Abstracts

Rationale: Developmental Epileptic Encephalopathy (DEE) represents a heterogeneous group of conditions wherein cognitive and behavioural deterioration occurs as a consequence of frequent seizures or interictal epileptiform abnormalities or due to the underlying etiology. Techniques for next generation sequencing such as Whole Exome Sequencing (WES), covers 1-1.5% of the human genome comprising of around 20000 genes facilitates the identification of familial or denovo pathogenic variants using a family trio design. Global Screening Array (GSA) consists of 6,54,027 markers including single nucleotide variants, small insertions and deletions and Copy Number Variants, to detect rare Mendelian mutations. In this study we performed a comparative analysis of WES with GSA to assess the cost effectiveness, genetic diagnosis yield and to characterize the molecular findings and inheritance patterns in patients with well-defined DEE phenotypes analysed in trios.

Methods: Genomic DNA extracted from peripheral blood sample of 4 probands and their biological parents were used for WES and GSA analysis. WES was done with Illumina Exome Sureselect Agilent V6 method and Infinium Global screening array-24 V3 beadchip was used to identify clinically relevant markers in trios. The Data were analysed using different bioinformatic tools and customised in house pipelines and annotated with publicly available databases to identify the risk variants associated with DEE. The variants were classified based on American College of Medical Genetics and Genomics (ACMG) classification criteria. Yield was considered based on identification of pathogenic/likely pathogenic variants and variants of unknown significance were documented.

Results: An average of 6,39,813 variants from GSA and 195,357 variants from WES were identified in 4 probands with DEE phenotypes of West Syndrome, Lennox Gastaut syndrome epilepsy, symptomatic myoclonic epilepsy and encephalopathy with continuous spike wave in sleep. Only an average of 12,112 variants were present in common for both GSA and WES which includes 4223 exonic variants, 5427 intronic variants, 27 splicing variants and remaining intergenic/3’UTR/5’UTR variants. The diagnostic yield of pathogenic variants from WES is 75% (3/4) and from GSA analysis is 25% (1/4) with a denovo variant identified by both techniques (Table 1). The cost of GSA ($66) compared favourably to WES ($342) which is 5 times more expensive.

Conclusions: Despite a wider coverage of genetic markers with GSA, the WES technique in trios does seem to suggest a higher yield in children suspected with DEE when compared to GSA in trios. Although WES in trios is more effective in identifying point mutations, a denovo variant could be identified by both techniques. In our study of rare DEE phenotypes of uncertain etiology, GSA has the extra advantage of reducing costs required to process a large number of samples. Larger comparative studies with segregation analyses are likely to throw further light on the preferred cost-effective approach to genetic analysis of DEE, especially from a low middle income country perspective.

Funding: Please list any funding that was received in support of this abstract.: Indian Council of Medical Research(ICMR) grant No.5/7/1658/CH/Adhoc/2019-RBMCH.