Chromosome Abnormalities
Chromosome abnormalities arise as a consequence of abnormal chromosome number (
numerical) or from structural rearrangements of one or more chromosomes (
structural).
3
The loss or gain of large chromosomal segments alters significant amounts of genetic material and often results in pregnancy loss or offspring that may not survive after birth. In the case of a surviving newborn, birth defects, intellectual disability, infertility, and shortened lifespan are common. The frequency of chromosomal abnormalities varies from 60% to 80% in first trimester abortions; 5% to 7% in infant and childhood deaths; 4% to 8% in structural congenital malformations; and almost 10% in neurodevelopmental disorders in infancy.
13,14,15
Numerical chromosome abnormalities involve the gain or loss of a whole chromosome (full aneuploidy); part of a chromosome (partial aneuploidy); or an extra set of chromosomes (polyploidy) (triploidy: 69 chromosomes; tetraploidy: 94 chromosomes).
In
trisomy, there is three of a particular chromosome. The most common numerical chromosome disorder in newborns is trisomy 21, observed in 1 every 800 live births. Trisomy 18 and trisomy 13 occur in 1 in 8000 and 1 in 20,000 live births, respectively
11,13,14 (
Table 11.1). Trisomy of other autosomes usually ends in spontaneous abortion.
In
monosomy, only one member of the pair is present. Among first-trimester abortuses, 45,X (monosomy of X chromosome) is the most common numerical disorder. About half of individuals with Turner syndrome have monosomy X. The most common features of girls with Turner syndrome are short stature and primary ovarian insufficiency. There is also a high rate of heart defects, renal and skeletal abnormalities, and webbed neck.
3
The prevalence of trisomy increases with maternal age and decreases with gestational age (because of an increase in pregnancy loss). The prevalence of trisomy 21 at 12 weeks is 30% higher than the prevalence at 40 weeks.
16 In contrast, 45,X has no relationship with maternal age.
A single cell division, soon after fertilization, may go awry resulting in a numerical chromosome abnormality in the daughter cells of that division and, consequently, in chromosomally abnormal cells from that original stem cell. These abnormal cells continue to divide and multiply alongside the subjacent chromosomally normal cells and eventually result in an individual who has two or more different cell lines—a
chromosomal mosaic (
Figure 11.2).
Chromosome mosaicism detected prenatally may also reflect
confined placental mosaicism (CPM). CPM refers to the discrepancy between the chromosomal complement of the fetus and its placenta, due to postzygotic mitotic errors during embryonic development. CPM can be detected prenatally in about 2% of viable human pregnancies at 10 to 12 weeks of gestation. CPM may also be caused by the trisomic zygote rescue, a genetic phenomenon in which a fertilized ovum containing three copies
of a chromosome loses one of these chromosomes to form a normal diploid chromosome complement. The most common placental-fetal dichotomy involves placental trisomy for chromosome 16.
17
Structural chromosomal abnormalities may result from the breakage and loss or addition of a variable-sized piece of a long or short arm (deletion, duplication), or the breakage and change in the order of segments within the same chromosome or between different chromosomes (translocation, inversion, insertion) (
Figure 11.3). The abnormality can be
balanced (without loss or gain of material) or
unbalanced (with loss or gain of chromosomal material, usually with abnormal phenotype). Parents with balanced structural chromosomal abnormalities are at risk of unbalanced offspring, the level of risk depending on the specific anomaly, chromosomes involved, size of the abnormal segments, and type of ascertainment.
9
There are two types of translocations, Robertsonian and reciprocal.
Robertsonian translocations involve the acrocentric (a chromosome in which the centromere is located quite near one end of the chromosome) chromosomes (chromosomes 13, 14, 15, 21, and 22). Carrier parents are associated with risks of offspring with unbalanced translocation ranging mostly from 4% to 20%, with higher risks for maternal carriers. Reciprocal translocations occur when there is exchange of genetic material between autosomes are associated, almost invariably, with much lower risks for unbalanced karyotypes, mostly below 3% and frequently around 1%.
3
Chromosome
inversions occur following breakage at two sites along a chromosome length, followed by inversion and reattachment. Inversions may involve the centromere (called
pericentric inversions) or not (called
paracentric inversions). Estimates of frequency range from about 0.12% to 0.7% (pericentric inversions) and about 0.1% to 0.5% (paracentric inversions).
