Prof.

Edvīns Miklaševičs
10.02.2020.

Medical Genetics

1
Nam ut medici causa morbi inventa
curationem esse inventam putant, sic
nos causa aegritudinis reperta medendi
facultatem reperiemus.
M. TVLLI CICERONIS TVSCVLANARVM DISPVTATIONVM LIBER TERTIVS

2
Content

■ Subject of medical genetics.

■ Causes of phenotypical variability.
■ Causes of diversity of allelic variants.
■ Somatic and generative allelic variants, their clinical
significance.

‹#›
Subject of medical genetics

4
 de’ Medici

Leopoldo

(1617 - 1675)

Giuliano (1479 -
Lorenzo (1449 - 1492)
1516)
Genetics

! The study of heredity and the variation of inherited

characteristics.

Oxford Dictionaries 8
Genetics vs Molecular biology

! The study of heredity and ! The branch of biology

the variation of inherited
characteristics.
that deals with the
structure and functions of
the macromolecules (e.g.
proteins and nucleic
acids) essential to life.

Oxford Dictionaries 9
 Genetics vs Molecular biology

Transfer of Structure and

DNA molecules function of DNA

from generation molecules.

to generation,
phenotype seg-
regation.

Museum
für Naturkunde
Berlin 10
Genetics - heredity and the variation of
inherited characteristics

Museum
für Naturkunde
Berlin 11
Genetics vs Molecular biology

! Crossing ! DNA analyzes

! Phenotype analyzes/trait segregation ! Southern hybridization
! Concordance tests ! PCR
! Statistics ! Sequencing
! Theory of probability ! Sanger
! NGS
! Spectrometry from UV to MS
! Molecular cytogenetics
! RNS analyzes
! Northern hybridization
! in situ hybridization
! PCR
! Expression analysis
! Protein analysis
! Animal models

12
Essentialist vs Nominalist

! Diseases exist somehow and in some way as entities

that attack their victims.

! Disease defined as a change within, an altered state,

or a deviation, in response to some stimulus.

13
bility emergence followed by disappearance. This pattern is a key point,
blem as we will see when we return to consider the evolutionary impli-
aken Human
cations of themortality curves
genetic theory of infectious diseases. The global in-
ts to fectious burden was caused mostly by primary infections, striking
par-
more
atter
artial
f the

ame
lle’s
nly a
and
arles
s his
ww.
pres- Fig. 1. Human mortality curves. Mortality curves at various periods of hu-
f an man history, from the Paleolithic period (<10,000 BC) to modern times (2000
y be AD). Contemporary data for the 2015,
Casanova United Kingdom
Proc. andSci.
Natl. Acad. Mozambique are avail-
USA, 112, E7118 - E7127.
‹#›
ales- able from the WHO site (www.who.int/topics/global_burden_of_disease). Older
bility emergence followed by disappearance. This pattern is a key point,
blem as we will see when we return to consider the evolutionary impli-
aken Human
cations of themortality curves
genetic theory of infectious diseases. The global in-
ts to fectious burden was caused mostly by primary infections, striking
par-
more
atter
artial
f the

ame Microbiology
lle’s
nly a
and
arles
s his
ww.
pres- Fig. 1. Human mortality curves. Mortality curves at various periods of hu-
f an man history, from the Paleolithic period (<10,000 BC) to modern times (2000
y be AD). Contemporary data for the 2015,
Casanova United Kingdom
Proc. andSci.
Natl. Acad. Mozambique are avail-
USA, 112, E7118 - E7127.
‹#›
ales- able from the WHO site (www.who.int/topics/global_burden_of_disease). Older
Causes of death in the USA, 1900 -
2010.

Cardiovascular diseases

Influenza

Oncological diseases

Tuberculose

Jones et al., 2012, N. Eng. J. Med., 366, 2333 - 2338.16

Continuity of disease across the lifetime

17
Continuity of disease across the lifetime

Schizophrenia

Bipolar disoders

Diabetes (T1 and T2)

Astma

Cardiovascular diseases
Oncological diseases

18
9 Other
Proportional Contribution to Premature
Death Proportional Contribution to Premature Death
Social
p-Ranked
Genetic circumstances
ry in OECD* 15%
predisposition
30%
Environmental
exposure
celand 5%
7 deaths/
live births) Health care
10%

itzerland
4 deaths/
000 births) Behavioral patterns
40%
Schroeder, 2007, N. Engl. J. Med. , 357, 1221 - 1228. ‹#›
Figure 1. Determinants of Health and Their Contribution
bility emergence followed by disappearance. This pattern is a key point,
blem as we will see when we return to consider the evolutionary impli-
aken Human
cations of themortality curves
genetic theory of infectious diseases. The global in-
ts to fectious burden was caused mostly by primary infections, striking
par-
more
atter
artial Genetics
f the

ame
lle’s
nly a
and
arles
s his
ww.
pres- Fig. 1. Human mortality curves. Mortality curves at various periods of hu-
f an man history, from the Paleolithic period (<10,000 BC) to modern times (2000
y be AD). Contemporary data for the 2015,
Casanova United Kingdom
Proc. andSci.
Natl. Acad. Mozambique are avail-
USA, 112, E7118 - E7127.
‹#›
ales- able from the WHO site (www.who.int/topics/global_burden_of_disease). Older
■ Understanding basic cause of disease and creating
new targets for prevention and therapy
■ Newborn screening
■ Identification of risk allele carrier and genetic
consulting
■ Family planning
■ New approaches in medicine
■ pharmacogenetics
■ gene therapy
■ targeted therapy

‹#›
Causes of phenotypical variability

22
Phenotype

Genes 23
 The ontogenic pyramid
Astolfi et al.

repositioning
repeats (long
aberrations.
hromosomes
ucleus, as in
the aegis of a

ineages, and
may display
age stage hu-
amatic insur-
tions, admit-
; see also the
in this issue]
rtions of zy-
erging germ
e insurgence
Conversely, a
Fig. (1). The “ontogenic pyramid”.
Astolfi etThe phenotype
al., 2010, (PHE)
Current may be 11, 379 - 386.
Genomics,
nd associated
seen as the result of four variables: the original zygotic genome 24
een environ-
1 cell Cell divisions 1012 - 1013
cells

25
 1 cell Cell divisions 1012 - 1013
cells

Retina 55
Intestinal epithelium 600
Germline 216

Lynch 2010, Trends Genet., 26, 345–352.

26
‹#›
‹#›
Fig. 3. Examples of twelve different ears (heights have been standardised). The numbers cross-reference with Fig. 5 and the Supplementary dataset.

