Chromosome Disorders

Professor Varban Ganev, MD, PhD, DSc

Faculty of Medicine
Sofia University “St. Kliment Ohridski”
University Hospital “Lozenetz”
The development of a reliable technique for chromosome analysis in 1956
soon led to the discovery that several previously described conditions were
due to an abnor-mality in chromosome number. Within 3 years, the causes
of Down syndrome (47,XX/XY, +21), Klinefelter syndrome (47,XXY), and
Turner syndrome (45,X) had been established. Shortly after, other autosomal
trisomy syndromes were reco-gnized, and over the ensuing years many other
multiple malformation syndromes were described in which there was loss or
gain of chromosome material.
To date, at least 20000 chromosomal abnormalities have been registered on
laboratory databases. On an individual basis, most of these are very rare,
but together they make a major contribution to human morbidity and
mortality. Chromosome abnormalities account for a large proportion of
spontaneous pregnancy loss and childhood disability, and also contribute to
malignancy throughout life as a consequence of acquired translocations and
other aberrations.
The basic principles of chromosome structure, function, and behavior
during cell division were described above, together with an account of
chromosome abnormalities and how they can arise and be transmitted in
families. In this chapter, the medical aspects of chromosome abnormalities,
and some of their specific syndromes, are described.
Incidence of Chromosome Abnormalities
Chromosome abnormalities are present in at least 10% of all spermatozoa
and 25% of mature oocytes. Some 15% to 20% of all recognized pregnancies
end in spontaneous miscarriage, and many more zygotes and embryos are so
abnormal that survival beyond the first few days or weeks after fertilization
is not possible. Approximately 50% of all spontaneous miscarriages have a
chromosome abnormality (Table 5.1) and the incidence of chromosomal
abnormalities in morphologically normal embryos is around 20%.
Chromosome abnormalities therefore account for the spontaneous loss of a
very high proportion of all human conceptions.
Table 5.1 Chromosome Abnormalities in Spontaneous Abortions
(Percentage Values Relate to Total of Chromosomally Abnormal
Abortuses).
From conception onward, the incidence of chromosome abnormalities falls
rapidly. By birth it has declined to a level of 0.5% to 1%, although the
total is higher (5%) in stillborn infants. Table 5.2 lists the incidence figures
for chromo-some abnormalities based on newborn surveys. It is notable
that among the commonly recognized aneuploidy syndromes, there is also
a high proportion of spontaneous pregnancy loss (Table 5.3). This is
illustrated by comparison of the incidence of conditions such as Down
syndrome at the time of chorionic villus sampling (11 to 12 weeks),
amniocentesis (16 weeks), and term (Figure 5.1).

Down Syndrome (Trisomy 21)

This condition derives its name from Dr Langdon Down, who first
described it in the Clinical Lecture Reports of the London Hospital in
1866. The chromosomal basis of Down syndrome was not established until
1959 by Lejeune and his colleagues in Paris.
Table 5.2 Incidence of Chromosome Abnormalities in the
Newborn.
Table 5.3 Spontaneous Pregnancy Loss in Commonly Recognized
Aneuploidy Syndromes.
Figure 5.1 Approximate incidence of trisomy 21 at the time of chorionic
villus sampling (CVS) (11–12 weeks), amniocentesis (16 weeks), and
delivery.
 Incidence
The overall birth incidence, when adjusted for the increasingly widespread
impact of antenatal screening, is approximately 1 : 1000 in the United
Kingdom, which has a national register. In the United States, the birth
incidence has been estimated at approximately 1 : 800. In the United
Kingdom, approximately 60% of Down syndrome cases are detected
prenatally. There is a strong association between the incidence of Down
syndrome and advancing maternal age (Table 5.4).

Clinical Features
These are summarized in Box 5.1.

The most common finding in the newborn period is severe hypotonia.

Usually the facial characteristics of upward sloping palpebral fissures,
small ears, and protruding tongue (Figures 5.2 and 5.3) prompt rapid
suspicion of the diagnosis, although this can be delayed in very small or
premature babies. Single palmar creases are found in 50% of children with
Down syndrome (Figure 5.4), in contrast to 2% to 3% of the general
population. Congenital cardiac abnormalities are present in 40% to 45% of
babies with Down syndrome, with the three most common lesions being
BOX 5.1 Common Findings in Down Syndrome.
Figure 5.2 A child with Down syndrome.
Figure 5.3 Close-up view of the eyes and nasal bridge of a child with Down
syndrome showing upward sloping palpebral fissures, Brushfield spots,
and bilateral epicanthic folds.
Figure 5.4 The hands of an adult with Down syndrome. Note the single
palmar crease in the left hand plus bilateral short curved fifth fingers
(clinodactyly).
 Natural History
Affected children show a broad range of intellectual ability with IQ scores
ranging from 25 to 75. The average IQ of young adults is around 40 to 45.
Social skills are relatively well-advanced and most children are happy and
very affectionate. Adult height is usually around 150 cm. In the absence of
a severe cardiac anomaly, which leads to early death in 15% to 20% of
cases, average life expectancy is 50 to 60 years. Most affected adults
develop Alzheimer disease in later life, possibly because of a gene dosage
effect—the amyloid precursor protein gene is on chromosome 21. This
gene is known to be implicated in some familial cases of Alzheimer disease.

Chromosome Findings
These are listed in Table 5.5. In cases resulting from trisomy 21, the
additional chromosome is maternal in origin in more than 90% of cases,
and DNA studies have shown that this arises most commonly as a result of
non-disjunction in maternal meiosis I. Robertsonian translocations
account for approximately 4% of all cases, in roughly one-third of which a
parent is found to be a carrier. Children with mosaicism are often less
severely affected than those with the full syndrome.
Table 5.5 Chromosome Abnormalities in Down Syndrome.
Efforts have been made to correlate the various clinical features in trisomy
Down syndrome with specific regions of chromosome 21, by studying
children with partial trisomy for different regions. There is some support
for a Down syndrome ‘critical region’ at the distal end of the long arm
(21q22), because children with trisomy for this region alone usually have
typical Down syndrome facial features. Chromosome 21 is a ‘gene-poor’
chromosome with a high ratio of AT to GC sequences. At present the only
reasonably well-established genotype-phenotype correlation in trisomy 21
is the high incidence of Alzheimer disease.

