Table 3.
Considerations and next steps after nondiagnostic clinical exome sequencing
| Type of variant | Action that can be taken |
|---|---|
| Small CNV not detectable by ES | Exon-level array may identify small CNVs. Alternatively, srGS or lrGS may detect small CNVs. |
| Regulatory variant located in a region not captured by ES | Depending on the specificity of the phenotype, consider more-targeted gene testing that includes sequencing of regulatory regions or srGS; consider RNA-seq or epigenetic signature testing. |
| Deep intronic variant that affects splicing | Consider a panel that may include known intronic variants. Either srGS, lrGS, or RNA-seq can also be used to identify or confirm the variant. |
| Variant in a gene not previously associated with the phenotype, not assessed and/or reported because of laboratory analysis and/or reporting criteria | Consider submission to Matchmaker exchange61 and referral to research group or consortia who can conduct a broader, gene discovery-oriented analysis (e.g., flag putatively deleterious variants in genes not previously associated with human disease and identify additional cases who harbor variants in this candidate gene). |
| Structural variant not detected by ES (e.g., a complex rearrangement or inversion) | OGM, srGS, or lrGS can be used to identify and clarify SVs missed by exome sequencing. |
| Repeat expansion | Depending on the specificity of the phenotype, consider a disease-targeted panel/gene testing or srGS or lrGS with repeat expansion detection. |
| Variants that cannot be phased | If parental samples are not available or a variant is de novo, then clinical srGS may phase if variants are close enough together. If not, either mate-pair sequencing or lrGS can be used. |
| Mosaic variants | Discuss reporting criteria and technical thresholds for variant calling with laboratory. If there is strong clinical suspicion for a specific genetic disease, consider targeted testing with higher sequencing depth. Consider high-depth exome sequencing; multiple-tissue/multiple-sample sequencing. |
ES, exome sequencing; CNV, copy-number variant; SV, structural variant; OGM, optical genome mapping; srGS, short-read genome sequencing; lrGS, long-read genome sequencing.