Bevan et al., 2014, J. Archeol. Sci., 49, 249 - 254.‹#›

 Darwin’s tubercle Superior crus of
antihelix expression

Crus helix expression

Folding of
antihelix
Tragus size
Antitragus
size

Helix rolling Lobe size Lobe attachment Ear protrusion

rs3827760

rs10212419
rs2080401
rs17023457

12.5
rs263156
12.0
11.5
11.0

rs1619249
10.5
rs1960918

10.0
9.5
9.0
8.5
8.0
–Log10 (P)

7.5
7.0
6.5
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0.0

Chr1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X XY

Figure 1 | Genome-wide associations of pinna traits. Variation in 10 pinna traits was evaluated in 5,062 individuals. The photographs at the top
indicate the location of the traits examined. At the bottom is shown a composite Manhattan plot for the seven traits showing genome-wide significant
Adhikari et al., 2015, Nat. Commun., 6: 7500.
association with at least one genome region. The rs numbers for the most significantly associated (index) SNP in each region are provided (Table 1).
‹#›

Each of the seven regions on the Manhattan plot is connected with the associated trait on the photos via a line of different colour (composite panels
 Darwin’s tubercle Superior crus of
antihelix expression

Crus helix expression

Folding of
antihelix
Tragus size
Antitragus
size

Helix rolling Lobe size Lobe attachment Ear protrusion

rs3827760

rs10212419
rs2080401
rs17023457

12.5
rs263156
12.0
EDAR

11.5
11.0

rs1619249
10.5
rs1960918

10.0
9.5
9.0
8.5
8.0
–Log10 (P)

7.5
7.0
6.5
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0.0

Chr1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X XY

Figure 1 | Genome-wide associations of pinna traits. Variation in 10 pinna traits was evaluated in 5,062 individuals. The photographs at the top
indicate the location of the traits examined. At the bottom is shown a composite Manhattan plot for the seven traits showing genome-wide significant
Adhikari et al., 2015, Nat. Commun., 6: 7500.
association with at least one genome region. The rs numbers for the most significantly associated (index) SNP in each region are provided (Table 1).
‹#›

Each of the seven regions on the Manhattan plot is connected with the associated trait on the photos via a line of different colour (composite panels
 EDAR pathway
EDA-A1/NF-jB €gren’s syndrome
signalling in Sjo

n
of
ck
d
of ■ EDAR pathway deter-
ly
v-
mines development of
d ectodermal appenda-
].
d ges (e.g. hair folicules,
lt teeth, glands), their
d
al localization, size and
n shape.
c-
l-
ne
he
n
ne
as Fig. 7. A simplified overview of the ectodysplasin/EDA-receptor/ Sisto et al., 2016, British Soc. Immunol.,
nuclear factor kappa B (EDA/EDAR/NF-jB) pathway. Trimeric ‹#›
es
receptor EDAR is activated by trimeric ligand EDA leading to the Clin. Experimen. Immunol.,184, 183–196.
Effect of allelic variant of the Edar gene
on the shape of ears
c

wt/wt Val370Ala/Val370Ala

Adhikari et al., 2015, Nat. Commun., 6: 7500.

‹#›
Allelic variants of the EDAR gene

ncbi.nml.nih.gov/clinvar‹#›
Allelic variants of the EDAR gene
NATURE COMMUNICATIONS | DOI: 10.1038/ncomms8500

b c

d e
100 ncbi.nml.nih.gov/clinvar
0.25
‹#›
Allelic variants of the EDAR gene
EDAR mutations in HED
AH van der Hout et al
676

van der Hout et al., 2008, Europ. J. Hum. Genet., 16, 673 - 679.
‹#›
Allelic variants of the EDAR gene
BMC Medical Genetics 2006, 7:80 http://www.biomedcentral.com/1471-2350/7/80

Lind et al., 2006, BMC Med. Genet., 7: 80.

‹#›
Classification of allelic variants

! pathogenic
! likely pathogenic
! uncertain significance
! likely benign
! benign

ACMG Guidelines 38
DIGNUM MEMORIA

1. Every gene has several (often very many) allelic

variants.
2. Diversity of allelic variants and their different
combinations produce phenotypic variability.
3. Allelic variants of the one and the same gene may be
phenotypically neutral, cause some phenotype
variations or severe pathology.
4. Allelic variants arise as a result of mutations.

‹#›
DIGNUM MEMORIA

1. All humans - with normal phenotype, or with

pathology - have the same genes.
2. Differences in the phenotypes - normal and
pathological - are caused not by presence, or
absence of some specific genes but by different
allelic variants of these genes.

‹#›
Causes of diversity of allelic variants

41
 RICHARD ET AL. MICROBIOL. MOL. BIOL.

G. 1. Repeated DNA sequences in eukaryotic genomes and mechanisms of evolution. The two main categories of repeated elements (tan
ats and dispersed repeats) are shown, along with subcategories, as described in the text. Blue arrows point to molecular mechanisms tha
ved in propagation and evolution of repeated sequences. REP, replication slippage; GCO, gene conversion; WGD, whole-genome du
SEG, segmental duplications; RTR, reverse transcription; TRA, transposition.
Richard et al., 2008, Microbiol. Molecular Biol. Rev., 72, 686 – 727. 42
! Alterations in number of chromosomes

! Remodeling of chromosomes

! Changes in gene dosage

! Micro- and mini-satellite instability

! Nucleotide substitutions, insertions, deletions

43
Mutations

! Germ - line and somatic

! Spontaneous and induced

44
Causes of mutations

! Endogenous

! Environmental

45
Causes of mutations

! Endogenous
» DNA replication errors
» reactive oxygen compounds arising as byproducts from
oxidative respiration

! Environmental

46
DNA replication

47
 The ontogenic pyramid
Astolfi et al.

repositioning
repeats (long
aberrations.
hromosomes
ucleus, as in
the aegis of a

ineages, and
may display
age stage hu-
amatic insur-
tions, admit-
; see also the
in this issue]
rtions of zy-
erging germ
e insurgence
Conversely, a
Fig. (1). The “ontogenic pyramid”.
Astolfi etThe phenotype
al., 2010, (PHE)
Current may be 11, 379 - 386.
Genomics,
nd associated
seen as the result of four variables: the original zygotic genome 48
een environ-
Causes of mutations

! Endogenous

! Environmental
» ultraviolet light
» ionizing radiation
» chemicals
- tobacco products
- food contaminants
- heterocyclic amines in overcooked meals

49
 Relative risk of melanoma associated with
Schulman and Fisher Page 11

exposure to indoor tanning

NIH-PA Author Manuscript
NIH-PA Author Manuscript

Figure 2. Schulman & Fisher 2009, Curr. Opin Oncol., 21, 144 –149.
Relative risk of melanoma associated with early first exposure to indoor tanning: estimates 50
(http://cdn2.artboom.info/wp-content/uploads/2011/11/Fernando-Vicente-11.jpg)
Fernando Vicente51
2FLARES (http://filament.io/flare?
Most common specific causes of death: 12-year
relative risk, current versus never-smoker
Number of deaths RR (95% CI)
samp
Current Never
base
smoker smoker thos
Chronic lung disease (J40–44) 1789 121 35·3 (29·2–42·5) neve
Cancer of lung (C34) 5633 698 21·4 (19·7–23·2) diffe
Aortic aneurysm (I71) 330 164 6·32 (5·17–7·71) body
Intestinal ischaemia (K55) 183 91 5·58 (4·27–7·29) Th
Cancer of mouth, pharynx, larynx, 204 91 4·83 (3·72–6·29) resu
nasal cavity, or sinuses (C00–14,30–32) smok
Coronary heart disease (I21–25) 2726 1732 4·47 (4·19–4·77) (424 2
Cirrhosis or alcoholic liver (K70,74) 478 256 3·35 (2·84–3·94) answ
Cancer of bladder (C67) 178 156 3·29 (2·61–4·15) of th
Cancer of oesophagus (C15) 450 397 3·10 (2·68–3·58) of n
Pneumonia (J12–18) 494 408 3·09 (2·68–3·56)
ex-sm
Cerebrovascular disease (I60–69) 1528 1458 3·06 (2·83–3·31)
at b
Cancer of pancreas (C25) 809 1082 2·30 (2·08–2·53)
(26 4
Cancer of kidney (C64) 246 360 2·10 (1·77–2·50)
(37 2
Cancer of stomach (C16) 247 329 2·00 (1·67–2·39)
comm
Diabetes (E10–14) 122 192 1·81 (1·43–2·31)
still
External causes* (V01–Y98) 487 677 1·76 (1·56–2·00)
Pirie et al., 2013, Lancet, 381, 133 – 141.havin
Pulmonary fibrosis (J84·1) 88 162 1·53 (1·16–2·01) 52
smok
espite female smokers.
ks by Because the absolute hazards of prolonged smoking
opped All-cause
are substantial,mortality: Illustration
so too are the of the
absolute benefi ts ofeffects of a 3-fold
rtality difference
cessation. Even in annual
cessation at death
about 50rates
years on
of agemortality from age
35 years
avoids at leastto age 80of years
two-thirds the continuing smoker’s
n non-
r than Smokers 53%
50 Non-smokers
cause
ate of
Hence, 40
died,
oking
nes in 30
Mortality (%)