Recurrence Risk
For straightforward trisomy 21, the recurrence risk is related to maternal
age (variable) and the simple fact that trisomy has already occurred
(∼∼1%). The combined recurrence risk is usually between 1 : 200 and
1 : 100. In translocation cases, similar figures apply if neither parent is a
carrier. In familial translocation cases, the recurrence risks vary from
around 1% to 3% for male carriers up to 10% to 15% for female carriers,
with the exception of very rare carriers of a 21q21q translocation, for
whom the recurrence risk is 100%. Prenatal diagnosis can be offered
based on analysis of chorionic villi or cultured amniotic cells. Prenatal
screening programs have been introduced based on the so-called triple or
 Patau Syndrome (Trisomy 13) and Edwards Syndrome (Trisomy
18)
These very severe conditions were first described in 1960 and share many
features in common (Figures 5.5 and 5.6). The incidence for both is
approximately 1 : 5000 and prognosis is very poor, with most infants dying
during the first days or weeks of life, though most cases are detected
prenatally, often leading to termination. In the unusual event of longer
term survival, there are severe learning difficulties. Cardiac abnormalities
occur in at least 90% of cases.
Chromosome analysis usually reveals straightforward trisomy. Both
disorders occur more frequently with advanced maternal age, the
additional chromosome being of maternal origin. Approximately 10% of
cases are caused by mosaicism or unbalanced rearrangements,
particularly Robertsonian translocations in Patau syndrome.

Triploidy
Triploidy (69,XXX, 69,XXY, 69,XYY) is a relatively common finding in
material cultured from spontaneous abortions, but is seen only rarely in a
liveborn infant. Such a child almost always shows severe intrauterine
growth retardation with relative preservation of head growth at the
Figure 5.5 Facial view of a child with
trisomy 13 showing severe bilateral cleft
lip and palate.
Figure 5.6 A baby with
trisomy 18. Note the
prominent occiput and
Syndactyly involving the third and fourth fingers and/or the second and
third toes is a common finding. Cases of triploidy resulting from a double
paternal contribution usually miscarry in early to mid-pregnancy and are
associated with partial hydatidiform changes in the placenta. Cases with a
double maternal contribution survive for longer but rarely beyond the
early neonatal period.
Hypomelanosis of Ito
Several children with mosaicism for diploidy/triploidy have been
identified. These can demonstrate the clinical picture seen in full triploidy
but in a milder form. An alternative presentation occurs as the condition
known as hypomelanosis of Ito. In this curious disorder, the skin shows
alternating patterns of normally pigmen-ted and depigmented streaks that
correspond to the embryological developmen-tal lines of the skin known as
Blaschko’s lines (see Figure 5.7). Most children with hypomelanosis of Ito
have moderate learning difficulties and convulsions that can be
particularly difficult to treat. There is increasing evidence that this cli-
nical picture represents a non-specific embryological response to cell or
tissue mosaicism. A similar pattern of skin pigmentation is sometimes seen
in women with one of the rare X-linked dominant disorders with skin
involvement, such as incontinentia pigmenti. Such women can be
Figure 5.7 Mosaic pattern of skin pigmentation on the arm of a child
with hypomelanosis of Ito.
Disorders of the Sex Chromosomes
Klinefelter Syndrome (47,XXY)
First described clinically in 1942. This relatively common condition with
an incidence of 1:1000 male live births was shown in 1959 to be due to the
presence of an additional X chromosome.
Clinical Features
In childhood the presentation may be with clumsiness or mild learning
difficul-ties, particularly in relation to verbal skills. The overall verbal IQ
is reduced by 10 to 20 points below unaffected siblings and controls, and
children can be rather self-obsessed in their behavior. Adults tend to be
slightly taller than average with long lower limbs. Approximately 30%
show moderately severe gynecomastia (breast enlargement) and all are
infertile because of the absence of sperm in their semen (azoospermia),
with small, soft testes. Fertility has been achieved for a small number of
affected males using the techniques of testicular sperm aspiration and
intracytoplasmic sperm injection. There is an increased incidence of leg
ulcers, osteoporosis, and carcinoma of the breast in adult life. Treatment
with testosterone from puberty onward is beneficial for the development of
 Chromosome Findings
Usually the karyotype shows an additional X chromosome. Molecular
studies have shown that there is a roughly equal chance that this will have
been inherited from the mother or from the father. The maternally derived
cases are associated with advanced maternal age. A small proportion of
cases show mosaicism (e.g., 46,XY/47,XXY). Rarely, a male with more than
two X chromosomes can be encountered, for example 48,XXXY or
49,XXXXY. These individuals are usually quite severely retarded and also
share physical characteristics with Klinefelter men, often to a more
marked degree.

Turner Syndrome (45,X)

