Cytogenetics and the evolution of medical genetics
Novel Deletion Variants Of 9q13–q21.12 And Classical Euchromatic Variants Of 9q12/qh Involve Deletion, Duplication And Triplication Of Large Tracts Of Segmentally Duplicated ...
Conventional cytogeneticsConventional G (GTL) (550 bands) and C (CBG) banding was performed using standard techniques on peripheral blood lymphocytes.
Families 1–3 and patients 1 and 2 with apparent proximal 9q deletions:
Family 1
This 9-year-old boy was referred for chromosome analysis because of learning difficulties and small genitalia. An interstitial deletion of 9q13–q21.12 was found in the proband and his father who was also considered to suffer from cognitive impairment (Figure 1, column 1).
Figure 1(Column 1) Results from patients with 9q13–q21.12 euchromatic deletion variants. Row 1: Note absence of the most proximal G-dark band q21.11 in the long arm. Row 2: Note also the absence of long arm signals in normal and variant chromosomes with BAC RP13-198D9 that defines the short boundary between segmentally duplicated and unique sequence euchromatin. Row 3: Note the absence of long arm signal on the variant chromosome and the presence of reduced signal strength on the normal 9 of the pSD detected by BAC RP11-246P17. Row 4: Note normal result with segmentally duplicated clone RP11-561O23. Row 5: Note very weak short arm signal that defines the long arm boundary between segmentally duplicated and unique sequence euchromatin with clone RP11-88I18. (Column 2) Results from a patient with the 9q13–q21.12 euchromatic duplication variant and a single extra euchromatic band. Row 1: Note presence of additional G-dark band in q12 in the long arm heterochromatin. Row 2: Single short arm signals in the normal and variant chromosomes with the boundary BAC RP13-198D9. Row 3: Weaker long arm signals on both normal and variant chromosomes of the pSD detected by clone RP11-246P17. Row 4: Extra weaker signal just above the strong long arm signal on the variant chromosome with the segmentally duplicated clone RP11-561O23. Row 5: Weak p arm signal and probable extra band just above strong long arm signal on the variant chromosome with boundary clone RP11-88I18. (Column 3) Results from a patient with 9q13–q21.12 euchromatic triplication variant and two extra euchromatic bands. Row 1: Note presence of two additional G-dark bands in q12 in the long arm heterochromatin. Row 2: Single short arm signals in normal and variant chromosomes with the boundary BAC RP13-198D9. Row 3: Weaker long arm signals on both normal and EV chromosomes of the pSD detected by clone RP11-246P17. Row 4: Two extra relatively weak signals within the chromosome 9 heterochromatic block with segmentally duplicated clone RP11-561O23. Row 5: Weak p arm signal stronger q arm signal and two extra but relatively weak signals within the chromosome 9 heterochromatic block with boundary clone RP11-88I18. (Column 4) Results from the patient with the 9p11.2–p13.1 euchromatic duplication variant and a single extra euchromatic band in the short arm. Row 1: Note presence of additional G-dark band in p12 in the short arm. Row 2: Single short arm signals in normal and variant chromosome with the boundary BAC RP13-198D9. Row 3: Double short arm signals on the variant chromosome, single short arm signal on the normal chromosome and weaker long arm signals on both chromosomes of the pSD detected by clone RP11-246P17. Row 4: Note the double short arm signals on the variant chromosome, single short arm signal on the normal chromosome with SD clone RP11-561O23. Row 5: Note stronger p arm signal on the variant chromosome with boundary clone RP11-88I18.
Families 2 and 3
The male proband in family 2 was referred with global developmental delay at the age of 8. A deletion of 9q13–q21.12 was found in the proband and his phenotypically normal mother. The male proband in Family 3 was referred with learning and behavioural problems and a possible diagnosis of Asperger syndrome at the age of 13. A deletion of 9q13–q21.12 was found in the proband and his phenotypically normal mother.
Patients 1 and 2
Both these male individuals were referred for recurrent miscarriages at the age of 33 and 38, respectively, and were found to have a deletion of 9q13–q21.12. Parental samples were requested but not received.