with 24%
g less 11 years
22%
ghout 20

rettes,
n half 10% 11 years
10
ed by 9%
s.
4%
s and 0
35 40 45 50 55 60 65 70 75 80
was of
Age (years)
years).
moker Figure 5: All-cause mortality: Illustration of the effects of a 3-fold difference in annual death rates on
so the mortality from age 35 years to age 80 years Pirie et al., 2013, Lancet, 381, 133 – 141.
53
an be This hypothetical example takes age-specific death rates in non-smokers to be two-thirds of the UK 2010 female
y, or
give Continuing cigarette smoker
0.23 24 Cigarette smoker until age 50
ALY Cigarette smoker until age 30
ety’s Lifelong non-smoker
35
who
lung cancer by age 75 (%)
Cumulative risk of death from

UK mean 21 Bq/m3
30

25

20

15
sible
rom 10
d the 5
that
0
nted 0 200 400 600 800
with Long term average radon (Bq/m3)
en in
Fig 1 | Cumulative risk of deathGray
fromet al.,lung cancer
2009, BMJ, bydoi:10.1136
338:a3110 age 75bmj.a3110 54
DSBs plays a major role in checkpoint phosphorylation following DNA dam- lon
activation, the relationship could be dif- age to form discrete foci ( H2AX foci) tiv
ferent. Moreover, the larger genome of was exploited to monitor unrepaired lon
Ionizing radiation
mammalian cells may confer a different
sensitivity threshold.
DSBs at the time of checkpoint release,
and mitotic entry and the formation of
the
tha
ref
dem
Transatlantic flight Moon walk Mars travel the
Fu
Background def
level Thoracic X-ray Diagnostic CT Tumour therapy che
DS
is r
bel
tak
10 µSv 100 µSv 1 mSv 10 mSv 100 mSv 1 Sv 10 Sv 100 Sv
Radiation dose
for
He
fro
cel
Cancer risk (estimated) 0.01 % 0.1 % 1 10 % rep
no data available data available
tiv
Figure 3 | Encounters with IR exposures and risk estimation. The chart displays
Nature the ionizing
Reviews | Cancer
che
radiation (IR) doses encountered from a range of situations, starting from the daily background radia-
tion level of ~5 Sievert ( Sv) to doses of almost 100 Sv delivered cumulatively during radiotherapy. des
Sv is the unit of the equivalent or effective dose, and is equal to the dose in Gy multiplied by a weight- ing
Löbrich & Jeggo, 2007, Nat. Rev. Cancer, 7, 861-869.55
ing factor for different radiation qualities and different tissues. For a whole-body exposure with X- or no
Type of Cancer Observed Expected SIR (95% CI)

Cancer incidence in 12California

Breast

Melanoma of the skin 7.20

flight 60

1.67 (0.86-2.92)
44.32 1.35 (1.03-1.74)

attendants
Lung and bronchus 3 7.90 0.37 (0.07-1.12)

Compared to women of all races, AFA members exhibited similarly elevated breast
cancer incidence (Table 5), as well as significantly more melanoma.

Table 6. Proportional Incidence Ratios of invasive cancers among female flight attendants, ages
20-64, 1988-1995 all races cancer reference proportions.
Type of Cancer Observed Expected SIR (95% CI)

Breast 60 42.73 1.40 (1.21-1.63)

Melanoma of the skin 12 5.60 2.14 (1.32-3.49)

Lung and bronchus 3 7.16 0.42 (0.08-1.24)

Cancer Incidence in California Flight Attendants – Page 9

56
 Fernando Vicente 11 - ARTBoom 21.01.15 20:17

Astolfi et al.

NEWS FEATURE (http://cdn2.artboom.info/wp-content/uploads/2011/11/Fernando-Vicente-11.jpg)

2FLARES (http://filament.io/flare?

THE HOTTEST ZONE

utm_source=flare_lite&utm_medium=deployment&utm_campaign=filament&utm_content=artboom.info/painting/fernando-

IMAGE CREATED BY J. ALLEN USING EO-1; SOURCE: NASA EO-1 TEAM

vicente-vanitas.html/attachment/fernando-vicente-11)0
(https://www.facebook.com/sharer/sharer.php?u=http://artboom.info/painting/fernando-vicente-
vanitas.html/attachment/fernando-vicente-11)1
Today, hundreds of farms (https://plus.google.com/share?
Radioactivity from Chernobyl
Shifting wind patterns carried radiation from the Chernobyl
blast across much of Europe (right). Plant operators are now in Wales still have their was first detected in western
url=http://artboom.info/painting/fernando-vicente-vanitas.html/attachment/fernando-vicente-
trying to lower water levels in a massive cooling pond (below) sheep tested for Chernobyl Europe by monitoring
11)00 (http://www.stumbleupon.com/submit?url=http://artboom.info/painting/fernando-vicente-
filled with radioactive water and sediments. radiation before herds can equipment at Forsmark nuclear
vanitas.html/attachment/fernando-vicente-11)1
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power station in Sweden.
url=http://artboom.info/painting/fernando-vicente-vanitas.html/attachment/fernando-vicente-
11&via=&text=Fernando Vicente 11 - ARTBoom)0×2FLARES

CHERNOBYL NUCLEAR POWER PLANT Fernando Vicente 11 See the full size image (
RUSSIA

PRIPYAT TOWN http://artboom.info/painting/fernando-vicente-vanitas.html/attachment/fernando-vicente-11 Page 2 of 3

COOLING POND BELARUS

CHERNOBYL
UKRAINE

g. (1). The “ontogenic pyramid”. The phenotypeRED FOREST

(PHE) PRIPYATmay
RIVER be Caesium-137 levels (kBq m–2) in 1986

en as the result of four variables: the original zygotic CHERNOBYL genome

Alpine regions were among
Kilometres the most contaminated areas
0 2 5 10 TOWN outside the former USSR. 1,480 185 40 10 2 No data

EN), the environments (ENV), the epigenome (EPI) and the

matic genome variations (SGV). The two headed arrows are
chief of the town’s Communist party office, National Cancer Institute (NCI) in Bethesda,
he was responsible for evacuating part of the Maryland. The latest results from the Ukrain-
epidemiologist at the Centre for Research in
Environmental Epidemiology in Barcelona,
1

eant to suggest complex reciprocalat theinteractions between

nuclear plant, he knew that them.
town. Because he worked as a senior engineer ian section of this cohort confirm previous
the disaster findings that the incidence of thyroid cancer is
Spain. “Some think they are doomed because
of their radiation exposure.” Further research
57
would have repercussions for decades to come. proportional to the size of the dose, with a par- could provide convincing evidence that Cher-
Somatic mutations

