Martina Owens 19.11.10

1. Explain the term ‘contiguous gene deletion syndrome’. Use examples to describe the phenotypic effects of such deletions (excluding imprinted genes). Outline the methods available for identifying contiguous gene deletions. Martina Owens 19.11.10

2. Essay Plan • Definition • Examples of contiguous gene deletion syndromes • X-linked • 1p36, Williams, Langer-Gideon, WAGR, Miller-Dieker, Smith Magenis, 22q11 • Methods available for identifying contiguous gene deletions • FISH, MLPA, aCGH, qPCR

3. Definition • A syndrome caused by a microdeletion that spans two or more genes tandemly positioned along a chromosome • Genes are generally not functionally linked • Phenotype observed is the result of a loss of the genes within the deletion

4. Examples of Contiguous Gene Deletions – Microdeletion syndromes

5. X chromosome deletions Microdeletions are relatively frequent at Xp21 and Xq Classic case: boy BB who had DMD, chronic granulomatous disease, retinitis pigmentosa and mental retardation BB had a deletion of in Xp21 that removed a contiguous set of genes and incidentally led to the identification of the DMD and CGD genes

6. Williams syndrome: clinical features • Characterised by: • Cardiovascular disease (elastin arteriopathy) - supravalvular aortic stenosis most common finding • Distinctive facies - "elfin" facial appearance with a low nasal bridge • Connective tissue abnormalities • Mental retardation • Specific cognitive profile - strengths in verbal short-term memory and language and extreme weakness in visuospatial construction are typical • Unique personality - affable and hyperverbal in childhood but become withdrawn in adulthood • Growth abnormalities • Endocrine abnormalities - hypocalcaemia (15%), hypercalciuria (30%), hypothyroidism (10%), and early (but not precocious) puberty (50%) Neurodevelopmental disorder due to microdeletion at 7q11

7. Williams syndrome: clinical features • Characterised by: • Cardiovascular disease (elastin arteriopathy) - supravalvular aortic stenosis most common finding • Distinctive facies - "elfin" facial appearance with a low nasal bridge • Connective tissue abnormalities • Mental retardation • Specific cognitive profile - strengths in verbal short-term memory and language and extreme weakness in visuospatial construction are typical • Unique personality - affable and hyperverbal in childhood but become withdrawn in adulthood • Growth abnormalities • Endocrine abnormalities - hypocalcaemia (15%), hypercalciuria (30%), hypothyroidism (10%), and early (but not precocious) puberty (50%) Neurodevelopmental disorder due to microdeletion at 7q11

8. Williams syndrome: clinical features • Characterised by: • Cardiovascular disease (elastin arteriopathy) - supravalvular aortic stenosis most common finding • Distinctive facies - "elfin" facial appearance with a low nasal bridge • Connective tissue abnormalities • Mental retardation • Specific cognitive profile - strengths in verbal short-term memory and language and extreme weakness in visuospatial construction are typical • Unique personality - affable and hyperverbal in childhood but become withdrawn in adulthood • Growth abnormalities • Endocrine abnormalities - hypocalcaemia (15%), hypercalciuria (30%), hypothyroidism (10%), and early (but not precocious) puberty (50%) Neurodevelopmental disorder due to microdeletion at 7q11

9. Williams syndrome: genotype-phenotype Incidence: 1 in 7,500 to 20,000 live births 1.55Mb deletion of ~ 26 genes (95% cases) or 1.84Mb (5% cases) (Bayes et al 2003)

10. Phenotype variable depending on size of deletion The Williams critical region is flanked by low copy repeats that predispose to homologous recombination Approximately 25-30% of cases, unaffected parent in whom the chromosome deletion originated has an inversion on chromosome 7 involving the WBSCR (Osborne et al 2001, Bayes et al 2003) Approximately 6% of the general population also have this inversion polymorphism (Hobart et al 2004).

