18.03.20 Microdup/del syndromes

Question 1

What are the different pathological mechanisms by which microdeletion/duplication syndromes can result in disease.

Answer 1

1. Haploinsufficiency
2. Affects imprinted genes
3. Recessive mutation is unmasked
4. Position effect
5. Trisomy for duplicated segment

Question 2

What are the two forms of syndrome associated with microdeletions and duplications? Give an example of each.

Answer 2

1. Single gene (Mendelian) syndrome – The phenotypic effects are due to the deletion/duplication of a single dosage-sensitive gene (e.g. Alagille syndrome, JAG1; CMT1A/HNPP, PMP22; Rubinstein-Taybi, CBP; Neurofibromatosis type 1, NF1). Neighbouring genes may also be deleted/duplicated, but as they are not dosage-sensitive they do not contribute to the phenotype.
2. Contiguous gene syndrome – A specific recognisable phenotype results from the loss or gain of multiple adjacent genes, some of which are dosage-sensitive (e.g. WAGR, Williams syndrome, DiGeorge/VCFS).

Question 3

What is the common basis for many microdeletion/duplication syndromes?

Answer 3

low copy repeats

Question 4

What are low copy repeats and which mechanism are they involved in which leads to microdeletion/duplications?

Answer 4

LCRs: DNA blocks of ~10-400kb with a high degree of homology (>97%) that occur multiple times throughout the genome and enable the erroneous coming-together of different chromosome regions during meiosis.

The misaligned repeats have the same sequence but not the same chromosomal location, so recombination is homologous but the sequences are not alleles. Hence this process is known as non-allelic homologous recombination (NAHR).

This mechanism generates many common non-pathogenic CNVs as well as pathogenic variations in gene dosage.

Question 5

What are the different outcomes of LCR/NAHR-based mechanism?

Answer 5

Depending on whether the NAHR is between LCRs on two homologous chromosomes (interchromosomal), on the chromatids of the same chromosome (intrachromosomal) or on the same chromatid (intrachromatid), as well as on the orientation and complexity of the LCRs, the outcomes vary (deletions/duplications/ inversions/isodicentric chromosomes).

Question 6

What are NAHR hotspots?

Answer 6

NAHR hotspots are positions within LCRs where crossovers preferentially occur, and rearrangement breakpoints are typically found.

Hotspots are usually in regions of identical nucleotide sequence at least ~200-450bp long. Because breakpoints cluster within defined regions at NAHR hotspots, the extent of many recurrent CNVs is essentially identical even in unrelated individuals.

Question 7

What is the minimal efficient processing segment?

Answer 7

The minimal efficient processing segment (MEPS) is the minimal stretch of identity required to enable homologous recombination.

The length of MEPS can be different between meiosis (~300-500bp) and mitosis (possibly shorter) and between different events.

The distance between LCRs could play a role in determining the lenth of the MEPs (the further away the LCRs, the longer the MEPs).

Question 8

Why do many microduplication syndromes remain undiagnosed?

Answer 8

microduplications generally result in a milder, more benign phenotype than microdeletions, since trisomy is usually better tolerated than monosomy.

In addition, some techniques such as FISH are far less sensitive at detecting microduplications than microdeletions, which may contribute to some going unidentified (although this is not the case for arrays, now more commonly used).

Question 9

Which factors influence reduced penetrance and variable expressivity in microdeletion/duplication syndromes?

Answer 9

1. Variable breakpoints
2. Differences in genetic background: additional variants (both common and rare) that modify expression
3. Unmasking of recessive variants on the second allele (or a “second hit” variant)
4. Epigenetic modifications, imprinting (e.g PWS/AS region)

Question 10

How has the discovery of microdeletion/duplication syndromes changed?

Answer 10

Early discoveries of microdeletion and microduplication syndromes relied on common clinical presentation (“phenotype-first” discovery), and the ability to detect chromosomal abnormalities by standard karyotype.

However many microdeletion/microduplications are relatively small (<5-10 Mb) and so would require high resolution banding, with many not visible at all (these would require detection by targeted methods e.g. FISH).

The switch to frontline microarrays (and increasingly, next generation sequencing) has since allowed more comprehensive and unbiased discovery of novel microdeletions and microduplications (including very rare rearrangements), with common phenotypic features identified after the fact.

Question 11

Give an example of disorders caused by reciprocal microduplication/microdeletion resulting from NAHR.