3 The risk to have a liveborn abnormal child due to recombination is between 1% and 5% when a parent has a pericentric inversion and much lower for paracentric inversions carriers. There are some inversions with a breakpoint within the heterochromatic regions of chromosomes 1, 9, 16, and Y, which are frequently seen, and they are considered normal variants.
All these chromosomal abnormalities can be diagnosed using classical cytogenetic techniques (conventional karyotype) or by molecular cytogenetics (fluorescence
in situ hybridization [FISH], quantitative fluorescence polymerase chain reaction [QF-PCR], multiplex ligation-dependent probe amplification [MLPA], CMA).
8
Some deletions and duplications in the genome involve a segment of a chromosome that is too small (from less than 1 kilobase [kb] to a few megabases [Mb]) to be readily seen through classical cytogenetic methods. These
microdeletions or
microduplications (CNV:
copy number variant) involve multiple disease genes, each potentially contributing to a phenotype independently. There are more than 200 microdeletion syndromes described to date (
Table 11.2). The most common microdeletion involves chromosome region 22q11.2 and has been associated with several distinct genetic disorders that are known to have overlapping clinical features (22qDS—deletion syndrome). These disorders include DiGeorge syndrome, velocardiofacial syndrome, isolated conotruncal cardiac defects, Cayler syndrome, and Opitz syndrome. The expanding, variable phenotype of individuals with 22q11 DS is now recognized.
18 The genetic changes of microdeletions can be studied by molecular cytogenetic techniques (FISH, MLPA, QF-PCR, CMA) or NGS (CNV-seq).
19
Single-Gene Disorders
Single-gene disorders (monogenic disorders), also referred to as Mendelian disorders, are those in which the phenotype is produced mainly by pathogenic variants in a specific gene, with little contribution from other genes or environmental influences. These disorders can be classified according to the patterns of inheritance dictated by Mendelian laws as being
autosomal dominant (AD),
autosomal recessive (AR), or
X-linked. Single-gene disorders may also display other non-Mendelian forms of inheritance such as
mitochondrial or
imprinting forms. It has been
estimated that approximately 1% of people in the general population have a single-gene disorder.
9
Autosomal dominant (AD) disorders are those in which the phenotype is caused by a pathogenic variant in a single copy of a gene on one of the 22 autosomes (the patient is heterozygous for the variant). An individual who carries a dominant gene pathogenic variant usually manifests the disorder. Examples of AD disorders are tuberous sclerosis, neurofibromatosis, and achondroplasia.
The following general principles characterize inheritance of
AD disorders (
Figure 11.4):
An individual who is affected has a 50% risk of transmitting the gene to each of his or her offspring.
Both males and females may be affected in equal proportions.
Both males and females are likely to transmit the disorder to male and female children.
An individual who is affected has one affected parent, or the disorder has appeared for the first time as a “de novo” variant in that individual (eg, approximately seven out of eight individuals with achondroplasia are due to a dominant de novo gene pathogenic variant).
The phenotype of a dominant gene pathogenic variant is determined by penetrance, which indicates whether or not that variant is expressed. Complete penetrance means that the dominant gene pathogenic variant expresses in all individuals who carry that variant (eg, neurofibromatosis 1 [NF 1] has complete penetrance after childhood, which means that all individuals who carry a pathogenic variant in the NF1 gene will manifest the disorder). Incomplete penetrance is expressed as a percentage, which means the number of individuals who carry the variant that expresses the phenotype. For example, 70% penetrance means that 70% of individuals with the pathogenic dominant gene variant expresses the phenotype. Incomplete penetrance may account for some AD disorders that seem to “skip” generations and may be a manifestation of the interaction of other genes.
The phenotype of a dominant gene is also determined by
expressivity or the variability in clinical expression (the range of phenotypic features).
Variable expressivity means that the dominant gene produces a range of phenotypic features from mild to severe; therefore, not all individuals will show identical phenotypes (eg, the phenotype of individuals with dominant pathogenic variants in genes associated with nonsyndromic holoprosencephaly is extremely variable, ranging from alobar holoprosencephaly to microforms with single central maxillary incisor).