11. 1p36 deletion syndrome: clinical features • characterized by: • typical craniofacial features • straight eyebrows with deep-set eyes • midface hypoplasia with broad and flat nasal root/bridge • long philtrum • pointed chin • large, late-closing anterior fontanel (77%) • microbrachycephaly (65%) • epicanthal folds (50%) • posteriorly rotated, low-set, abnormal ears. • developmental delay/mental retardation of variable degree (100%) • hypotonia (95%) • seizures (44-58%) • structural brain abnormalities (88%) • congenital heart defects (71%) • eye/vision problems (52%) • hearing loss (47%) • skeletal anomalies (41%) • abnormalities of the external genitalia (25%) • renal abnormalities (22%)

12. 1p36 deletion syndrome: genotype-phenotype Incidence: 1 in 5,000 to 1 in 10,000 live births with a with a 2:1 female to male ratio • Size of the deletion varies among affected individuals – results in variability of symptoms between patients • >100kb (>95%) • >5Mb (~25%)

13. Langer-Giedion syndrome: clinical features Autosomal dominant disorder • Characterized by: • intellectual deficit • redundant skin • multiple cartilaginous exostoses - affects mainly the extremities of the long bones • characteristic facies • bulbous nose • wide prominent philtrum and thin upper lip • abnormal ears • sparse hair • small mandible • cone-shaped phalangeal epiphyses. • Growth retardation, microcephaly, hypotonia and hearing problems have also been reported. • Prevalence is unknown

14. Langer-Giedion syndrome: genotype-phenotype Caused by a microdeletion in chromosome 8q23.3-q24.13 leading to the loss of at least two genes: TRPS1 and EXT1 • EXT1 • encodes an endoplasmic reticulum-resident type II transmembrane glycosyltransferase involved in the chain elongation step of heparan sulphate biosynthesis • mutations in this gene cause the type I form of multiple exostoses TRPS1 • transcription factor that represses GATA-regulated genes • plays a role in regulating growth of bone and cartilage • loss of functional TRPS1 protein contributes to short stature, cone-shaped ends of the long bones (epiphyses), and distinctive facial features in people with Langer-Giedion syndrome

15. WAGR syndrome: clinical features • Affected children are predisposed to develop • Wilms tumour (a tumour of the kidneys) (45%) • Aniridia (absence of the iris) • - Identified in neonatal period. ~1/3 patients with sporadic aniridia will have WAGR • Genitourinary anomalies • mental Retardation Subset of WAGR syndrome patients shows severe childhood obesity (WAGRO) Incidence: <1/100,000

16. WAGR syndrome: genotype-phenotype Due to a microdeletion in the 11p13 region of chromosome 11 WAGRO patients have a deletion involving 11p14-p12

17. Miller-Dieker syndrome: clinical features Autosomal dominant congenital disorder characterised by a developmental defect of the brain, caused by incomplete neuronal migration. Clinical features: • lissencephaly (‘smooth brain’) • microcephaly (normal at birth) • wrinkled skin over the glabella and frontal suture • prominent occiput • downward slanting palpebral fissures • small nose and chin • cardiac malformations • hypoplastic male external genitalia • growth retardation, and mental deficiency with seizures and EEG abnormalities • Life expectancy is grossly reduced, with death most often occurring during early childhood

18. Miller-Dieker syndrome: genotype-phenotype Caused by a deletion of 17p13.3 ~50% have a microscopically visible deletion, and the remainder have a submicroscopic deletion Deletions of PRP8, RILP, SREC, PITPNα, SKIP, MYO1C have also observed in MDS patients

19. Smith-Magenis syndrome: clinical features • Characterized by: • distinctive facial features that progress with age • developmental delay • mild-moderate mental retardation • cognitive impairment • behavioural abnormalities • - significant sleep disturbance • - stereotypies • - maladaptive and self-injurious behaviours Infants have feeding difficulties, failure to thrive, hypotonia, hyporeflexia, prolonged napping and generalized lethargy. Incidence: 1 in 25,000