This condition was first described clinically in 1933. The absence of a Barr
body, consistent with the presence of only one X chromosome, was noted in
1954 and cytogenetic confirmation was forthcoming in 1959. Although
common at conception and in spontaneous abortions (Table 5.1), the
incidence in live-born female infants is low, with estimates ranging from
1:5000 to 1:10.000.
 Clinical Features
Presentation can be at any time from pregnancy to adult life. Increasingly,
Turner syndrome is being detected during the second trimester as a result
of routine ultrasonography, showing either generalized edema (hydrops)
or swelling localized to the neck (nuchal cyst or thickened nuchal pad)
(Figure 5.8). At birth many babies with Turner syndrome look entirely
normal. Others show the residue of intrauterine edema with puffy
extremities (Figure 5.9) and neck webbing. Other findings may include a
low posterior hairline, increased carrying angles at the elbows, short
fourth metacarpals, widely spaced nipples, and coarctation of the aorta,
which is present in 15% of cases.
Figure 5.8 Ultrasonographic scan at 18 weeks’
gestation showing hydrops fetalis. Note the halo of
fluid surrounding the fetus.
Figure 5.9 The foot of an infant with
Turner syndrome showing edema and
small nails.
Table 5.6 Chromosome Findings in Turner Syndrome.
Intelligence in Turner syndrome is normal. However, studies have shown
some differences in social cognition and higher order executive function
skills according to whether the X chromosome was paternal or maternal in
origin. The two main medical problems are short stature and ovarian
failure. The short stature becomes apparent by mid-childhood and without
growth hormone treatment the average adult height is 145 cm. This short
stature is due, at least in part, to haploinsufficiency for the SHOX gene,
which is located in the pseudoautosomal region. Ovarian failure
commences during the second half of intrauterine life and almost
invariably leads to primary amenorrhea and infertility. Estrogen
replacement therapy should be initiated at adolescence for the
development of secondary sexual characteristics and long-term prevention
of osteoporosis. In vitro fertilization using donor eggs offers the prospect of
pregnancy for women with Turner syndrome.
 Chromosome Findings
These are summarized in Table 5.6. The most common finding is 45,X
(sometimes erroneously referred to as 45,X0). In 80% of cases, it arises
through loss of a sex chromosome (X or Y) paternal meiosis. In a
significant proportion of cases, there is chromosome mosaicism and those
with a normal cell line (46,XX) have a chance of being fertile. Some cases
with a 46,XY cell line are phenotypically male, and all cases with some Y-
chromosome material in their second cell line must be investigated for
possible gonadal dysgenesis-intracellular male gonads can occasionally
become malignant and require surgical removal.
XXX Females
Birth surveys have shown that approximately 0.1% of all females have a
47,XXX karyotype. These women usually have no physical abnormalities
but can show a mild reduction of between 10 and 20 points in intellectual
skills and sometimes quite oppositional behavior. This is rarely of
sufficient severity to require special education. Studies have shown that the
additional X chromosome is of maternal origin in 95% of cases and usually
arises from an error in meiosis I. Adults are usually fertile and have
children with normal karyotypes.
As with males who have more than two X chromosomes women with more
than three X chromosomes show a high incidence of learning difficulties
the severity being directly related to the number of X chromosomes.
XYY Males
This condition shows an incidence of about 1:1000 in males in newborn
surveys but is found in 2% to 3% of males who are in institutions because
of learning difficulties or antisocial criminal behavior. However, it is
important to stress that most 47,XYY men have neither learning difficulty
nor a criminal record, although they can show emotional immaturity and
impulsive behavior. Fertility is normal.
Physical appearance is normal and stature is usually above average.
Intelligence is mildly impaired with an overall IQ score of ID to 20 points
below a control sample. The additional Y chromosome must arise either as
a result of non-disjunction in paternal meiosis II or as a post-zygotic event.
 Fragile X Syndrome
This condition, which could equally well be classified as a single gene
disorder rather than a chromosome abnormality, has the unique
distinction of being both the most common inherited cause of learning
difficulties and the first disorder in which a dynamic mutation (triplet
repeat expansion) was identified in 1991. It affects approximately 1:5000
males and accounts for 4% to 8% of all males with learning difficulties.
Martin and Bell described the condition in the 1940s before the
chromosome era, and it has also been known as Martin-Bell syndrome.
The chromosomal abnormality was first described in 1969 but the
significance not fully realized until 1977.
Clinical Features
Older boys and adult males usually have a recognizable facial appearance
with high forehead, large ears, long face, and prominent jaw (Figure 5.10).
After puberty most affected males have large testes (macro-orchidism).
There may also be evidence of connective tissue weakness, with
hyperextensible joints, stretch marks on the skin (striae) and mitral valve
prolapse. The learning difficulties are moderate to severe and many show
autistic features and/or hyperactive behavior. Speech tends to be halting
and repetitive. Female carriers can show some of the facial features, and
 The Fragile X Chromosome
The fragile X syndrome takes its name from the appearance of the X
chromo-some, which shows a fragile site close to the telomere at the end of
the long arm at Xq27.3 (Figure 5.11). A fragile site is a non-staining gap
usually involving both chromatids at a point at which the chromosome is
liable to break. In this condi-tion, detection of the fragile site involves the
use of special culture techniques such as folate or thymidine depletion,
which can result in the fragile site being detectable in up to 50% of cells
from affected males. Demonstration of the fragile site in female carriers is
much more difficult and cytogenetic studies alone are not a reliable means
of carrier detection, in that, although a positive result confirms carrier
status the absence of the fragile site does not exclude a woman from being
a carrier.
Figure 5.10 A family affected by fragile X syndrome. Two
sisters, both carriers of a small FRAXA mutation inherited
from their father, have had affected sons with different
Figure 5.11 X chromosome from several males with fragile X
syndrome.
 The Molecular Defect
The fragile X locus is known as FRAXA and the mutation consists of an
increase in the size of a region in the 5’-untranslated region of the fragile X
learning difficulties (FMR-1) gene. This region contains a long CGG
trinucleotide repeat sequence. In the DNA of a normal person, there are
between 10 and 50 copies of this triplet repeat and these are inherited in a
stable fashion. However, a small increase to between 59 and 200 renders
this repeat sequence unstable, a condition in which it is referred to as a
premutation. Alleles of 51 to 58 are referred to as intermediate. A man
who carries a premutation is known as a 'normal transmitting male',
although it has been recognized that these premutation carriers are at
increased risk of a late-onset neurological condition named 'fragile X
tremor/ataxia syndrome' (FXTAS). All of his daughters will inherit the
premutation and have normal intelligence, but they are also at small risk
of FXTAS in later years. When they have sons, there is a significant risk
that the premutation will undergo a further increase in size during meiosis,
and if this exceeds 200 CGG triplets, it becomes a full mutation.
The full mutation is unstable not only during female meiosis but also in
somatic mitotic divisions. Consequently, in an affected male gel
electrophoresis shows a 'smear-' of DNA consisting of many different-sized
alleles rather than a single band (Figure 5.12). Note that a normal allele
and premutation can be identified by polymerase chain reaction (PCR),
whereas Southern blotting is necessary to detect full mutations as the long
GGC expansion is often refractory to PCR amplification. At the molecular
level, a full mutation suppresses transcription of the FMR-1 gene by
hypermethylation, and this in turn is thought to be responsible for the
clinical features seen in males and in some females with a large expansion
(Table 5.7). The FMR-1 gene contains 17 exons encoding a cytoplasmic
protein that plays a crucial role in the development and function of
cerebral neurons. The FMR-1 protein can be detected in blood using
specific monoclonal antibodies.
Figure 5.12 Southern blot of DNA from
a family showing expansion of the CGG
triplet repeat being passed from a
normal transmitting male through his
obligate carrier daughter to her son
with fragile X learning difficulties.
Table 5.7 Fragile X Syndrome: Genotype-Phenotype Correlations.
Another fragile site adjacent to FRAXA has been identified at Xq2S. This
is known as FRAXE. The expansion mutations at FRAXE also involve
CGG triplet repeats and occur much less frequently than FRAXA
mutations. Some males with these mutations have mild learning
difficulties, whereas others are just as severely affected as men with
FRAXA. FRAXE may show up as a fragile site cytogenetically but the PGR
test is separate. A third fragile site, FRAXF, has been identified close to
FRAXA and FRAXE. This does not seem to cause any clinical abnormality.

