Table 1.

Clinically available genetic testing modalities in epilepsy

Test	Scope	Indication	Advantages	Disadvantages
CMA	Targeted and untargeted (includes known disease loci as well as a survey across the chromosomes)	Unexplained epilepsy, especially with intellectual disability and/or autism Suspected chromosomal microdeletion or duplication syndrome	Simultaneous targeted and untargeted approach May provide information about regions of homozygosity in consanguineous individuals, thereby possibly suggesting specific genes Relatively fast (few weeks)	Rarely, can miss a chromosomal rearrangement such as a ring chromosome abnormality, but high-resolution clinical CMA typically detects small deletions at the site of rearrangements
Karyotyping	Untargeted	Suspected monosomy, trisomy or chromosomal rearrangement; maternal history of recurrent pregnancy losses; generally recommended if strong suspicion and CMA result is negative	Fast (few days)	Lower resolution than CMA
Single-gene testing	Targeted	Syndromes usually associated with specific gene(s)	Faster and less expensive than gene-panel testing	Not all commercially available tests include deletion and duplication testing as well as sequencing
Gene-panel testing	Semi-targeted	Syndrome associated with several epilepsy-related genes, or syndrome not clearly related to specific gene	If several genes may be candidates for a syndrome, this option is more time-efficient than serial single-gene testing, and faster than WES and WGS	Not all commercially available tests include deletion and duplication testing, as well as sequencing Expensive
WES	Untargeted (but analysis should include targeted examination of specific genes of interest)	Epilepsy syndrome without specific gene associations	Currently, difficult to derive copy number information from WES data	Incidental findings Expensive Coverage of specific genes not guaranteed because of limitations in capture technology
WGS	Untargeted (but analysis should include targeted examination of specific genes or regions of interest)	Epilepsy syndrome without specific gene associations	Also enables evaluation for copy number abnormalities	Incidental findings Expensive Not yet covered by insurance

Abbreviations: CMA, chromosomal microarray analysis; WES, whole exome sequencing; WGS, whole genome sequencing.