20
In examining the pedigree of a family with possible
AD disorders, attention is usually given to whether the disease has a vertical pattern of inheritance.
21
Autosomal recessive (AR) disorders are those in which the phenotype is due to pathogenic variants present in both copies of a gene on one of the 22 autosomes (the patient is homozygous [two
identical pathogenic variants] or compound heterozygous [two different pathogenic variants in both alleles of a gene]). Examples of
AR disorders are cystic fibrosis, Tay-Sachs disease, and spinal muscular atrophy.
Inheritance of
AR disorders is characterized by the following general principles (
Figure 11.5):
Two unaffected individuals who are heterozygous or carriers of one pathogenic recessive gene variant have a 25% risk of having an affected offspring in each pregnancy (one of four children will be affected; three of four will be phenotypically normal with two of these being carriers).
Carriers of pathogenic recessive gene variants are at risk of affected offspring only if their partners are also carriers of pathogenic variants in the same gene.
Both males and females may be affected in equal proportions.
Carriers of single recessive pathogenic variants do not manifest the disease, are healthy (in some cases they may have changes at the biochemical or cellular level).
Carriers of recessive pathogenic variants may be recognized after the birth of an affected child, after the diagnosis of an affected family member, or as the result of a genetic screening program.
In examining the pedigree of a family with possible AR disorder, attention is usually given to whether the disease has a horizontal pattern of inheritance.
Every person is a carrier of some
AR pathogenic variants, but, as recessive diseases have a low prevalence in the general population, the chance that both partners are carriers of variants in the same gene is low (1%-2%) unless there is consanguinity or they belong to specific ethnic groups. Hence, couples who share the Mediterranean, Ashkenazi Jewish, Black, or Asian extraction are at risk for beta-thalassemia, Tay-Sachs and Canavan disease, sickle cell disease, and alpha-thalassemia, respectively.
22,23
X-linked disorders are those in which the phenotype is due to a pathogenic variant in a gene on the X chromosome, and they are usually recessive. Given that the male has only one X chromosome and the female has two, both the risk and severity of X-linked disease will vary between the sexes. Examples of X-linked recessive disorders are hemophilia A and Duchenne muscular dystrophy (DMD), and of an X-linked dominant disorder is incontinentia pigmenti.
The following general principles characterize inheritance of
X-linked disorders (
Figure 11.6):
In X-linked recessive disorders:
Males will usually manifest the fullest expression of the disorder, whereas random X inactivation will largely influence expression in females.
Affected men will produce carrier daughters, while their sons will be healthy.
The male-to-male transmission does not occur because a male never contributes his X chromosome to a son.
Females heterozygotes have a risk of 50% of male children affected in each conception, while half of the female daughters will be carriers.
Females heterozygotes are generally asymptomatic but may manifest some sign(s) of the disease in question (eg, female carriers of DMD are generally asymptomatic but may manifest cardiomyopathy or cardiac conduction defects).
X-linked dominant traits are characterized by an affected male transmitting the condition to all his
daughters and none of his sons; an affected female has a 50% likelihood of transmitting the disorder to her sons or daughters. Rarely, an X-linked dominant trait may be lethal in affected males, resulting in a disorder that appears to occur, clinically, only in females and in which an affected female has a 50% likelihood of transmitting the trait to her daughters. These affected women have an increased frequency of miscarriage due to affected male fetuses.
In examining the pedigree of a family with possible X-linked disease, attention is usually given to whether the disease has occurred in maternal nephews, uncles, or first cousins and through the female line.
Pathogenic variants in single gene disorders can be diagnosed using molecular techniques (eg, Sanger sequencing, NGS, PCR, MLPA). Carrier screening tests for some disorders are also available using biochemical tests (eg, quantification of hexosaminidase A enzyme activity in plasma or leukocytes to assess in Tay-Sachs disease carrier status).
8
Non-Mendelian Patterns of Inheritance
Some disorders do not follow the classic Mendelian patterns of inheritance. There are several mechanisms described below.