Genetic Counseling and the Fragile X Syndrome

This common cause of learning difficulties presents a major counseling
problem. Inheritance can be regarded as modified or atypical X-linked. All
of the daughters of a normal transmitting male will carry the premutation.
Their male offspring are at risk of inheriting either the premutation or a
full mutation. This risk is dependent on the size of the premutation in the
mother, with mutations greater than 100 GGG repeats almost invariably
increasing in size to become full mutations.
For a woman who carries a full mutation there is a 50% risk, that each of
her sons will be affected with the full syndrome and that each of her
daughters will inherit the full mutation. Because approximately 50% of
females with the full mutation have mild learning difficulties, the risk that
a female carrier of a full mutation will have a daughter with, learning
difficulties equals 1/2 * 1/2 (i.e., 1/4 ). Prenatal diagnosis can be offered
based on analysis of DNA from chorionic villi but in the event of a female
fetus with a full mutation accurate prediction of phenotype cannot be
made.
The fragile X syndrome is a condition for which, population screening
could be offered, either among selected high-risk groups such as males
with learning difficulties or on a widespread general population basis.
Such programs will have to surmount major ethical, financial, and
logistical concerns if they are to achieve widespread acceptance.
 Chromosome Deletion and Microdeletion Syndromes
Microscopically visible deletions of the terminal portions of chromosomes
4 and 5 cause the Wolf-Hirschhorn (4p-) (Figure 5.13) and cri-du-chat (5p-
) (Figure 5.14) syndromes respectively. In both conditions severe learning
difficulties is usual, often with failure to thrive. However, there is
considerable variability, parti-cularly in Wolf-Hirschhorn syndrome, and
no clear correlation of the phenotype with the precise loss of chromosomal
material. Cri-du-chat syndrome derives its name from the characteristic
cat-like cry of affected neonates-a consequence of underdevelopment of the
larynx. Both conditions are rare, with estimated incidences of
approximately 1:50,000 births. Not all cases have cytogenetically visible
chromosome deletions, and clinicians can ask for specific fluorescent in-
situ hybridization (FISH) analysis if microarray-CGH is not available.
Figure 5.13 A child with deletion 4p
syndrome—Wolf-Hirschhorn
Figure 5.14 Facial view of a 2-year-old
boy with cri-du-chat syndrome.
 Microdeletions
Through high-resolution prometaphase banding and FISH, several
previously unexplained syndromes have been shown to be due to sub
microscopic or micro-deletions. Some microdeletions involve loss of only a
few genes at closely adjacent loci, resulting in contiguous gene syndromes.
For example, several boys with Duchenne muscular dystrophy (DMD)
have been described who also have other X-linked disorders, such as
retinitis pigmentosa and glycerol kinase deficiency. The loci for these
disorders are very close to the DMD locus on Xp21. Examples of well
known microdeletion syndromes are given in Table 5.8, all of them
relatively rare.
Table 5.8 Microdeletion Syndromes.
 Microarray-CGH
The 1990s witnessed the development of FISH-based analysis of all
chromosome telomeres using subtelomeric probes. This led to the diagnosis
of some cases of learning difficulty/dysmorphic patients, not detected by
multiplex ligation-dependent probe amplification. In recent few years this
has been rapidly superseded by extensive microarray comparative
genomic hybridization (CGH) testing and a number of new microdeletion
(and to a lesser extent microduplication) syndromes have emerged. At high
resolution, this new technology is yielding significant results in about 20%
of cases of well selected, previously unknown dysmorphic patients with
developmental delay/learning disability. This compares to a positive pick-
up rate of 4% to 5% from standard karyotyping on patients considered
likely to have a. chromosome disorder. Examples of these new and
emerging syndromes are shown in the following section.
 Lessons from Microdeletion Syndromes
Retinoblastoma
It was originally observed that approximately 5% of children presenting
with retinoblastoma had other abnormalities, including learning
difficulties. In some of these, a constitutional interstitial deletion of a
region of chromosome 13q was identified. The smallest region of overlap
was 13q14, which was subsequently shown to be the position of the locus
for the autosomal dominant form of retinoblastoma due to mutations in
the RBI gene.

Wilms' Tumor
Some children with the rare renal embryonal neoplasm known as Wilms'
tumor (or hypernephroma) also have aniridia, genitourinary
abnormalities, and retardation of growth and development. This
combination is referred to as the WAGE syndrome. Chromosome analysis
in these children often reveals an interstitial deletion of 11p13 (Figure
5.15). The deletion genes include PAX6, which is responsible for the
aniridia (Figure 5.16). Confirmation is made by FISH probe analysis (or
direct gene mutation analysis in cases of pure aniridia).
Loss of the WT1 gene causes the development of Wilms' tumor. Knowing
this, it can now be predicted whether a newly diagnosed child with deletion
11p13 is at high risk of developing a Wilms’ tumor, using a separate FISH
analysis at the WT1 locus. It is important to note that, however, that the
genetics of Wilms' tumor is complex, with other loci sometimes involved.