61
 Somatic mutations
T T TCTTGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCATAAAAATTCAAAAAA
T T TGTGGCAGCGTGTCTTAAAAATTCAAAGAA
T T TGTTGCAGCGTGTCTTAAAAATTCTAAAAA
T T TGTTGCACCGTGTCTTAAAAATTCAAAAAA
C T TGTTGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTATCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAA-AATTCAAAAAA
T T TGTTCCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAAAAATTCAAAAAG
T T TGTTGCAGCGTGTCTAAAAAATTCAAAAAA
T T TGATGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAAAAATGCAAAAAA
T T TGTTGCAGCCTGTCTTAAAAATTCAAAAAA

62
St. Jerome

Caravaggio (c. 1605–1606). San Gerolamo63

 Somatic mutations
T T TCTTGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCATAAAAATTCAAAAAA
T T TGTGGCAGCGTGTCTTAAAAATTCAAAGAA
T T TGTTGCAGCGTGTCTTAAAAATTCTAAAAA
T T TGTTGCACCGTGTCTTAAAAATTCAAAAAA
C T TGTTGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTATCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAA-AATTCAAAAAA
T T TGTTCCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAAAAATTCAAAAAG
T T TGTTGCAGCGTGTCTAAAAAATTCAAAAAA
T T TGATGCAGCGTGTCTTAAAAATTCAAAAAA
T T TGTTGCAGCGTGTCTTAAAAATGCAAAAAA
T T TGTTGCAGCGTGTCTTAAAAATTCAAAAAA

64
Somatic mutations

65
Tissue-specific frequencies of mutations
as a function of age in mouse lines

Figure 3. Lynch 2010, Trends Genet., 26, 345–352.

Tissue-specific frequencies of mutations as a function of age in mouse lines carrying Lac
66
 Mutation rate per nucleotide site (x 10-9)

Tissue Per generation Per cell division

Retina 55.45 0.99

Intestinal epithelium 162.00 0.27

Fibroblast 1.34

Lymphocytes 1.47

Average 1.02

Lynch 2010, Trends Genet., 26, 345–352.

67
! At age of 15 years the average somatic cell will have
acquired at least 10-7 to 10-6 per coding nucleotide.
» 100 to 1000 mutations per non-replicating diploid cell.
» Proliferative cells (e. g. intestinal epithelium, epidermis) could
contain 1000 to 10 000 mutations.

Lynch 2010, Proc. Natl. Acad. Sci. USA, 107, 961 - 968.
68
! With a diploid genome size of 6 × 109 sites and ~1013
cells per soma, the body of a middle-aged human
might then contain >1016 mutations (not including
insertions, deletions, or other larger scale mutations).

Lynch 2010, Trends Genet., 26, 345–352.

69
Somatic mutations

70
 The ontogenic pyramid
Astolfi et al.

repositioning
repeats (long
aberrations.
hromosomes
ucleus, as in
the aegis of a

ineages, and
may display
age stage hu-
amatic insur-
tions, admit-
; see also the
in this issue]
rtions of zy-
erging germ
e insurgence
Conversely, a
Fig. (1). The “ontogenic pyramid”.
Astolfi etThe phenotype
al., 2010, (PHE)
Current may be 11, 379 - 386.
Genomics,
nd associated
seen as the result of four variables: the original zygotic genome 71
een environ-
Somatic mosaicism

72
73
Somatic mosaicism

74
Somatic mosaicism

! Two or more genetic or cytogenetic cell lines within the

cells of the body (may or may not include the germline
cells).

75
Clinical,L Ehistological
TTERS and molecular
analysesa of nevus sebaceous Figure 1 Clinical, histological and
(a) Nevus sebaceous presenting a
plaque on the scalp. (b) Histopath
(from subject no. 52) comprise ep
sebaceous and apocrine glands, a
is present at the left and right ma
(c) Sanger sequencing chromatog
(left) and nevus sebaceous (right)
arrowhead indicates a c.37G>C p

all secondary tumors had t

Supplementary Table 1). Our
arising within sebaceous nevi c
lying lesion and, therefore, tha
the nevus sebaceous.
Material from previously p
b with Schimmelpenning syndr
sis. One subject showed an ext
the scalp, neck, trunk and rig
2 mm growth retardation, dispropo
malities and multiple bone fra
c C G GNonlesional
C G G
skin
T G T C G
Nevus sebaceous
G C G/C G T G T hypophosphatemic rickets13.
individual were available for
sebaceous lesions, two biopsie
reminiscent of a keratinocytic
tadenoma papilliferum that h
HRAS WT HRAS c.37G>C nevus sebaceous and blood le
tion was present in all77five le
Groesser et al., 2012, Nat. Genet., 44, 783 - 788.
To confirm genetic mosaicism and to demonstrate a genotype- cystadenoma papilliferum, w
 Diagnostic methods for somatic
VIEWS
mosaicism
a Hypothetical pedigree of somatic mosaicism b Hypothetical pedigre

WT
MUT

WT
ITARY TYROSINAEMIA WT
Blood MUT
MUT
osomal-recessive disorder
ine metabolism that is WT Normal
deficiency of the enzyme skin
MUT
lacetoacetate hydrolase.
order typically causes
d renal problems early in WT Abnormal
is associated with MUT skin
ogical deterioration and
ma. Figure 2 | Diagnostic methods for somatic and germ-line mosaicism. a | Hypothetical pedigree of S
NEUROFIBROMATOSIS TYPE I and (below) molecular
Youssoufian & analysis
Pyeritz showing somatic
2002, Nat. Rev.mosaicism.
Genet., 3,The
748three-generat
- 758.
78
ENEIC ORGAN occurrence of a sporadic mutation (shown in red) in a second-generation male (represented as squares) m
 es derived mosaicism for activating HRAS and KRAS mutations involving the
g from 12% skin, skeletal, ocular and central nervous systems is the underlying
nocytes. InSchimmelpenning - Feuerstein - Mims
genetic cause of Schimmelpenning syndrome.
ndividuals
n 13. These
syndrome
mutation in a b C T G G/A T G G C
cells of the
ng genetic Nevus
sebaceous
ary tumors
pilliferum,
he associ- C T G G T G G C

xclusively;
Nonlesional
skin

elpenning
xtensive C T G G T G G C
ell as
otograph
omatograms Blood
found in
ytes showed
OMIM #163200
Groesser et al., 2012, Nat. Genet., 44, 783 - 788.
79
Schimmelpenning - Feuerstein - Mims
syndrome

! Patient at 10 years old with a

large hyperkeratotic
epidermal nevus involving
the skull, face, and neck.

OMIM #163200
Amato et al., 2010, AJNR Am. J. Neuroradiol., 31, E47–E4880
 The timing of post-zygotic mutation influences
the distribution of mutant cells in the individual
Campbell et al. P

Campbell et al., 2015, Trends

Genet., 31, 382–392.

81
 Inflammatory nevus affecting the left side of the
Campbell et al.
body of a 1-month-old individual with CHILD
syndrome

Author Manuscript

Campbell et al., 2015, Trends Genet., 31, 382–392.