Mitochondrial Inheritance
Mitochondrial disorders are a heterogeneous group of diseases produced by dysfunction of mitochondria. Each cell has hundreds of mitochondria located in the cytoplasm. Each mitochondrion has its own genome. Mitochondrial disorders can be caused by genetic defects either at the nuclear or at the mitochondrial DNA (mtDNA). When pathogenic variants are located in the nuclear DNA, the disorder will be inherited in the usual autosomal recessive or dominant patterns (eg, Leigh syndrome). On the contrary, if the genetic defect is encoded in the mitochondrial genome, the pattern of inheritance of these disorders will be mitochondrial, which are described below (eg, Leber hereditary optic neuropathy).
The following general principles characterize
mitochondrial inheritance24:
The mother transmits mitochondrial DNA because only maternal mitochondria are transmitted to the offspring (sperm mitochondria are eliminated during fertilization).
Males and females can be equally affected.
The phenotype will be affected by mitochondrial heteroplasmy, which is the coexistence of normal and abnormal mitochondrial DNA molecules within each cell (each cell contains multiple mitochondria, and each mitochondrion contains multiple copies of mitochondrial DNA). Mitochondria divide through mitosis and segregate to daughter cells during cell division. An mtDNA pathogenic variant present in one mitochondrion will generate more abnormal mitochondria that will segregate to daughter cells. The proportion of normal and abnormal mitochondria will vary in different cells and different tissues, therefore affecting the expression and severity of the disorder depending on the eventual abnormal mitochondrial load in various tissues.
The mother of an affected individual has the mtDNA pathogenic variant and may or may not have symptoms.
Males with an mtDNA pathogenic variant will not transmit the variant to offspring.
Females with an mtDNA will transmit the variant to all her offspring, and the phenotype will vary according to the number of abnormal mitochondria in different tissues.
An individual is unique in the proportion of normal and abnormal mitochondrial DNA in different organs.
Uniparental Disomy
Uniparental disomy (UPD) is the inheritance of both members of a chromosome pair from the same parent, resulting in disomy of that chromosome (n = 2). UPD arises more frequently as a consequence of the “
rescue” of a trisomic conception by loss of one chromosome and retention of the other two chromosomes from the same parent (
uniparental heterodisomy: two different homologous chromosomes from the same parent). UPD may also occur as a result of duplication of the chromosome in a monosomic pregnancy (
uniparental isodisomy: two identical homologous chromosomes from the same parent) (
Figure 11.7). This process is uncommon but contributes to the occurrence of some well-known clinical disorders when it involves chromosomes with “imprinting” or genomic imprinting (
Table 11.3).
15
This derivation of a pair of homologs from one parent cannot be detected cytogenetically. Molecular cytogenetic techniques using DNA markers facilitate UPD detection (eg, MLPA, SNP-array).
8,9 The indication for UPD study in most instances has been either a genetic disorder (eg, Prader-Willi syndrome) or an abnormality found on prenatal diagnosis. For example, trisomy 15 CPM (trisomy 15 is found in chorionic villi, but the amniotic fluid is euploid and further assessment should be conducted to determine UPD of chromosome 15).
Imprinting
The
imprinting or
genomic imprinting is an epigenetic mechanism by which the expression of specific genes depends on the sex of the parent of origin. If an “epigenetic mark” inactivates an imprinted gene (eg, DNA methylation), gene function will depend entirely on the active gene inherited from the other parent. It is a regulation process of gene expression where the function of the gene changes without changing its sequence. Under normal circumstances in the human genome, most genes are both expressed; only a minority of human genes are imprinted according to whether the chromosome has been inherited in the sperm or the ovum. Imprinting thus produces a differential activation status of the two alleles of a locus or loci. For example, if inactivation of the inherited maternal allele occurs, only the allele of paternal origin will be functionally active; and
vice versa. There are disorders produced by loss or change in the “imprinting” pattern of a gene or chromosome segment, for example, in UPD of one entire chromosome or chromosome segment subject to imprinting (chromosomes 6, 7, 11, 14, 15, 20). UPD has been described most commonly in the Prader-Willi, and Angelman syndromes. About two-thirds of patients with Prader-Willi syndrome have a recognizable cytogenetic deletion in one chromosome 15q11-q13 region. Another approximately 30% of cases are due to maternal UPD.
