Table 4.

Different methods of genetic testing

Technology	Strengths	Limitations	Example diagnostic application
Sequencing approaches
Sanger sequencing	Accuracy Low cost per reaction	Not scalable Insensitive to large SVs	Single gene test Single variant testing—for a pre-specified variant during cascade family evaluation
Panel sequencing	Balances reasonably comprehensive coverage (e.g. all genes associated with a particular phenotype) against cost Often highly optimized for complete and uniform capture of region of interest	Usually exonic only Needs updating as knowledge changes (e.g. new gene-disease associations discovered)	First line diagnostic test for proband
WES	Comprehensive coverage of all genes Off-the-shelf design Can run a single wet-lab workflow, and introduce specificity at analysis stage Can update analysis to incorporate new knowledge without regenerating data—adaptable Enables analyses for secondary findings	Larger target requires more sequencing (c.f. panels) May be less optimized than more focused panel More costly and complex to store and process data (c. 10–100× more data than panel) Will not detect non-coding variants May not detect all variant classes	Diagnosis in proband for very heterogeneous conditions (e.g paediatric and syndromic cardiomyopathies) Second line test if panel negative in specific circumstances, for example with informative family structure
WGS	Comprehensive genetic characterization—all genes, all elements, all variant types Will also detect common variants for PRS, pharmacogenetics and other applications Enables analyses for secondary findings	More costly and complex to store and process data (∼100× more data than WES)	Diagnosis in proband for very heterogeneous conditions Second line test if panel negative Definitive and future-proof genetic characterization if funds permit—e.g. hold data in medical record for iterative targeted interpretation according to clinical needs
Non-sequencing approaches
Allele-specific PCR	Quick, cheap, accurate	Pre-specified variants only	Testing a single variant in a large family (more likely Sanger sequencing now)
Array comparative genomic hybridization	Cheap screening for SVs/CNVs High-resolution (compared with cytogenetic approaches)	Insensitive to other variant classes	Screening for structural variants, including aneuploidy, e.g. in structural congenital heart disease
Droplet digital PCR	Low cost, high-sensitivity, detection of genome dose for SV/CNV detection at a pre-specified locus	Scalability limited by multiplexing of pre-specified PCR amplicons targeting regions of interest	Confirmation of putative CNVs detected in high-throughput sequence data
DNA SNP arrays	Genome wide Relatively cheap	Pre-specified variants only Accuracy poor for many rarer variants	Recreational ancestry analysis Polygenic risk Pharmacogenetics

CNV, copy number variant; PCR, polymerase chain reaction; PRS, polygenic risk score; SNP, single-nucleotide polymorphism; SV, structural variant; WES, whole-exome sequencing; WGS, whole-genome sequencing.