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Keywords: Chromosomal deletions; Copy number/structural variation; FISH; Genetic testing; Diagnostics

D.M. Ranaweera 1; D.C. de Silva 2; N. Panchananthan 1; M. Kajan 1; D. Samarasinghe 3; S. Perera 3; R. Morawakkorala 3; S. Gunewardene 4; N.V. Chandrasekharan 1

1) Department of Chemistry, University of Colombo, Colombo 3, Sri Lanka; 2) Department of Physiology, University of Kelaniya, Sri Lanka; 3) Lady Ridgeway Children’s Hospital, Colombo 8, Sri Lanka; 4) Department of Physics, University of Colombo 3, Sri Lanka

Introduction: Williams-Beuren syndrome (WBS), caused by the loss of 23 genes including elastin (ELN) on chromosome 7q11.23, is associated with heart malformations, developmental delay, hypercalcaemia and characteristic facies. Genetic testing enables confirmation of diagnosis, improves management and genetic counselling. Sri Lanka (average household income $115/month) has a free health service but genetic testing costs are borne by parents, making it mostly unaffordable.

Materials and Methods: Suspected WBS cases (n=24) were recruited following ethical clearance and informed consent. Molecular diagnosis was performed using semi quantitative polymerase chain reaction (semiqPCR) (target ELN; control CFTR), quantitative PCR (qPCR) (target ELN; control TES) using dyes SYBR green and EvaGreen; 10 results (n=10) validated by fluorescent in-situ hybridization.

Results: Among 19/24 (79%) clinically typical cases, an ELN deletion was identified by semiqPCR and qPCR. Nine cases had their diagnosis confirmed by FISH. Five clinically atypical cases were not found to have a deletion (2 familial cases, one isolated SVAS, two unknown) on semiqPCR and qPCR (EvaGreen dye). There was a discrepancy for two patients with qPCR (SYBR green dye): one duplication (FISH negative); one deletion (parents declined FISH). The cost of consumables for semiqPCR, qPCR and FISH was around $6, $7 and $225 respectively.

Conclusion: The semiq and qPCR using EvaGreen, although not the gold standard, appear to offer a molecular diagnostic test that is more affordable for Sri Lankan families and when used with clinical data, is a useful diagnostic tool in a resource limited healthcare setting.

Acknowledgements- University of Colombo Research Grant AP/3/2/2014/RG/02