25,26
Trinucleotide-Repeat Expansion
There are specific genes with a region of triplet repeats (trinucleotide) that are susceptible to expansion when there is transmission from parent to offspring (eg, fragile X syndrome, Huntington disease). This process is termed anticipation. During meiosis, gametes can increase the number of triplet repeats, and when the gene reaches a critical number, it may alter its expression and produce phenotypic abnormalities. The reason for repeat expansion (or not) is unknown. Some regions of triplet repeats may expand only during female meiosis (eg, fragile X) and others may expand during male meiosis (eg, Huntington disease).
Fragile X syndrome is an X-linked disorder produced by CGG trinucleotide expansion in the FMR1 (fragile X mental retardation 1) gene and present in 1 out of every 4500 males. It is the most common single cause of inherited intellectual disability in males. The prevalence of females affected with the syndrome is approximately one-half the male prevalence.
FMR1 alleles are classified according to the number of repeats in exon 1 into four groups (
Table 11.4):
normal alleles: 5 to 44 repeats;
intermediate alleles (gray zone or borderline): 45 to 54 repeats;
premutation alleles: 55 to 200 repeats;
full-mutation alleles: more than 200 CGG repeats. It is also important to assess the methylation pattern of the repeat region.
27,28
Fragile X syndrome occurs in individuals with an
FMR1 gene with full mutation usually accompanied by aberrant methylation, which produces a loss-of-function of the gene. The chance of expansion of a premutation to a full mutation when transmitted to offspring depends on the sex of the parent and the number of trinucleotide CGG repeats present in the parental gene
27,28,29,30:
Intermediate allele: offspring are not at increased risk for fragile X syndrome, although almost 14% may expand into the
premutation range when transmitted by the mother.
16 They are not known to expand to
full mutations.
Premutation alleles: Premutation carriers do not have fragile X syndrome. Women with alleles in this range have a 50% risk of transmitting a
premutation in each pregnancy. They are also at risk to repeat expansion and having children with fragile X syndrome. The risk of a maternal
premutation becoming a
full mutation in her offspring depends on the number of CGG trinucleotide repeats. The larger the size of the
premutation repeat, the more likely the expansion to a fully expanded CGG repeat. For small
premutations, AGG interrupters in the FMR1 gene may help
evaluate the risk of expansion. The presence of AGG decreases the risk of expansion of a premutation allele to a full mutation allele during maternal transmission.
Premutation carriers also have an increased risk of FMR1-related primary ovarian insufficiency (POI), and fragile X-associated tremor/ataxia syndrome (FXTAS) (both males and females). Males are considered “transmitting males” because the father does not expand to
full mutations (the
premutation is inherited by all of his daughters and none of his sons).
28
Detection of the CGG triplet repeat with concurrent ascertainment of the methylation status is the standard diagnostic test for fragile X syndrome.
30
Germline Mosaicism
Germline or gonadal mosaicism occurs in a phenotypically normal individual when a pathogenic disease variant is present only in some germ cells and, therefore, increases the risk for having multiple affected children with the disease. It may explain the recurrence of some dominant diseases in unaffected parents such as osteogenesis imperfecta type 2.
Germline mosaicism is also common in DMD, an X-linked disease; therefore the empiric recurrence risk after the birth of a child with DMD disease caused by apparently de novo pathogenic variants may be higher than expected in the general population.
21
Multifactorial or Polygenic Disorders
Multifactorial or polygenic disorders are relatively common (about 1% of newborns) and occur due to the interaction of genetic and environmental factors. Most malformations limited to one organ or system belong to this category (eg, anencephaly). Although they have a slight tendency to recur, they do not follow Mendelian inheritance patterns. The occurrence of a defect of multifactorial origin implies a risk of recurrence of 3% to 5% for the siblings and offspring of the affected. This risk is lower than what one would expect if a single gene was affected but higher than that observed in the general population. Recurrence increases with the number of affected relatives, the severity of the defect, and sex of the affected proband. The risk is higher if the sex of the affected person is the least prevalent for this anomaly. For example, the risk of recurrence is higher for bilateral cleft lip with cleft palate (8%) than for unilateral cleft lip (4%); and for pyloric stenosis, which occurs more frequently in men, when the defect occurs in a woman.
3,8,9 Most traits inherited from parents, such as height, hair and eye color, have a multifactorial or polygenic inheritance mechanism.
The advance in the understanding of the human genome allowed the discovery of the genetic origin and reclassification of some defects thought previously to be multifactorial.