20. Smith-Magenis syndrome: genotype-phenotype MS critical region maps to 17p11.2 and spans less than 650 kb 17p11.2p12: one of the most recombination-prone regions of the genome Low-copy number repeats (proximal, middle, and distal SMS REPs) flanking the common deletion region form substrates for inter- and intrachromosomal recombination All SMS patients with a 17p11.2 deletion are deleted for RAI1 (~10% patients have a mutation in RAI1) Regulates transcription through chromatin remodelling by interacting with other proteins in chromatin as well as proteins in the basic transcriptional machinery. May be important for embryonic and postnatal development. Possible role in neuronal differentiation

21. Smith-Magenis syndrome: genes involved RAI1: responsible for most SMS features - other genes in the 17p11.2 region contribute to the variability and severity of the phenotype in 17p11.2 deletion cases Patients with the 17p11.2 develop cardiovascular and renal/urinary tract abnormalities compared to patients with a mutation in RAI1 17p11.2p12 is also associated with hereditary neuropathy with liability to pressure palsies (HNPP) and Charcot–Marie–Tooth disease type 1A

22. 22q11.2 deletion syndrome: clinical features • Variable phenotype that includes a combination of: • Congenital heart disease (particularly conotruncal malformations) (74%) • Palatal abnormalities (69%) • Characteristic facial features (~100% - may be subtle) • Hypocalcaemia (~50%) • Learning difficulties (90%) • Skeletal abnormalities (e.g. polydactyly) • Genitourinary tract anomalies (e.g. renal agenesis) (37%) • Severe dysphagia (30%) • Growth hormone deficiency • Autoimmune disease (thrombocytopenia, juvenile rheumatoid arthritis, vitiligo, neutropenia, hemolytic anaemia) • Hearing loss (sensorineural and conductive) (77%) • Psychiatric illness (~50%) DiGeorge: identified in the neonatal period with congenital heart defect, hypocalcaemia and immunodeficiency VCFS: velopharyngeal incompetence, congenital heart disease, characteristic facial features and dev delay Incidence: 1 in 4,000 live births

23. 22q11.2 deletion syndrome: genotype-phenotype Up to 90% of DiGeorge patients and ~100% of Velocardiofacial syndrome patients have a hemizygous deletion of 22q11.2 Deletion is linked to low copy number repeats (LCR A-D) Unequal meiotic exchange is the dominant mechanism of deletion

24. 22q11.2 deletion syndrome: genotype-phenotype • TBX1: • probably responsible for many of the syndrome's characteristic signs (heart defects, cleft palate, distinctive facial features, hearing loss, hypocalcaemia and possibility behavioural problems). • important roles in the formation of tissues and organs during embryonic development (especially muscles and bones of the face and neck, large arteries that carry blood out of the heart, structures in the ear, and glands such as the thymus and parathyroid) • COMT1: • enzyme involved in the metabolic degradation of catecholamines • increased risk of behavioural problems and psychiatric problems

25. Methods available for identifying contiguous gene deletions • FISH: • commercially available probes for most deletion • may have difficulties detecting small deletions • may be difficult to characterise the deletion for syndromes associated with variable deletions • MLPA: • commercially available kits available • ‘microdeletion syndrome’ and ‘mental retardation’ kits available to test for >1 syndrome • can be confirmed using FISH probes • aCGH: • important in diagnosing cases with unknown genetic aetiology • qPCR: • Copy number of individual genes

26. References GeneTests (www.ncbi.nlm.nih.gov/sites/GeneTests) Kang S-HL et al, 2007, Clin Genet: 72: 329–338 (1p36) Kobrynski et al, 2007, The Lancet: 370: 9596 (22q11) Fischbach et al, 2005, Pediatrics; 116: 984-988 (WAGR)