Answer 11

1) CMT1A and HNPP are caused by a reciprocal 1.4Mb duplication/deletion encompassing the dosage-sensitive PMP22 gene at 17p11.2. The recurrent deletion/duplication results from NAHR between two LCRs known as CMT1A-REPs. The two CMT1A-REP copies share 24,011bp of 98.7% sequence identity.
2) SMS and PTLS are caused by recurrent 3.7Mb deletion/duplications generated by NAHR between LCRs. Three ~250kb LCRs are present: distal (D), middle (M) and proximal (P) SMS-REPs. The SMS-REPM is inverted in orientation. The common ~4Mb del/dup occurs due to NAHR between the SMS-REPD and P. Smaller deletions occur by NAHR between the SMS-REPD and M.

Question 12

Give an overview of SMS, including incidence.

Answer 12

SMS is characterized by:

1. distinctive facial features (brachycephaly, broad face with synophrys and tented upper lip, brachydactyly),
2. short stature
3. developmental delay
4. cognitive impairment
5. hypotonia in infancy
6. behavioural abnormalities including sleep disturbance, sterotypies, tantrums and self-injurious behaviour.

SMS results from deletions of 17p11.2 (70% of those affected) as well as loss of function point mutations in the critical gene RAI1.
The incidence of SMS is estimated to be 1:25,000 births. Virtually all cases of SMS occur de novo.

Question 13

Give an overview of PTLS.

Answer 13

PTLS is a neurological disorder associated with mild intellectual disability, developmental delay, autistic features, hypotonia and failure to thrive in infancy. Most cases of PTLS result from de novo duplications of the same 17p11.2 region involved in SMS.

Question 14

Which microdeletion is associated with Williams syndrome? What is the mechanism underlying this recurrent deletion?

Answer 14

1) contiguous gene deletion of the Williams-Beuren syndrome critical region (WBSCR) at 7q11.23
2) ) that encompasses a number of genes implicated in the phenotype e.g. the elastin gene (ELN) is responsible for connective tissue abnormalities and CV disease.

The WBSCR is flanked by low copy repeats that predispose to NAHR. In 95% of individuals with WS the deletion comprises 1.55 Mb; in 5% it comprises 1.84 Mb. The size of deletion reflects which LCR blocks are involved

Question 15

What is the incidence of Williams syndrome

Answer 15

1 in 7500

Most cases are de novo occurrences, but occasionally, parent-to-child transmission is observed.

In approximately 25% of cases, the unaffected parent in whom the chromosome deletion originated has a paracentric inversion on chromosome 7 involving the WBSCR.

Question 16

What are the clinical features of Williams syndrome?

Answer 16

Williams syndrome (WS) is characterized by:

1. CVD (commonly supravalvar aortic stenosis, SVAS),
2. distinctive facies (‘elfin’)
3. connective tissue abnormalities
4. intellectual disability (usually mild),
5. overfriendly personality,
6. growth abnormalities
7. endocrine abnormalities.

Question 17

What is the incidence and clinical presentation of 7q11.23 microduplication syndrome?

Answer 17

Reciprocal to William deletion

1 in 7,500-20,000

1. Typical facial features include prominent and/or broad forehead, long eyelashes, low-hanging columnella of nose, short philtrum, high-arched palate, mild facial asymmetry, thin vermilion of the upper and lower lips, and retrognathia.
2. Severe impairment in expressive language in contrast to the relative strength in language exhibited by individuals with WS.

Question 18

What is the pathological mechanism underlying the 15q11-13 deletion in PWS?

Answer 18

PWS: 75% of patients with PWS have a paternal deletion (5-6Mb) which results from NAHR between complex >500kb LCRs.

Four large clusters of complex repeats have been termed BP1 to BP4.

The typical deletion is one of two sizes: extending from the distal breakpoint (BP3) to one of two proximal breakpoints (BP1 or BP2).

PWS is a contiguous gene disorder, with studies thus far indicating that the complete phenotype is due to the loss of expression of several genes (including SNURF-SNRPN, MKRN3, NDN, MAGEL2, C15orf2, PWRN1).

Question 19

What is the common deletion underlying DiGeorge syndrome?

Answer 19

The majority of affected individuals (85%) have a large (3Mb) deletion encompassing approximately 40 genes (including TBX1); a subset of individuals have a smaller atypical or ‘‘nested’’ deletion.

The deleted regions are flanked by LCRs (A-D).