OMIM # 308050

82
A
 Mosaic overgrowth with fibroadipose hyperplasia is
caused by somatic activating mutations in PIK3CA
overgrowth in individuals
A mutations. (a–e) Subject a b c f
emity overgrowth with a
se tissue at ages 12 months
gressing to massive leg
upper-body adipose
which time above-knee
leg had been undertaken (c).
th at 35 years old.
howing overgrowth,
of the left foot and rotational d
oot. (f,g) Anterior (f) and h
ubject N7, showing leg
surgery and massive
oot, which was partially e
(h) and left (i) feet of subject
mited overgrowth confined to
. Informed consent to publish
ned from the identifiable

Lindhurst et al., 2012, Nat. Genet., 44, 928 - 933.83

 of human mesodermal lineages has more benign consequences than
implied by the mouse
Mosaic models overexpressing
overgrowth mutant Pik3ca.
with fibroadipose It is of
hyperplasia
is
caused by somatic activating mutations in PIK3CA
overgrowth in individuals
a Ala(a–e)HisSubjectHis
A mutations. a bc c f
GC AC AT C AT Bone N7
emity overgrowth with a dermal
Arm
se tissue at ages 12 months fibroblasts
Fat
gressing to massive leg N7
upper-body adipose deep-tissue
Fibrous fibroblasts
which time above-knee Leg tissue
leg had been undertaken (c). N7
th at 35 years old. Muscle osteoblasts
howing overgrowth, N99
of the leftGfoot
C A CA
and rotational
T T C A T d Skin dermal
fibroblasts
oot. (f,g) Anterior His
(f) and h
ubject N7,Ala showing Leuleg His N99
growth plate
b
surgery and massive His1047
oot, which was partially e N45
dermal
(h) andABDleft (i) feet C2
of subject Helical Kinase
N RBD fibroblasts
domain domain domain C
mited overgrowth confined to
1 1,068
. Informed consent to publish
nedFigure
from the3 identifiable
Identification of PIK3CA mutations in affected cells and tissues.
(a) The PIK3CA c.3140A>T mutation (p.His1047Leu) identified in cultured
dermal fibroblasts from the affected left leg but not the unaffected right
Lindhurst et al., 2012, Nat. Genet., 44, 928 - 933.84
 The timing of post-zygotic mutation influences
the distribution of mutant cells in the individual
Campbell et al. P

Campbell et al., 2015, Trends

Genet., 31, 382–392.

85
 sequencing data c.1633G>A (p.Glu545Lys) variant being recurrent.
for de novo muta- The differences in mutation burden between HME cases prompte
De novo somatic mutations in components of the
(Supplementary us to examine this burden in anatomically defined brain regions i
PI3K-AKT3-mTOR pathway cause hemimega-
lencephaly
a
HME-1563 HME-1564 HME-1565

Right Left

HME-1573 HME-1855 HME-1916

Blood Brain
b
Lee et al., 2012, Nat.Genet., 44, 491 - 496.86
 sequencing data c.1633G>A (p.Glu545Lys)
counts countsvariant being recurrent.
counts counts allele (%)
for de novo muta- The differences in mutation burden between
47 HME 16% cases prompte
De
PIK3CA
(Supplementary
novo somatic
c.1633G>A (HME-1573)
mutations
0
us to examine 0this burden
AKT3 c.49C>T (HME-1565)
121
in components
9
49 in anatomically
9
of
defined
23
the
brain
28% regions i
PI3K-AKT3-mTOR
MTOR c.4448C>T (HME-1563)
pathway
0 298
cause
17
hemimega-
159 9.7%
lencephaly
a c PIK3CA c.1633G>A (p.Glu545Lys) AKT3 c.49C>T (p.Glu17Lys) MTOR c.4448C>T (p.Cys1483Tyr)
HME-1563(HME-1573) HME-1564(HME-1565) HME-1565(HME-1563)
Blood Brain Blood Brain Blood Brain
A (0%) G (100%) A (36.6%) G (63.4%) G (100%) A (0%) G (59.6%) A (40.4%) T (0%) C (100%) T (8.1%) C (91.9%)
80 60 10 10 10 10
70 50 8 8 8
60 8
40
Intensity

50 6 6 6 6
40 30
30 4 4 4 4
20
20 2 2 2 2
10 10
0 0 0 0 0 0
Right
5,950 6,000 5,950 Left6,000 6,950 7,000 6,950 7,000 5,450 5,500 5,450 5,500
Mass
HME-1573 HME-1855 HME-1916

VOLUME 44 | NUMBER 8 | AUGUST 2012 NATURE GENETICS

Blood Brain
b
Lee et al., 2012, Nat.Genet., 44, 491 - 496.87
 6–30% in parietal, cen- family by binding to the pleckstrin homology (PH) domain. A
y, in HME-1563,
De novo where family proteins
somatic mutationscan directly phosphorylate the
in components ofmTOR
the protein, wh
ct regionsPI3K-AKT3-mTOR
of the central is the product of the MTOR
pathway cause The identification of de novo m
gene.hemimega-
rden to be quite variable, tions in these three genes, which are central to the mTOR pathwa
lencephaly
ion. These data indicate evidence that disrupted signaling underlies HME.

a Orbital
A (25.0%) G (75.0%)
Frontal
A (36.0%) G (64.0%)
80 25
HME-1573 (PIK3CA) 70 20
60

Intensity
50 15
40
Orb 30 10
20 5
10
0 0
Fr
5,950 6,000 5,950 6,000

Co Central operculum Occipital

A (39.5%) G (60.4%) A (21.0%) G (79.0%)
70 60
60 50
Occ 50
40 40
30 30
20 20
10 10
0 0
5,950 6,000 5,950 6,000
Mass

b Parietal
G (73.1%) A (26.9%)
Central operculum
Lee et al., 2012,GNat.Genet.,
(69.6%) 44, 491
A (30.4%)
- 496.88
HME-1565 (AKT3) 50
50
Somatic mosaicism for activating
mutations in the PIK3CA gene
! Somatic mosaicism for activating mutations in PIK3CA
[OMIM 171834] has been associated with a variety of
asymmetrical overgrowth syndromes, including fibroadipose
hyperplasia, CLOVES syndrome [OMIM 612918],
segmental overgrowth affecting muscle and fat, and
megalencephaly phenotypes such as hemimegalencephaly
(HME) and megalencephaly-capillary malformation-
polymicrogyria syndrome (MCAP) [OMIM 602501].

! The phenotypic heterogeneity in these syndromes, as well

as their severity, is attributed in part to the location of the
cells bearing the mutation and to the proportion of cells
affected in each of the patient’s tissues.

Cohen et al., 2014, Am. J. Med. Genet.,164A, 2360 – 2364.