Patients 3–5 with additional euchromatic band(s) within 9q12/qh:
Patient 3 was ascertained when her mother was referred for a previous trisomy 18 and an increased nuchal translucency of 4.3 mm at 12 weeks gestation conferring a 1 in 7 risk of trisomy 21. Extra material within 9q12/qh was found in chorionic villus cultures but the mother had normal chromosomes 9 and the father was unavailable. The pregnancy resulted in a newborn dysmorphic female and the euchromatic variant was confirmed in an otherwise karyotypically normal perinatal blood sample (Figure 1, column 2).
Patient 4 was a male aged 16 years referred for learning difficulties and obesity. Testing for fragile X and Prader Willi syndromes gave normal results. Extra material was found within 9q12.
Patient 5 was a male ascertained with oligoasthenoteratospermia at the age of 27. Two additional bands were found within the 9q12/qh heterochromatin (Figure 1, column 3). Parental samples were not obtained.
Patient 6 with additional euchromatic band within 9p12:
Patient 6 was a male aged 15 years referred for chromosome analysis with spastic paraparesis and poor balance. An additional G-dark band was observed within 9p12 (Figure 1, column 4). Parental samples were not obtained.
Molecular cytogeneticsFluorescence in situ hybridisation (FISH) was carried out with build 36.1. Sanger Institute 1 Mb and 37 k cloneset BACs (www.Ensembl.Org/Homo_sapiens/cytoview) spanning the 9p21 to 9q22 region (Table 1). Bacterial stabs were cultured by standard techniques and minipreps of DNA were made using the Qiagen miniprep kit (www.Qiagen.Com). DNA clones were labelled by nick translation with Spectrum Orange or Spectrum Green d-UTP and hybridisation was performed according to the manufacturer's protocols (www.Vysis.Com). Dual colour FISH was also carried out with cosmid cCMP9.27 specific for satellite III DNA and BAC RP11-15J10 (Figure 2). Slides were examined with an Olympus BX55 fluorescence microscope and images captured using SmartCapture software (www.Digitalscientific.Co.Uk).
Table 1 Segmentally duplicated BACs in normal individuals and extent of deletion, duplication and triplication in patients with euchromatic variants Figure 2Result from patient with the 9q12 euchromatic variant with a single extra euchromatic band. Note the alternating pattern of green Spectrum Green-labelled satellite III using cosmid cCMP9.27 and red Spectral Orange-labelled signals from the highly segmentally duplicated clone RP11-15J10 illustrated by the additional paralogous sub-telomeric RP11-15J10 signals.
Mapping and gene contentSDs and copy number variations were identified from the Human Genome Segmental Duplication Database (http://projects.Tcag.Ca/humandup/). The gene content of the segmentally duplicated region was obtained from the Ensembl database (v36) using the MartView data export tool (http://www.Ensembl.Org/Multi/martview).
Molecular cytogenetic resultsFISH on the proband and father from Family 1 gave normal proximal 9q signals with BACs from the Sanger 1 Mb cloneset that mapped to the region of interest between bands q13 and q21.13 according to the Ensembl (http://www.Ensembl.Org) and NCBI (http://www.Ncbi.Nih.Gov/mapview) web browsers (BACs** in Table 1). However, immediately centromeric to these 1 Mb clones, 37 k tiling path clones including BAC RP11-88I18 gave an additional weak but positive short arm signal, and BAC RP11-561O23 gave strong signals in both the long arm and short arms (Figure 1, column 1). Further BACs that mapped specifically in genome browsers to 9q13, q12, p11.2, p12 or 9p13.1 gave signals in both 9p and 9q in the normal homologue but no signal on the long arm of the euchromatic variant chromosomes (see eg BAC RP11-246P17 in Table 1 and Figure 1, column 1, row 2).
A panel of fully sequenced tiling path BACs was then used to map the extent of this segmentally duplicated pericentromeric region in normal individuals and the results in these and individuals with euchromatic variants are shown in Table 1 (with the extent of the segmentally duplicated region in light grey). All 9p clones telomeric (distal) to RP11-402N8 had signals at a single locus within 9p13 and all 9q clones telomeric (distal) to RP11-88I18 had a single signal within 9q. All of the clones centromeric to these showed signals in both 9p and 9q. This region extends over ∼31.6 Mbs from BAC 402N8 to BAC 88I18 and contains 44 SDs, 17 copy number variants and sequences derived from 93 known and 49 novel genes.