Angelman and Prader-Willi Syndromes

These two conditions have special place in medical genetics as paradigms for
genomic imprinting. Children with Angelman syndrome (Figure 7.24) have
inappropriate laughter, convulsions, poor coordination (ataxia), and severe
learning difficulties. Children with Prader-Willi syndrome (Figure 7.22) are
extremely floppy (hypotonic) with poor feeding in infancy, and later develop
hyperphagia and obesity, with mild-to-moderate learning difficulties. A large
proportion of children with these disorders have a microdeletion involving
15q11-13.
In contrast, a deletion occurring at the same region on the maternally
inherited chromosome 15 causes Angelman syndrome. Non-deletion cases
also exist and are often due to uniparental disomy, with both number 15
chromosomes being paternal in origin in Angelman syndrome, and maternal
in origin in Prader-Willi syndrome. These parent- of-origin effects are
Figure 5.15 A, Metaphase spread showing the number 11 chromosomes
(double arrows). The chromosome indicated by the single arrow has an
interstitial deletion in the short arm. See Figures 5.11 and 5.12. B, FISH
showing failure of a PAX6 locus specific probe (red) to hybridize to the
deleted number 11 chromosome shown in A from a child with WAGR
syndrome. The green probe acts as a marker for the centromere of each
number 11 chromosome.
Figure 5.16 A baby with deletion 11p13
presenting with aniridia on routine neonatal
examination.
 DiGeorge/Sedlagkova/Velocardiofacial Syndrome
DiGeorge syndrome affects approximately 1:4000 births, is usually sporadic,
and is characterized by heart malformations (particularly those involving the
cardiac outflow tract), thymic and parathyroid hypoplasia, cleft palate and
typical fades. The molecular defect is a 3-Mb microdeletion on chromosome
22 (22q11.2). Dr Eva Sedlagkova from Prague reported a large series of
children with a congenitally short palate in 1955, 10 years earlier than
DiGeorge, and these patients clearly had the same condition. A similar
phenotype was described by Shprintzen and referred to as velocardiofacial
syndrome. Because of the confusion of eponyms and other terms given to this
condition over the years, “deletion 22q11 syndrome” now has the most
widespread acceptance (at the molecular level the deleted DNA segment is
still called the DiGeorge Critical Region).
Figure 5.17 shows individuals with deletion 22q11.2 at different ages. Because
it is the most common of the microdeletion syndromes, it has been intensely
researched. It is variable and many affected individuals are able to
reproduce, so the condition follows autosomal dominant inheritance in some
families. The 3 Mb deletion occurs because this region is flanked by two
identical sequences of DNA known as low-copy repeats (LCRs) of the type
that occur frequently throughout the genome. At meiosis the chromosomes
can be 'confused' when they align, such that the downstream DNA sequence
aligns with the upstream. If recombination occurs between these two flanking
regions, a deletion of 3 Mb results on one chromosome 22. It is possible that
the phenotypic features may be due largely to haploinsufficiency for the
TBX1 gene that lies within the region.
Figure 5.17 Deletion 22q11 (DiGeorge/Sedláĝková/velocardiofacial)
syndrome. A, A young infant. B, A young child. C, An older child. D, The
same individual (shown in C) as an adult age 49 years.
Those diagnosed should be investigated for cardiac malformations,
calcium and parathyroid status, immune function, and renal anomalies.
About half have short stature and a small proportion of these have partial
growth hormone deficiency. About 25% have schizophrenia-lite episodes
in adult life.