89
 NATUREjVol 4

Fertilized egg Gestation Infancy Childhood Adulthood Early clonal Benign Early invasive Late invasive Chemotherapy-
resistant
expansion tumour cancer cancer recurrence

Intrinsic
mutation processes Environmental
and lifestyle exposures Mutator
Passenger mutation phenotype Chemotherapy
Driver mutation
Chemotherapy
resistance mutation 1–10 or more
driver mutations

10s–1,000s of mitoses 10s–100s of mitoses 10s–100,000 or more

depending on the organ depending on the cancer passenger mutations

lineage of mitotic cell divisions from the fertilized egg to a cancer other processes, for example DNA repair defects, m
hin a cancer showing the timing of the somatic mutations the mutational burden. Passenger mutations do not have a
e cancer cell and the processes that contribute to them. cancer cell, but driver mutations will cause a clonal expansi
y be acquired while the cell lineage is phenotypically normal, chemotherapy can be associated with resistance mutations
the intrinsic mutations acquired during normal cell division predate the initiation of treatment.
of exogenous mutagens. During the development of the
Stratton et al., 2009, Nature, 458, 719 - 724.91
Comprehensive catalogue of somatic mutations
from a malignant melanoma genome

33,345 somatic substitutions

88% sensitivity
97% specificity

31 Somatic rearrangements

41 Copy number changes

36 Small insertions & deletions

92
! At age of 15 years the average somatic cell will have
acquired at least 10-7 to 10-6 per coding nucleotide.
» 100 to 1000 mutations per non-replicating diploid cell.
» Proliferative cells (e. g. intestinal epithelium, epidermis) could
contain 1000 to 10 000 mutations.
! The intestinal epithelium of 60 years old person is
expected to harbour > 109 independent mutations. This
implies that nearly every genomic site has acquired a
mutation in at least one cell in this single organ.

Lynch 2010, Proc. Natl. Acad. Sci. USA, 107, 961 - 968. 93
Causes of death in the USA, 1900 - 2010

Jones et al., 2012, N. Eng. J. Med., 366, 2333 - 2338.

94
 tions at all detected alleles . Using stringent criteria (Supplementary us to examine this burden in anatomically defined brain regio
Fig. 3), we identified 26 candidate somatic
mutations specific to HME brain. We then a
prioritized variants for those likely to sub- HME-1563 HME-1564 HME-1565
stantially alter function by considering the
biological importance of evolutionarily Astolfi et al.
conserved sequences (Online Methods).
With this prioritization, the top three mis-
sense mutations were found in PIK3CA
(c.1633G>A; p.Glu545Lys) in HME-1573,
Right Left
AKT3 (c.49C>T; p.Glu17Lys) in HME-1565
and MTOR (c.4448C>T; p.Cys1483Tyr) in HME-1573 HME-1855 HME-1916
HME-1563 (Fig. 1), suggesting these as can-
didate genes involved in HME. None of these
mutations were found in any blood sample
(with a range of 49–298 reads per allele)
T h e n e w e ng l a n d j o u r na l o f m e dic i n e
but were identified in 9–17 reads from the
affected hemisphere compared with 23–159
images in clinical medicine
reference reads (9.7–28% of reference reads).
Blood Brain
Visualization of the reads in the Integrative b Lindsey R. Baden, M.D., Editor
Mut Ref Mut Ref Mut
Genomics Viewer suggested that the base Segmental Neurofibromatosis counts counts counts counts allele (%)
quality of the mutant alleles was similar to
PIK3CA c.1633G>A (HME-1573) 0 121 9 47 16%
A B C
AKT3 c.49C>T (HME-1565) 0 49 9 23 28%
Figure 1 MRI and mutation analysis in
hemimegalencephaly. (a) Axial T2-weighted MTOR c.4448C>T (HME-1563) 0 298 17 159 9.7%
brain MRI of cases identified with mutations.
Arrows indicate the affected hemispheres, c PIK3CA c.1633G>A (p.Glu545Lys) AKT3 c.49C>T (p.Glu17Lys) MTOR c.4448C>T (p.Cys1483Ty
showing thickened cortical mantle, changes in (HME-1573) (HME-1565) (HME-1563)

ig. (1). The white matter signal

“ontogenic and alterations
pyramid”. in ventricular
The phenotype (PHE) may Blood
be
A (0%) G (100%)
Brain
A (36.6%) G (63.4%) G (100%)
Blood
A (0%)
Brain
G (59.6%) A (40.4%)
Blood
T (0%) C (100%)
Brain
T (8.1%) C (91.9%
shape, resulting in increased hemispheric size
en as the result of four variables: the original zygotic genome
and midline shift of falx cerebri. (b) Sequencing
80
70
60 10 10 10 10
50 8 8 8 8
GEN), the environments
counts from exome (ENV), the ofepigenome
sequencing each of three (EPI) and
60 the
40
Intensity

50 6 6 6 6
omatic genomebrain-blood paired (SGV).
variations samples. Mut,
Themutation;
two headed arrows 30 are
40 30
4 4 4 4
20

A
ref, reference. (c) Mass spectrometry validation 20 2
eant to suggest complex reciprocal interactions between 10
of mutations. Wild-type sequences (blue) and
them. that had been present on the left side of her trunk since birth. She had no
4-year-old
10 girl presented 2for evaluation of cutaneous nodules 2Dong-Lai Ma, M.D.,2Ph.D.
0 0 0 0 0Peking Union Medical College
0 Hospital
rom Sgaramella & Astolfi [39], with permission.
de novo mutations (red) are correlated with 5,950
history of seizures or developmental delay, and there was no family history Beijing, China
6,000 5,950 6,000 6,950 7,000 6,950 7,000 5,450 5,500 5,450 5,500
of similar cutaneous findings. Physical examination revealed numerous soft, non- mdonglai@sohu.com
results from next-generation sequencing. Mass distributed across
tender papules and nodules between 2 and 12 mm in diameter,
the left upper abdomen (Panel A) and wrapping around to the left back (Panels B Jin Hu, M.D.
ossible; representative cells should derive from tissuesand C). The remainder of the physical examination was unremarkable; axillary Affiliated Children’s Hospital
95
freckles, café au lait macules, and Lisch nodules were not observed. Results of a Beijing, China
DIGNUM MEMORIA
1. During each cell division new allelic variants are always
produced.
2. Huge majority of new allelic variants doesn’t influence cell’s
function as they
1. appear in regions containing no genes or introns;
2. doesn’t change significantly function of proteins which they
encode;
3. cause death of the cell.
3. In rare cases new allelic variants change properties of proteins
which they encode and this results in human pathology.
4. Somatic allelic variants can’t be transferred to the next
generations.
5. Severity of symptoms is determined by localization and number
of cells harbouring pathogenic allelic variants.

‹#›
Germ - line mutations

97
Germ - line mutations
REAL Genetics starts here!

98
Clinical,L Ehistological
TTERS and molecular
analysesa of nevus sebaceous Figure 1 Clinical, histological and
(a) Nevus sebaceous presenting a
plaque on the scalp. (b) Histopath
(from subject no. 52) comprise ep
sebaceous and apocrine glands, a
is present at the left and right ma
(c) Sanger sequencing chromatog
(left) and nevus sebaceous (right)
arrowhead indicates a c.37G>C p

all secondary tumors had t

Supplementary Table 1). Our
arising within sebaceous nevi c
lying lesion and, therefore, tha
the nevus sebaceous.
Material from previously p
b with Schimmelpenning syndr
sis. One subject showed an ext
the scalp, neck, trunk and rig
2 mm growth retardation, dispropo
malities and multiple bone fra
c C G GNonlesional
C G G
skin
T G T C G
Nevus sebaceous
G C G/C G T G T hypophosphatemic rickets13.
individual were available for
sebaceous lesions, two biopsie
reminiscent of a keratinocytic
tadenoma papilliferum that h
HRAS WT HRAS c.37G>C nevus sebaceous and blood le
tion was44,present
Groesser et al., 2012, Nat. Genet., in all99five le
783 - 788.
To confirm genetic mosaicism and to demonstrate a genotype- cystadenoma papilliferum, w
 Loose skin / deep creases
Distinctive facial features
Costello syndrome