Question 20

What proportion of 22q11 deletions are de novo?

Answer 20

About 93% of probands have a de novo deletion of 22q11.2 and 7% have inherited the 22q11.2 deletion from a parent. There is significant intrafamilial variability in expression and the deletion can be inherited from an apparently normal parent

Question 21

What is the prevalance and phenotype of DiGeorge syndrome?

Answer 21

The prevalence of 22q11.2 deletion syndrome has been estimated to range from 1:4000 to 1:6395, but given the variable expression, this may be an underestimate.

Very variable phenotype with any combination of the following: cardiac defects, thymic hypoplasia, cleft palate, learning difficulties, speech and language difficulties, hypocalcemia and a distinctive facial appearance.

Question 22

What cytogenetically abnormality is associated with Miller-Dieker syndrome? What is the distinctive clinical features?

Answer 22

MDS is a contiguous gene deletion syndrome of 17p13.3 characterised by lissencephaly, microcephaly and severe mental retardation.

The deletion may be cytogenetically visible or FISH visible and includes LIS1 and YWHAE genes.

Approximately 80% of individuals with MDS have a de novo deletion involving 17p13.3 and approximately 20% have inherited a deletion from a parent who carries a balanced chromosome rearrangement.

Question 23

What cytogenetically abnormality is associated with Langer-Giedion syndrome ? What is the distinctive clinical features?

Answer 23

LGS, also known as trichorhinophalangeal syndrome type II, is characterised by mild to moderate learning difficulties, fine sparse growing scalp hair, dystrophic brittle nails, short fingers with cone-shaped epiphyses, pear-shape bulbous nose and bony exotoses.

LGS is a rare contiguous gene deletion syndrome resulting from the loss of several genes at 8q24.

Loss of EXT1 is responsible for the multiple exotoses and loss of TRPS1 is thought to contribute to bone and craniofacial abnormalities.

Most cases of LGS arise from de novo deletions.

Question 24

What cytogenetically abnormality is associated with Wilms tumour-aniridia-genitourinary anomalies-mental retardation (WAGR) ? What are the clinical features?

Answer 24

WAGR is a contiguous gene deletion syndrome that results from deletions of 11p13 which include the genes PAX6 and WT1.

Loss of WT1 results in genitourinary abnormalities (often cryptorchidism in males) and renal anomalies, with high risk of developing Wilms tumour.

Loss of PAX6 is responsible for aniridia (absence of the iris) which is usually the first noticeable sign of WAGR.

Question 25

What cytogenetically abnormality is associated with Neurofibromatosis type 1 (NF1) ? What are the clinical features?

Answer 25

Neurofibromatosis 1 (NF1) is characterized by multiple café-au-lait spots, neurofibromata, learning difficulties and iris Lisch nodules.

NF1 is caused by heterozygous loss of function mutations in the NF1 gene at 17q11.2 as well as by an LCR-mediated 1.5Mb deletion that encompasses NF1 and other flanking genes and pseudogenes.

Question 26

Give two examples of terminal microdeletion syndromes.

Answer 26

1) Wolf-Hirschhorn syndrome - del 4pter

2) Cri-du-chat sydnrome - del 5pter

Question 27

What is the incidence of WHS?

Answer 27

1 in 50,000

About 50%-60% of individuals with WHS have a de novo pure deletion of 4p16 and about 40%-45% have an unbalanced translocation with both a deletion of 4p and a partial trisomy of a different chromosome arm.

Question 28

What are some of the clinical features of WHS?

Answer 28

1) Typical craniofacial features (‘Greek warrior helmet appearance’): broad bridge of the nose, microcephaly, high forehead, hypertelorism, epicanthus, highly arched eyebrows, short philtrum, downturned mouth, micrognathia, and poorly formed ears with pits/tags.
2) growth delay
3) developmental delay
4) intellectual disability of variable degree
5) seizures

Question 29

What is the incidence of CDC syndrome?

Answer 29

1:20,000 – 1:50,000

Most cases (85%) of Cri-du-chat result from a de novo deletion, with around 15% being the result of an unbalanced translocation.

Question 30

What are some of the clinical features of CDC syndrome?

Answer 30

1) Distinctive cat-like cry (due to anomalies of the larynx and epliglottis)
2) severe developmental delay/intellectual disability,
3) microcephaly, low birth weight
4) hypontonia in infancy and distinctive facial features including hypertelorism, low-set ears, small jaw and rounded face.