Duplication 22q11.2
The misaligned pairing at meiosis, of the LCRs that flank the 3 Mb region
at 22q11.2 that causes DiGeorge syndrome, predicts that gametes
duplicated for this ENA segment would be present in equal numbers.
However, duplication 22q11.2 syndrome is seldom seen in clinical practice,
suggesting that it might be subclinical in its effects.
Some patients have been reported but there is no consistent phenotype.
Some cases bear similarity to the deletion 22q11.2 phenotype, but marked
variability occurs. The problems range from isolated mild learning
difficulties to multiple abnormalities with non-specific dysmorphic
features, congenital heart disease, cleft palate, hearing loss, and postnatal
growth deficiency. More cases maybe diagnosed using microarray-CGH.
 Williams Syndrome
Williams syndrome occurs because of a microdeletion at chromosome 7q11
and diagnosis can be confirmed by FISH. The clinical phenotype was first
reported by Williams in 1961 and later expanded by Beuren (hence,
sometimes, Williams-Beuren syndrome). Hypocalcaemia is a variable
feature in childhood and sometimes persists, whilst supraval vular aortic
stenosis (SVAS) and peripheral pulmonary artery stenosis are congenital
abnormalities of the great vessels. Haploinsufficiency at 7q11 leads-to loss
of one copy of the gene that encodes elastin, a component of connective
tissue. This is probably the key factor causing SVAS and the vascular
problems that are more common in later life. Individuals have a
characteristic appearance (Figure 5.18) with mild short stature, a full
lower lip, and sloping shoulders. Equally characteristic is their behavior.
They are typically very outgoing in childhood-having a 'cocktail party
manner'-but become withdrawn and sensitive as adults. All are
intellectually impaired to the extent that they cannot lead independent
lives, and the majority do not reproduce, although parent-child
transmission has been reported.
Figure 5.18 A person with Williams syndrome as a baby (A), a
young child (B), an older child (C), and in his early forties (D).
 Smith-Magenis Syndrome
This microdeletion syndrome is due to loss of chromosome material at
17p11.2, often visible cytogenetically. As with DiGeorge syndrome, the
mechanism of deletion in many cases involves homologous recombination
between flanking LCRs. The physical characteristics are not highly
distinctive (Figure 5.19), but congenital heart disease occurs in one-third,
scoliosis develops in late childhood in more than half, and hearing
impairment in about two-thirds. The syndrome is most likely to be
recognized by the behavioral characteristics: as children, patients exhibit
self-harming (head-banging, pulling out nails, and inserting objects into
orifices), a persistently disturbed sleep pattern, and characteristic “self-
hugging". Some degree of learning difficulty is the norm. The sleep
pattern can often be managed by judicious use of melatonin.
Deletion 1p36 Syndrome
A new microdeletion syndrome that emerged through improved
cytogenetic techniques and the use of FISH in the 1990s is 1p36 syndrome
which, in keeping with today's approach to nomenclature, has no eponym.
The features are hypotonia, microcephaly, growth delay, severe learning
difficulties, epilepsy (including infantile spasms), characteristically straight
eyebrows with slightly deep-set eyes, and midface hypoplasia (Figure 5.20).
Figure 5.19 A young person with
Smith-Magenis syndrome; the facial
features are not highly distinctive, but
the philtrum is usually short. As
babies, chromosome studies are often
requested because the possibility of
Down syndrome is raised.
Figure 5.20 A child with deletion
1p36 syndrome—very straight
eyebrows, epilepsy, and learning
 Deletion 9q34 Syndrome
Another of the relative new microdeletion syndromes, this was first
reported as a condition featuring significant learning difficulties, hypotonia,
obesity, brachy-cephaly, arched eyebrows, synophrys, anteverted nostrils,
prognathism, sleep disturbances, and behavioural problems. Many patients
have severe speech delay and not all manifest obesity. The case pictured
here (Figure 5.21) bears a passing resemblance to Angelman syndrome.
Some patients with the phenotypic features but no microdeletion have been
shown to have mutations in the euchromatin histone methyl transferase 1
(EHMTl) gene, which lies within the region. The syndrome might therefore
be mainly due to haploinsufficiency for this gene.
Deletion 17q21.31 Syndrome
This new condition has a prevalence of approximately 1:16,000 and is
probably significantly underdiagnosed. The main features are severe
developmental delay, hypotonia, and characteristic facial dysmorphisms
including a long face with a high forehead and tubular or pear-shaped nose,
a bulbous nasal tip, large ears, and everted lower lip (Figure 5.22).
Individuals tend to be friendly. Other clinically important features include
epilepsy, heart defects, kidney anomalies, and long slender fingers.
Figure 5.21 A child with deletion 9q34
syndrome. She has arched eyebrows,
narrow upslanting palpebral fissures,
brachycephaly, prognathism, and
severe learning difficulties. She was
initially investigated for possible
Angelman syndrome.
Figure 5.22 This person shows the
characteristic facial features of
deletion 17q21.31 syndrome. The
face is long and the nose somewhat
tubular or pear-shaped, and the
nasal tip bulbous. There is
developmental delay.
 Deletion 1q21.1 Syndrome
This condition was first identified in three individuals from a cohort of 505
with congenital heart disease. The phenotype is broad and includes mild-
moderate mental retardation, small head size, growth retardation, heart
defects, cataracts, hand deformities and skeletal problems, learning
disabilities, seizures, and autism. On the other hand, however, some
individuals with the aberration are only slightly affected, or apparently
unaffected. A mother and her child, both with the deletion, are shown in
Figure 5.23. Variable penetrance and lack of highly distinctive features make
genetic counseling for this aberration highly problematic. Some experts
regard it as a susceptibility locus rather than a clinically distinct syndrome.
Chromosome disorders and behavioral phenotypes. The distinctive behavior
of children with Williams syndrome—their outgoing 'cocktail party
manner'—has been recognized as part of the condition for a long time. As
the micro deletion conditions have emerged, it has been increasingly clear
that patterns of behavior can reliably be attributed to certain disorders. This
is very striking in Smith-Magenis syndrome, but also apparent to a lesser
extent in deletion 22q11, cri-du-chat, and Angelman and Piader-Willi
syndromes. It is also apparent in the aneuploidies (Down and Klinefelter
syndromes), as well as in 47,XXX and 47,XYY and fragile X syndromes.
Figure 5.23 A, This mother and child have deletion 1p21.1 syndrome. They
bear a resemblance to each other and there is evidence of mild
development delay and small head size. B, The same child nearly a year
Behavioral phenotypes have therefore become an area of considerable
interest to clinical scientists and the observations lend support to the belief
that behavior to some extent at least, is genetically determined. In studying
chromosome disorders we are of course looking at genetically abnormal
situations, and from this we cannot necessarily extrapolate directly to
'normal-situations. For the latter, twin studies have provided substantial and
valuable information. This field of study remains complex and
understandably controversial. However, most now accept that behavior is a
complex interaction of genetic background, physical influences during early
development (e.g. fetal well-being), nurturing experiences, family size,
culture, and belief systems.
Disorders of Sexual Differentiation
The process of sexual differentiation has been described before. Given the
complexity of the sequential cascade of events that takes place between 6 and