The boundaries between this segmentally duplicated region and flanking unique sequences were within contigs NT_00843.17 in the short arm and NT_023935.17 in the long arm. Cytogenetically, these boundaries lie within the 4 kb overlap between BACs RP13-198D9 and RP11-402N8 in 9p13.1 and within the 118 kb gap between BACs RP11-88I18 and RP11-274B18 in 9q21.12. Centromeric to contig NT_008413.17 in 9p, 17 contigs extending over ∼8 Mb between band p13.1 and the centromere are shown in build 36.1 of the human genome. These contigs each contain between one and 10 BACs. All of the probes tested from these contigs were segmentally duplicated or highly segmentally duplicated (Table 1 and data not shown). Similarly, there are 16 contigs spanning ∼4 Mb between the 9q heterochromatin and NT_023935.17 in the long arm. All of the clones tested from these contigs were either segmentally duplicated or highly segmentally duplicated (Table 1 and data not shown). We considered these SD-containing clones gave three signal patterns:
partial segmental duplication (pSD in Table 1) with a strong signal in either 9p or 9q and a much weaker signal in the opposite arm.
SD (in Table 1) with strong signals in both 9p and 9q. Some loci also had additional, clearly separated signals in 9p in addition to the proximal 9q signals (SD+ in Table 1).
high-level segmental duplication (hSD in Table 1) with signals in both 9p and 9q as well as sub-telomeric 9p and other chromosomes including the ancestral 2q13–q14.1 fusion site at which chromosome 2 was formed in man.20
All eight individuals carrying the euchromatic 9q13–q21.12 deletion variant gave the same results; none of the unique sequence clones were deleted, whereas the long arm signals from the majority of segmentally duplicated clones were consistently absent ('No' in Table 1, column 7) except for the 9q21.11/q21.12 clones 561O23 and 88I18 near the distal boundary of the segmentally duplicated region. This variant may be described as var(9)del(9)(q13q21.12).
In the three patients with euchromatic duplication or triplications variants and one or two additional bands within 9q12/qh, most of the segmentally duplicated BACs showed single, double or multiple additional signals ('Yes' in Table 1, column 8) (Figure 2). In each duplication and triplication variant, these included the overlapping distal BACs 561O23 and 88I18 but not the four BACs adjacent to the short arm boundary of the segmentally duplicated region (Table 1). These variants may be written as var(9)dup(9)(q13q21.12) or var(9)trp(9)(q13q21.12).
In the single patient with the euchromatic duplication variant and an additional band within 9p12, segmentally duplicated BACs showed two or more additional signals in proximal 9p ('Yes' in Table 1, column 9) (Figure 1, columns 1–4). The duplicated tract included BACs from the proximal boundary of the segmentally duplicated region but not the five BACs adjacent to the long arm boundary. This variant may be expressed as var(9)dup(9)(p11.2p13.1).
Chromosomal Abnormalities
Chromosomal abnormalities, alterations and aberrations are at the root of many inherited diseases and traits. Chromosomal abnormalities often give rise to birth defects and congenital conditions that may develop during an individual's lifetime. Examining the karyotype of chromosomes (karyotyping) in a sample of cells can allow detection of a chromosomal abnormality and counselling can then be offered to parents or families whose offspring are at risk of growing up with a genetic disorder.
Types of chromosomal abnormalityA chromosomal abnormality may be numerical or structural and examples are described below:
Numerical abnormalitiesThe normal human chromosome contains 23 pairs of chromosomes, giving a total of 46 chromosomes in each cell, called diploid cells. A normal sperm or egg cell contains only one half of these pairs and therefore 23 chromosomes. These cells are called haploid.
The euploid state describes when the number of chromosomes in each cell is some multiple of n, which may be 2n (46, diploid), 3n (69, triploid) 4n (92, tetraploid) and so on. When chromosomes are present in multiples beyond 4n, the term polyploid is used.
