritance: relationship between µ, H, and A (cntd.), µ differes between sexes (µ f =µ m ) cntd. 2µ f +µ m 2(µ f +µ m ) people 2µ f +µ m µ f +µ m chromosomes µ m gametes µ f +µ m +µ f =2µ f +µ m µ 2µ f +µ f +µ m m people +µ f +µ m

28 Relationship between µ, H, and A (cntd.), µ differs between sexes N fem. =N male. =1000, µ m =2/1000, µ f =1/1000 4/1000 6/1000 people 4/1000 6/2000 chromosomes X: 2/1000 Y: 0/1000 gametes X: (3+1)/1000 X: (3+1)/1000 Y: 0/ 1000 X: 4/1000 people X: 4/1000 X: 2/1000

29 Sporadic case 2

30 X-linked recessive disease mutation de novo (µ f µ m ) or inherited? 1/2 ~2 (µ f +µ m ) L1= µ f +µ m µ f ~1 L2=1 µ f =µ f L1: I2 is a carrier L2: de novo mutation LR= (µ f +µ m ) / µ f. if µ f =0.2µ m, then LR=1.2/0.2=6, tzn.: Only 1/7 of sporadic cases are due to de novo mutations

31 X-linked recessive disease mutation de novo (µ f µ m ) or inherited? 0,92 P mother as a carrier 0,87 0,82 0,77 0,72 0, µ m /µ f

32 Hemophilia Hemophilia A and hemophilia B are X-linked disorders of coagulation caused by mutations in the F8 and F9 genes, respectively. Mutations of F8 cause deficiency or dysfunction of clotting factor VIII; mutations of F9 cause deficiency or dysfunction of clotting factor IX. Hemophilia A has an incidence of 1 in 5000 to 10,000 newborn males. Hemophilia B is far rarer, with an incidence of 1 in 100,000. Subcutaneous hematoma of the forehead in a young heophiliac boy, days after a minor contusion. The appearance of the forehead returned to normal in 6 months Hemophilia A Factor VIII α ~3 Rosendaal Hemophilia B Factor IX α ~4 Sommer 2001.

33 Duchenne muscular dystrophy an exception to the rule? De novo mutations arise with comparable frequency during oogenesis and spermatogenesis The dystrophin gene is a very large (>2mB) and contains many repetitive regions. Furthermore, a greater than 30- fold(!) reduction in dystrophin activity must occur before the DMD phenotype is observed Sommer High frequency of large deletions (60% to 65%), large duplications (5% to 10%), and small deletions, insertions, or nucleotide changes (25% to 30%). Most de novo large deletions arise during oogenesis, whereas most de novo nucleotide changes arise during spermatogenesis