14 weeks of embryonic lifes it is not surprising that errors can occur. Many
of these errors can lead to sexual ambiguity or to discordance between the
chromosomal sex and the appearance of the external genitalia. These
disorders are also sometimes referred to as various forms of intersex (Box
5.2).
BOX 5.2 Disorders of Sexual Differentiation and Development.
 True Hermaphroditism
In this extremely rare condition an individual has both testicular and
ovarian tissue, often in association with, ambiguous genitalia. When an
exploratory operation is carried out in these patients, an ovary can be
found on one side and a testis on the other. Alternatively, there can be a
mixture of ovarian and testicular tissue in the gonad, which is known as an
ovotestis. Host patients with true hermaphroditism have a 46,XX
karyotype, and in many of these individuals the paternally derived X
chromosome carries Y chromosome-specific DNA sequences as a result of
illegitimate crossing over between the X and Y chromosomes during
meiosis I in spermatogenesis (Figure 5.24).
A small proportion of patients with true hermaphroditism are found to be
chimeras with both 46,XX and 46,XY cell lines, a situation analogous to
freemartins in cattle.
Figure 5.24 FISH showing hybridization of a Y
chromosome paint to the short arm of an X
chromosome in a 46,XX male.
 Male Pseudohermaphroditism
In pseudohermaphroditism there is gonadal tissue of only one sex. The
external genitalia can be ambiguous or of the sex opposite to that of the
chromosomes. Thus in male pseudohermaphroditism there is a 46,XY
karyotype with ambiguous or female genitalia.
The most widely recognized cause of male pseudohermaphroditism is
androgen insensitivity. In this condition, which is also known as testicular
feminization syndrome, the karyotype is normal male and the external
phenotype is essentially that of a normal female. Internally the vagina ends
blindly and the uterus and fallopian tubes are absent. Testes are located in
the abdomen or in the inguinal canal, where they can be mistaken for
inguinal herniae. This condition is caused by the absence of androgen
receptors in the target organs, so that, although testosterone is formed
normally, its peripheral masculinizing effects are blocked. Androgen
receptors are encoded by a gene on the X-chromosome in which both
deletions and point mutations have been identified. Curiously, expansion
of a CAG repeat in the first exon of this androgen receptor gene causes a
neurological disorder known as Kennedy disease, or spino-bulbar
muscular atrophy. This is a rare example of the phenomenon sometimes
called a 'gene within a gene'.
Other causes of male pseudohermaphroditism include:
1 An incomplete form of androgen insensitivity known as Reifenstein
syndrome in which affected males have hypospadias, small testes, and
gynecomastia.
2 Enzyme defects in testosterone synthesis such as 5a
a-reductase deficiency
in which the external genitalia are ambiguous at birth but undergo
masculinization (virilization) at puberty.
3 Chromosome mosaicism (45,X/46,XY), in which most individuals are
normal males but a small proportion have ambiguous or female external
genitalia.
4 Campomelic dysplasia, which is caused by mutations in the SOX9 gene
on chromosome 17. SOX9 is believed to be an important gene in the
regulatory pathway by which SRY causes masculinization of the
undifferentiated fetal gonads.
5 The Smith-Lemli-Opitz syndrome, which is caused by deficiency of 7-
dehydrocholesterol reductase, an enzyme involved in cholesterol biosyn-
thesis. Some severely affected male infants have female external genitalia.
 Female Pseudohermaphroditism
In female pseudohermaphroditism, the karyotype is female and the
external genitalia are virilized so that they either resemble those of a
normal male or are ambiguous. Congenital adrenal hyperplasia (CAH) is
by far the most important cause of female pseudohermaphroditism. This
can be caused by several different enzyme defects in the adrenal cortex, all
of which show autosomal recessive inheritance. Reduced cortisol
production leads to an increase in adrenocortico-trophic hormone
secretion, which in turn causes hyperplasia of the adrenal glands. In the
most common form of CAH, because of a 21-hydroxylase deficiency,
hormone synthesis switches from the manufacture of cortisol and
aldosterone to the androgen pathway, leading to striking virilization of a
female fetus. The lack of cortisol and aldosterone usually leads to rapid
collapse within days of birth, which can prove fatal unless appropriate
hormone and electrolyte supplementation is initiated.
Rarer causes of female pseudohermaphroditism include an androgen-
secreting tumor and maternal androgen ingestion during pregnancy.
Chromosomal Breakage Syndromes
Constitutional and acquired chromosome abnormalities that predispose to
mali-gnancy are considered before. In addition to these conditions, it is
recognized that a small number of hereditary disorders are characterized
by an excess of chromosome breaks and gaps as well as an increased
susceptibility to neoplasia.
Ataxia Telangiectasia
This is an autosomal recessive disorder that presents in early childhood
with ataxia, oculocutaneous telangiectasia (Figure 5.25), radiation
sensitivity, and susceptibility to sinus and pulmonary infection. There is a
10% to 20% risk of leukemia or lymphoma. Cells from patients show an
increase in spontaneous chromosome abnormalities, such as chromatid
gaps and breaks, which are enhanced by radiation. The gene for ataxia
telangiectasia is called ATM and maps to chromosome 11q23. The protein
product is thought to act as a ‘checkpoint’ protein kinase, which interacts
with the TP53 and BRCA1 gene products to arrest cell division and
thereby allow repair of radiation-induced chromosome breaks before the S
phase in the cell cycle.
Figure 5.25 Ocular telangiectasia in a child with ataxia
telangiectasia.
 Bloom Syndrome
Children with this autosomal recessive disorder are small with a light-
sensitive facial rash and reduced immunoglobulin levels (IgA and IgM).
The risk of lymphoreticular malignancy is approximately 20%. Cultured
cells show an increased frequency of chromosome breaks, particularly if
they are exposed in vitro to ultraviolet light. The gene for Bloom syndrome
maps to chromosome 15q26, where it encodes one member of a group of
enzymes called the DNA helicases. These are responsible for unwinding
double-stranded DNA before replication, repair, and recombination.
Normally the Bloom syndrome gene plays a major role in maintaining
genome stability. When defective in the homozygous state, DNA repair is
impaired and the rate of recombination between sister chromatids is
increased dramatically. This can be demonstrated by looking for sister
chromatid exchanges (see the following section).
 Fanconi Anemia
This autosomal recessive disorder is associated with upper limb
abnormalities involving the radius and thumb (Figure 5.26), increased
pigmentation, and bone marrow failure leading to deficiency of all types of
blood cells (i.e., pancytopenia). There is also an increased risk of neoplasia,
particularly leukemia, lymphoma, and hepatic carcinoma. Multiple
chromosomal breaks are observed in cultured cells (Figure 5.27) and the
basic defect lies in the repair of DNA strand cross-links. There are five
known subtypes of Fanconi anemia, each caused by recessive mutations at
different autosomal loci. The most common, type A, maps to chromosome
16q24.
Xeroderma Pigmentosa
This exists in at least seven different forms, all of which show autosomal
recessive inheritance. Patients present with a light-sensitive pigmented
rash and usually die from skin malignancy in sun-exposed areas before the
age of 20 years. Cells cultured from these patients show chromosome
abnormalities only after exposure to ultraviolet light. These disorders are
due to defects in the nucleotide excision repair pathway. This involves
endonuclease cleavage 5′ and 3′ to each damaged nucleotide, excision of