Loose skin / deep creases

Life-threatening complications
Life-threatening complications
Cardiac arrhythmia
Hypertrophic cardiomyopathy
Cardiac
Malignancy arrhythmia

Hypertrophic cardiomyopathy
Malignancy
OMIM #218040
ults and, for the fourth image on the first panel, Rick Guidotti/Positive Exposure. 100
Costello Syndrome Professional Advisory Board
Costello syndrome

! Dysphagia / Feeding difficulty / Gastrostomy tube (g-

tube) (95%)
! Postnatal short stature (97%)
! Characteristic facial features (98%)
! Thick lips (95%)
! Loose skin (94%)
! Abnormal palmar skin creases (99%)
! Developmental delay / Mental
retardation (100%)

OMIM #218040
101
Costello Syndrome Professional Advisory Board
 Diagnostic methods for somatic and
germ-line mosaicism
a Hypothetical pedigree of somatic mosaicism b Hypothetical pedigree of germ-line mosaicism

WT
Blood
MUT

WT
A WT Sperm
Blood MUT
MUT
rder
is WT Normal
me skin
MUT
se.
s
ly in WT Abnormal
MUT skin
nd
Figure 2 | Diagnostic methods for somatic and germ-line mosaicism. a | Hypothetical pedigree of SEGMENTAL
NEUROFIBROMATOSIS TYPE I and (below) molecular analysis showing somatic mosaicism. The three-generation pedigree illustrates the
occurrence of a sporadic mutation (shown in red) in a second-generation male (represented as squares) manifested as a café-au-lait
skin lesion that is typical of neurofibromatosis type I (NFI). Although this disorder is typically inherited as an autosomal-dominant trait,
e
none of the offspring of the affected individual show the abnormality. Moreover, molecular
Youssoufian analysis
& Pyeritz reveals
2002, a putative
Nat. deletion
Rev. Genet., 3,(MUT)
748 - 758.
self 102
in the NF1 gene in DNA obtained from the abnormal skin of the affected patient. By contrast, only wild-type (WT) DNA is noted in
Mutation rate in germline cells

! Base substitution
» 1.1 - 1.7 x 10-8 per generation
! Indels
» 0.9 - 0.14 x 10-9 per site per generation
! Copy number variations
» 0.16 per haploid genome per generation

Lynch 2016, Genetics, 202, 869 – 875.

103
Mutation rate per nucleotide per cell
division

!Somatic cells - 1.02 x 10-9

!Germline cells - 5 x 10-11

Lynch 2016, Genetics, 202, 869 – 875.

104
! With a diploid genome size of ~ 6 billion bases, an
average newborn contains ~ 100 de novo mutations.

Lynch 2016, Genetics, 202, 869 – 875.

105
! de novo mutations are more often inherited from father
than mother.

Haldane 1947, Ann.Eugen., 13, 262 - 271.

106
 has gone (FIG. 4), and610/23,
through Duchenne ormuscular
more than dystrophy, an X-linked
25 times as ear and rises sh
ANEUPLOID
recessive trait.
many chromosome replications as an egg. Conversely, other dominan
Having an unbalanced

Cell divisions during oogenesis and chromosome number.

The20,
for a man of age genes
thisfor both ofisthese
number onlydiseases
about 7are enormous.
times as 23age could be th
An example is trisomy. many. TheThat for Duchenne muscular dystrophy has 55 exons
ratio of germ-cell divisions between males cation and ineff
and that for neurofibromatosis has 59 (REF. 24). The neu-
and females is high, but it is not sufficient to account for expected to det
spermatogenesis rofibromatosis gene has one of the highest mutation
the high male:female
two FGFRDuchenne
mutation ratios observed for the
rates — 10–4 per gene per generation25 — and thecell death at o
RETis. similar. Many of the mutations arefor by an increa
genes and rate
The acceleration in mutation
intragenic deletions, which rate
arewith
morepaternal
commonage in largerer factor might
genes. This is not because deletions are produced lesseither external
often in smaller genes, but rather because deletionsshould certainl
removing a part of these large genes could, in smallersarily in a non-l
genes, delete the whole gene and more. This could lead
to early lethality, which would not be detected. Exceptions to
The following hypothesis arises: whereas base substi-There are som
tutions occur primarily in males and are age-dependent,
show only a sl
small chromosomal changes (mainly intragenic dele-
mutation ratio
tions) are not age-dependent because they occur by dif-
ferent mechanisms. The data indicate that the rate oftraits are neuro
occurrence of deletions is actually higher in females thannant condition
in males. For Duchenne muscular dystrophy, 93% of(FIG. 4), and Duc
point mutations were from sperm, whereas 87% of dele-recessive trait.
tions were maternal23. The data from neurofibromatosis The genes fo
are consistent with this view, although the numbers areThat for Duche
small — 16 out of 21 deletions were maternal, whereas 9and that for neu
out of 11 point mutations were paternal24. Therefore,rofibromatosis
only a small paternal age effect is expected for diseasesrates — 10–4 p
like neurofibromatosis, because only part of the muta-
Duchenne rate
tions are base substitutions (FIG. 4). Retinoblastoma26 and
Wilms tumour27 are two further examples of diseases
intragenic delet
where only a small paternal age effect is observed,genes. This is n
because a significant fraction of the new mutations areoften in smalle
not base substitutions. removing a pa
The best known example of a maternal age effectgenes, delete th
occurs in Down syndrome. It has long been known thatto early lethality
transmission of an extra chromosome leading to TRISOMY The followin
is much more common from females than fromtutions occur p
Figure 2 | Cell divisions during oogenesis and spermatogenesis. S, stem cells; G, gonial
cells; M, meiotic cells. The total number of cell divisions in the life history of an egg is 24. In males males28. About 0.3% of liveborns are ANEUPLOID, with thesmall chromos
this depends on the number of stem-cell divisions, which is greater in older males. (Figure most common being trisomy 21 leading to Down syn-tions) are not a
adapted from REF. 22.) drome. The trisomy rate at conception is, of course,
ferent mechan
Crow 2000, Nat. Rev. Genet., 1, 40 occurrence
- 47.107 of d
42 | OCTOBER 2000 | VOLUME 1 www.nature.com/reviews/geneticsin males. For D
Cell divisions in germ cells prior to
meiosis

• 24 cell divisions from • 30 cell divisions prior

zygote to an ovum to puberty (15 yrs)

• stem cell divisions 23

times a year

• 4 gonial and 2
meiotic divisions

108
! Number of chromosome replications from the zygote to
a sperm produced by man at age T is
- NT = 30 + 23(T - 15) + 5

Crow 2006, J. Radiat. Res., 47 Sup.B, B75 - B82.

109
Number of cell divisions

Age Number of Cell Divisions

20 150

30 380

45 725

110
 Event Frequency Reference

Mutation rate per base per Conrad et al., 2011, Nat.

10 e-8 Genet., 43, 712 - 714.
replication

Orioli et al., 1995, Am. J.

Sporadic achondroplasia 10 e-5 - 10 e-4 Med. Genet., 59, 209 -
217.

Tolarova et al., 1997,

Sporadic Apert syndrome 10 e-6 - 10 e-5 Am. J. Med. Genet., 72,
394 - 398.

Miyamoto et al., 1997,

Rett syndrome 10 e-6 - 10 e-5 Brain Dev., 19, 492 -
494.

