A 2.3kb whole gene deletion of FOXG1 detected using the BlueGnome Cytochip ISCA (v2.

0) 8x60k oligo array

SIAN JOSE, Sian M Morgan, Annie Procter, Andrew Fry and Peter Thompson.
Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK.

INTRODUCTION
Rett syndrome is a severe neurodevelopmental disorder that is caused by mutation of the MECP2 gene at Xq28. It is characterised by a period of normal development in early life, followed by developmental regression, characteristic hand movements, seizures and severe mental retardation. Variants of Rett syndrome have been described based on differences in clinical phenotype, such as the severe infantile encephalopathy variant, characterised by early onset seizures and caused by mutations in CDKL5. Another variant Rett syndrome phenotype has been described, referred to in the literature as the congenital variant of Rett syndrome, in which patients do not seem to have the period of normal development characteristic of classical Rett syndrome but instead manifest symptoms from birth. Here we present a patient with congenital variant Rett syndrome who was found to have a 2.3kb deletion at 14q12 consistent with a whole gene deletion of the Forkhead box G1 (FOXG1) gene. This is the smallest array CGH imbalance to date reported by our laboratory.

FOXG1
In 2008, Ariani et al published a paper describing a 3 year old female with a Rett like phenotype and a de novo, 3Mb deletion at 14q12 including the FOXG1 gene. This gene encodes a brain-specific transcription factor that is critical for forebrain development. Since then there have been several papers describing deletions and mutations of FOXG1 in patients with a congenital Rett syndrome phenotype.

PATIENT HISTORY
This patient was first referred to the Genetics Service for assessment in 2008 at age 5 months because of developmental delay, microcephaly and gastro-oesophageal reflux. A normal G-band analysis was reported at this time In 2009, sequence analysis of MECP2 and CDKL5 was carried out. The results for both were normal. In 2011, the patient had further G band analysis with increased counts, as well as MLPA analysis for congenital Rett syndrome. MLPA testing was carried out using the FOXG1/TCF4 P075A1 kit from MRC Holland. Array CGH analysis was carried out in late 2011 using the BlueGnome CytoChip ISCA (v2.0) 8x60k oligo array and analysed using BlueFuse Multi (v2.4) with base pair positions based on NCBI build 36. Test DNA was referenced against same sex control DNA.

TABLE 1: PHENOTYPIC FEATURES REPORTED IN ASSOCIATION WITH FOXG1 MUTATIONS

Kortum F et al, Kortum F et al, Jacob FD et al, Ariani F et al, 2011 2011 2009 2008 Disease aetiology No. patients Prenatal microcephaly Postnatal microcephaly Profound mental retardation Absent speech Seizures Gastro-oesophageal reflux Hypoplastic corpus callosum Stereotypic movements Dyskinesia Disturbed sleep Dysmorphism FOXG1 mutation 11 Y Y Y Y Y Y Y Y Y
Dysregulation of gene expression Deletion (3Mb) Deletion (3Mb)

Our patient Deletion (2.3kb) 1 Y Y Y Y Y Y Y Y Y Y

1 Y Y Y Y Y Y

1 Y Y Y Y Y Y

1 Y Y Y Y

Y Y Y Y

Y Y Y Y

RESULTS MLPA
Chart showing MLPA calls using the FOXG1/TCF4 P075_A1 kit
1.2

ARRAY CGH
aCGH showed a deletion of 2.3kb at 14q12: arr 14q12(28,306,275-28,308,564)x1

0.8

0.6

This is consistent with a whole gene deletion of FOXG1

0.4

0.2

MLPA showed a heterozygous whole gene deletion of FOXG1. Further MLPA studies showed that this deletion had arisen de novo

CONCLUSION
This is the smallest whole gene deletion of FOXG1 reported to date in the literature, and the smallest copy number change reported by our laboratory. This is supported by data from DECIPHER where overlapping patients were reported to have much larger losses (2.9Mb-19.1Mb). As can be seen in table 1, some phenotypic features are common to all patients reported in the literature, namely postnatal microcephaly, profound mental retardation, absent speech and seizures, which are also present in our patient. The consistency and similarity of phenotypic features in patients with FOXG1 aberrations supports a FOXG1 core phenotype as suggested by Kortum F et al, 2011. There does not seem to be a strong genotype phenotype relationship depending on the aetiology of the syndrome, although dysmorphism seems to be recorded more frequently in deletion cases. The finding in this case demonstrate the power of oligonucleotide array CGH in the diagnostic laboratory and emphasises the potential increased resolution for analysis that is now possible if there is sufficient published literature to support interpretation.
REFERENCES Ariani F, Hayek G, Rodinella D et al (2008). FOXG1 Is Responsible for the Congenital Variant of Rett Syndrome. Am J Hum Genet. 83, 89-93. Jacob FD, Ramaswamy V, Andersen J and Bolduc FV (2009). Atypical Rett syndrome with selective FOXG1 deletion detected by comparative genomic hybridization: case report and review of the literature. Eur J Hum Genet. 17, 1577-1581. Kortum F, Das S, Flindt M et al (2011). The core FOXG1 syndrome phenotype consists of postnatal microcephaly, severe mental retardation, absent language, dyskinesia and corpus callosum hypogenesis. J Med Genet. 48, 396-406.