the damaged nucleotide(s), and finally restoration of the damaged strand
Figure 5.26 Bilateral radial aplasia with absent thumbs in an
infant with Fanconi anemia.
Figure 5.27 Multiple chromosome breaks and gaps in a metaphase
spread prepared from a child with Fanconi anemia.
Chromosome Breakage and Sister Chromatid Exchange
Strong evidence of increased chromosome instability is provided by the
demon-stration of an increased number of sister chromatid exchanges (SCEs)
in cultured cells. An SCE is an exchange (crossing over) of genetic material
between the two chromatids of a chromosome in mitosis, in contrast to
recombination in meiosis I, which is between homologous chromatids. SCEs
can be demonstrated by differences in the uptake of certain stains by the two
chromatids of each metaphase chromosome after two rounds of cell division
in the presence of the thymidine analogue 5-bromodeoxyuridine (BUdR),
which becomes incorporated in the newly synthesized DNA (Figure 5.28).
There are normally about 10 SCEs per cell, but the number is greatly
increased in cells from patients with Bloom syndrome and xeroderma
pigmentosa. In the latter condition, this is apparent only after the cells have
been exposed to ultraviolet light.
It is not clear how SCEs relate to the increased chromosome breakage
observed in these two disorders, but it is thought that the explanation could
involve one of the steps in DNA replication. It is also of interest that the
number of SCEs in normal cells is increased on exposure to certain
carcinogens and chemical mutagens. For this reason the frequency of SCEs in
Figure 5.28 Chromosome preparation showing sister chromatid
exchanges (arrow).
Indications for Chromosomal/Microarray-CGH
Analysis
It should be apparent from the contents of this chapter that chromosome
abnormalities can present in many different ways. Consequently it is
appropriate to consider the indications for chromosome analysis, which
increasingly means microarray-CGH, under a number of different
headings
BOX (Box 5.3). for Chromosome Analysis.
5.3 Indications
 Multiple Congenital Abnormalities
Every child with multiple congenital abnormalities should have
chromosome studies undertaken. This is important for several reasons:
1. Establishing a chromosomal diagnosis will prevent further potentially
unpleasant investigations being undertaken.
2. Information about the prognosis can be provided, along with details of
the relevant support group and an offer of contact with other families.
3. A chromosomal diagnosis should facilitate accurate genetic risk
counseling.
Although it can be very distressing for parents to be told that their child
has a chromosome abnormality, they will often be relieved that an
explanation for their child’s problems has been found.
 Unexplained Learning Difficulties
Chromosome abnormalities cause at least one-third of the 50% of learning
difficulties that are attributable to genetic factors. Although most children
with a chromosome abnormality have other features such as growth
retardation and physical anomalies, this is not always so. If the fragile X
syndrome is a possibility, it is important that the cytogenetics laboratory is
informed so that the correct culture conditions are used, although in most
centers the fragile X syndrome is now diagnosed by molecular methods
rather than chromosome analysis. If standard karyotyping and fragile X
syndrome testing is negative, great reliance will increasingly be placed on
microarray CGH.
 Sexual Ambiguity
The birth of a child with ambiguous genitalia should be regarded as a
medical emergency, not only because of the inevitable parental anxiety, but
also because of the importance of ruling out the potentially life-threatening
diagnosis of salt-losing congenital adrenal hyperplasia. A chromosome
analysis should be among the first investigations undertaken.
Disorders of sexual development presenting in later life with problems
such as delayed puberty, primary amenorrhea or male gynecomastia are
also strong indications for chromosome analysis as a first-line
investigation. This can provide a diagnosis such as Turner syndrome
(45,X) or Klinefelter syndrome (47,XXY). Alternatively a normal
karyotype will stimulate a search for other possible explanations, such as
an endocrine abnormality.
 Infertility and Recurrent Miscarriage
Unexplained involuntary infertility should prompt a request for
chromosome studies, particularly if investigations reveal evidence of
azoospermia in the male partner. At least 5% of such men are found to
have Klinefelter syndrome. More rarely a complex chromosome
rearrangement such as a translocation can cause such severe mechanical
disruption in meiosis that complete failure of gametogenesis ensues.
At least 15% of all recognized pregnancies end in spontaneous
miscarriage; in 50% of cases this is because of a chromosome abnormality.
Unfortunately, some couples experience recurrent pregnancy loss—usually
defined as more than three spontaneous miscarriages. Often no
explanation is found and many such couples go on to have successful
pregnancies. However, in 3% to 6% one partner is found to carry a
chromosome rearrangement that predisposes to severe imbalance through
malsegregation at meiosis. Consequently it is now standard practice to
offer chromosome analysis to all such couples.
 Unexplained Stillbirth/Neonatal Death
The presence of growth retardation and at least one congenital
abnormality in a stillbirth or neonatal death would be an indication for
chromosome studies based on analysis of blood or skin collected from the
baby before or as soon after death as possible. Skin fibroblasts continue to
be viable for several days after death. Chromosome abnormalities account
for 5% of all stillbirths and neonatal deaths, and not all of these babies
have multiple abnormalities that would immediately suggest a
chromosomal cause.
Malignancy and Chromosome Breakage Syndromes
Certain types of leukemia and many solid tumors, such as retinoblastoma
and Wilms’ tumor, are associated with specific chromosomal abnormalities
that can be of both diagnostic and prognostic value. Clinical features
suggestive of a chromosome breakage syndrome, such as a combination of
photosensitivity and short stature, should also lead to appropriate
chromosome fragility studies, such as analysis of sister chromatid
exchanges.
Further Reading
De Grouchy J, Turleau C: Clinical atlas of human chromosomes. 2nd ed
1984 John Wiley Chichester
A lavishly illustrated atlas of known chromosomal syndromes.
Donnai D, Karmiloff-Smith A: Williams syndrome: from genotype
through to the cognitive phenotype. Am J Med Genet (Semin Med Genet).
97:164–171 2000
A review dealing with one microdeletion syndrome in detail and the efforts to
understand how the phenotype can be explained by the molecular findings.
Gardner RJM, Sutherland GR: Chromosome abnormalities and genetic
counseling. 2nd ed 1996 Oxford University Press Oxford
A useful updated guide to genetic counseling in families with a chromosome
disorder.
Hagerman RJ Silverman AC: Fragile X syndrome. Diagnosis, treatment
and research. 1991 Johns Hopkins University Press Baltimore
A detailed account of the clinical and genetic aspects of the fragile X
syndrome.
Further Reading
Jacobs PA, Browne C, Gregson N, Joyce C, White H: Estimates of the
frequency of chromosome abnormalities detectable in unselected newborns
using moderate levels of banding. J Med Genet. 29:103–108 1992
A review of the results of more than 14,000 prenatal diagnoses with estimates
of the incidence of chromosome abnormalities in term infants.
Ratcliffe S: Long term outcome of children of sex chromosome
abnormalities. Arch Dis Child. 80:192–195 1999
A very useful and clear description of the cognitive and social outcomes of
long-term follow-up studies of sex chromosome aneuploidies.
Schinzel A: Human cytogenetics database. 1994 Oxford University Press
Oxford
A regularly updated computerized database of all known chromosome
abnormalities. This is an invaluable aid to diagnosis and counseling.