111
Paternal age effect mutations

! Spontaneous germline point mutations in humans tend

to be paternal in origin with a male/female mutation
ratio of 2-7, and show only a modest effect of parental
age on mutation rate.

! However a different pattern is evident in some

congenital disorders, which arise from specific point
mutations that are 2-3 orders of magnitude more
common than expected.

Goriely et al., 2009, Nat. Genet., 41, 1247.

112
Paternal age effect mutations

! The causative mutations nearly always originate from

the healthy fathers (male/female ratio >10) who, on
average, are 2-6 years older than the population mean.

! The best documented examples of paternal age effect

mutations occur in the genes FGFR2, FGFR3, HRAS,
PTPN11 and RET.

! In all cases the mutations exhibit dominant inheritance

and encode missense substitutions with gain-of-
function properties.

Goriely et al., 2009, Nat. Genet., 41, 1247.

113
! Positive germline selection!

114
Crow 2006, J. Radiat. Res., 47 Sup.B, B75 - B82. 115
Mutation levels at the FGFR3 K650 codon in
sperm from 78 men (aged 22.1-73.9 years)

Goriely et al., 2009, Nat. Genet., 41, 1247.

116
 Relative frequency of de novo achondroplasia
and Apert syndrome for different paternal
R E Vages
IEWS

Figure 3 | Relative frequency of de novo achondroplasia and Apert syndrome for different paternal ages. The ordinate is the
ratio of the observed number of mutations (O) to the number expected (E), if all paternal ages are associated with the same frequency
of mutation. The blue line gives the actual data; the red line is the best-fitting exponential curve. (Figure adapted from REF. 4.)

much higher (at least 10%), with most dying very early stand out. Essentially all the mutations occur in males
Crow 2000, Nat. Rev. Genet., 1, 40 - 47.
in the prenatal period. For trisomy 21, 93% of 436 infor- and the paternal age dependence is strong. Other traits117
onality

escents/Adults
classic facial features
often curly hair Astolfi et al.
bromata
apilloma
eratosis, hyperpigmentation
ature
and orthopedic problems
velopmental delay) / MR
ntal retardation)

credits go to the parents of the above children and adults and, for the fourth image on the first panel, Rick Guidotti/Posi

Fig. (1). The “ontogenic pyramid”. The phenotype (PHE) may be

Figure 1 Three patients of various ages with the cardiofaciocutaneous syndrome. The face is typical, with a broad forehead, bulbous tip of the nos
seen as the result of four variables: the original zygotic genome
low-set ears, sparse scalp hair and absent eyebrows with ulerythema ophryogenes. The upper panel shows the same child at 10 months (left) an
6 years (right), describing the evolution of the phenotype. All of these children carry a BRAF mutation. Parents of patients gave written consent to
(GEN), the environments (ENV), the epigenome (EPI) andimages.
publish these the
somatic genome variations (SGV). The two headed arrows are
meant to suggest complex reciprocal interactions between them.
From Sgaramella & Astolfi [39], with permission.

possible; representative cells should derive from tissues

originating from each of the three layers of an animal gas-
trula or from plant embryo structures; cells easy to be iso- 118
lated as pure and uncontaminated as possible would be pref-
 Astolfi et al.

Bellus et al.: FGFR3 Lys650Asn and Lys650Gln 1413

Renate Marquis-Nicholson, Salim Aftim

726 Am. J. Hum. Genet. 64:722–731, 1999

Fig. (1). The “ontogenic pyramid”. The phenotype (PHE) may be

seen as the result of four variables: the original zygotic genome
(GEN), the environments (ENV), the epigenome (EPI) and the
somatic genome variations (SGV). The two headed arrows are
meant to suggest complex reciprocal interactions between them.
From Sgaramella & Astolfi [39], with permission.
Figure 1: Fetal phenotype: skeletal radiographs of anteroposterior
possible; representative cells should derive from Figure
tissues 2 Photographs of patients. Note the mild shortening of the arms and normal facial appearance in patient 1, who has G1950C

originating from each of the three layers of an animal gas-

(Lys650Asn) and is shown at age 15 years (A–D), whereas patient 4, who has G1950T (Lys650Asn)
and patient
and is shown
ExoSAP-IT at age 15 mo
(Affymetrix,
5, who has A1948C (Lys650Gln) and is shown at age 20 mo (G), have more-prominent dysmorphic facial features.
(E and
Santa F), California,
Clara,
USA) prior to bidirectional DNA sequencing using
R

trula or from plant embryo structures; cells easy to be

lated as pure and uncontaminated as possible would be
ters (pelvic
pref-
Lys650Asn
iso-index, fibula:tibia length ratio, and L1:L4 between hand bonesM13 forward and reverse primers and Big-Dye
(4.5 years) and wrist bones (2.5 119
Terminator, Version 3.0 (Applied Biosystems Ltd.,
interpediculate-distance ratio) was performed according years). Karyotype and levels of alkaline phosphatase,
Carlsbad, California, USA). An amount of 20 µL of
Th
par
we
to the method of Matsui et al. (1998). SDs (Z scores) calcium, and phosphorus were normal. Cognitive, ver-
DIGNUM MEMORIA

1. Human somatic cells commonly accumulate new allelic variants

about 50 times more rapidly than germ-line cells do.
2. Formation of new allelic variants is random and inevitable
process which happens simultaneously in several/many
gametes.
3. Germ-line mutations don’t change phenotype of carrier but if
they lead to new pathogenic allelic variants they can be
transmitted to the next generation and cause pathology.
4. de novo traits are more often inherited paternally than
maternally as there are more DNA replication cycles during
spermatogenesis.
5. de novo traits are more often inherited from elder fathers.

‹#›
Diseases discussed in this lecture

1. CATSHLS syndrome [OMIM # 610474]

2. CHILD syndrome [OMIM # 308050]
3. CLOVES syndrome [OMIM 612918]
4. Costello syndrome [OMIM #218040]
5. Megalencephaly - capillary malformation - polymicrogyria
syndrome [OMIM 602501]
6. Schimmelpenning - Feuerstein - Mims syndrome [OMIM
#163200]

‹#›
Glossary

■ Acanthosis nigricans - a skin condition characterized

by areas of dark, velvety discoloration in body folds
and creases. The affected skin can become thickened.
Most often, acanthosis nigricans affects armpits, groin
and neck.
■ Brachydactyly - abnormally short digits.
■ Dysphagia - difficulty in swallowing.
■ Genu varum - condition in which the knees of an
affected individual are wide apart, while the ankles and
feet are together when he/she stands up.
■ Hyperplasia - abnormal increase in volume of a tissue
or organ.
‹#›
Glossary

■ Lordosis - refers to the inward curve of the lumbar

spine (just above the buttocks).
■ Megalencephaly - Also called macrencephaly, a
condition in which there is an abnormally large, heavy,
and usually malfunctioning brain.
■ Microcephaly - is a rare neurological condition in
which an infant's head is significantly smaller than the
heads of other children of the same age and sex.

‹#›
Glossary

■ Naevus sebaceus - Is a congenital, hairless plaque

that typically occurs on the face or scalp.The condition
is named for an overgrowth of sebaceous glands in the
area of the nevus.
! Rhizomelic dwarfism - is a type of dwarfism where
the dominant feature is proximal (i.e. femoral, humeral)
limb shortening.
! Thanatophoric - relating to, affected with, or being a
severe form of congenital dwarfism which results in
early death.

124