Aneuploidy refers to the presence of an extra chromosome or a missing chromosome and is the most common form of chromosomal abnormality. In the case of Down's syndrome or Trisomy 21, there is an additional copy of chromosome 21 and therefore 47 chromosomes. Turner's syndrome on the other hand arises from the absence of an X chromosome, meaning only 45 chromosomes are present.
Occasionally, aneuploid and regular diploid cells exist simultaneously and this is called mosaicism. The condition involves two or more different cell populations from a single fertilized egg. Mosaicism usually involves the sex chromosomes, although it can involve autosomal chromosomes.
In contrast to mosaicism, a condition called chimaerism occurs when different cell lines derived from more than one fertilized egg are involved.
Structural abnormalitiesStructural abnormalities occur when the chromosomal morphology is altered due to an unusual location of the centromere and therefore abnormal lengths of the chromosome's short (p) and long arm (q).
Some of the most common chromosomal abnormalities include:
What's To Know About DiGeorge Syndrome?
DiGeorge syndrome is a chromosomal disorder that typically affects the 22nd chromosome. Several body systems develop poorly, and there may be medical problems, ranging from a heart defect to behavioral problems and a cleft palate.
The condition is also known as 22q11.2 deletion syndrome. Around 90 percent of people with the condition have a small deletion on the 22nd chromosome at the q11.2 location.
This deletion is now known to be responsible for several previously-named syndromes that now all fall under the 22q11.2 deletion syndrome.
Other names include velocardiofacial syndrome, conotruncal syndrome, Shprintzen syndrome, and CATCH22.
DiGeorge syndrome is thought to affect 1 in 4,000 people. However, the features vary widely. As a result, underdiagnosis and misdiagnosis are likely to occur.
Fast facts on DiGeorge syndromeHere are some key points about DiGeorge syndrome.
DiGeorge syndrome results from the deletion of the 22q11.2 segment in one of the two copies of chromosome 22. It affects approximately 30 to 40 genes.
Many of these genes are not yet fully understood.
The syndrome usually starts as a random event during fertilization, either on the maternal or paternal side. It may happen during the time of fetal development.
Most cases are not inherited, and there is rarely a family history of the condition.
However, in around 10 percent of cases, it is passed from a parent to a child.
Share on PinterestDiGeorge syndrome is a genetic condition that features a missing segment in one chromosome.If a child has DiGeorge syndrome, parents or caregivers may notice that they have:
Heart problems are most likely to affect the aorta.
The syndrome can involve a wide range of signs and symptoms.
Other symptoms may include hearing impairment, visual abnormalities, and altered kidney function
Due to the significant variability of DiGeorge syndrome, the type and severity of symptoms are typically determined by the organ system affected.
DiGeorge syndrome is most commonly diagnosed with a blood test called a FISH analysis (Fluorescent In Situ Hybridization).
A health care provider is likely to request a FISH analysis if a child has symptoms that may indicate DiGeorge syndrome, or if there are signs of a heart defect. Certain types of heart defect are strongly associated with the condition.
Treatment depends on the organ systems involved. It can involve a wide range of health professionals.
Share on PinterestTreatment often requires coordinating care between a variety of different health specialists.Different conditions caused by DiGeorge syndrome need different types of treatment.
Hypoparathyroidism
Treatment includes supplementation with vitamin D or calcium and with parathyroid hormone.
Limited thymus gland function can affect the immune system's ability to fight infection, and there may be frequent mild or moderate infections. Treatment and vaccine scheduling is usually the same as for children without the condition. The immune function usually becomes stonger as the child gets older.
Severe thymus dysfunction poses a risk of severe infection. Thymus tissue transplantation, bone marrow transplant, stem cell transplant, or transplant of disease-fighting blood cells may be necessary.
Other treatments
Other treatments include:
Currently, there is no cure for DiGeorge syndrome, and it is a lifelong condition. The outlook depends on the organ system affected and the severity of the condition.
However, some of the problems tend to improve with age, such as heart and language problems. Most people can expect to live a normal life, but they may continue to experience infections and other problems. Adults with the condition can often live independently.
As with most medical conditions, early diagnosis and treatment is essential. It is also important to attend all medical appointments, as ongoing monitoring can help an individual maintain a good level of health.
Anyone who is concerned about the risk of diGeorge syndrome should speak to their health provider.
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