Table 2.
Genetic testing performed at our institution.
| Genetic Test | Number of patients | Number of tests | Positive 1 N (%) | Negative 1 N (%) | VUS N (%) | No result N (%) |
|---|---|---|---|---|---|---|
| FISH | 7 | 8 | 1 (13%) | 7 (88%) | 0 (0%) | 0 (0%) |
| Karyotype | 42 | 44 | 7 (16%) | 36 (82%) | 0 (0%) | 1 (2%) |
| Chromosomal microarray2 | 82 | 84 | 14 (17%) | 46 (55%) | 24 (29%) | 1 (1%) |
| Chromosomal deletion/duplication test | 14 | 14 | 3 (21%) | 11 (79%) | 0 (0%) | 0 (0%) |
| Single gene sequencing2,3 | 70 | 122 | 18 (15%) | 97 (80%) | 11 (9%) | 0 (0%) |
| Single gene or gene panel deletion/duplication | 29 | 36 | 3 (8%) | 28 (78%) | 2 (6%) | 3 (8%) |
| Methylation analysis | 4 | 4 | 0 (0%) | 3 (75%) | 0 (0%) | 1 (25%) |
| Gene panel2,4 | 45 | 49 | 7 (14%) | 29 (59%) | 14 (29%) | 1 (2%) |
|
Mitochondrial genetic testing2 (nuclear gene panel or mitochondrial genome) |
10 | 12 | 1 (8%) | 6 (50%) | 6 (50%) | 0 (0%) |
| Clinical exome sequencing | 14 | 14 | 6 (43%) | 4 (29%) | 4 (29%) | 0 (0%) |
| Research exome/genome sequencing5 | 16 | 17 | 6 (35%) | 8 (47%) | 36 (18%) | 0 (0%) |
Testing performed elsewhere included FISH for 20 infants, karyotype for 45, chromosomal microarray for 45, single gene tests for 12, gene panels for 13, deletion/duplication tests for 9, methylation studies for 5, mitochondrial genetic tests for 3, and ES for 6.
“Positive” includes pathogenic or likely pathogenic variants (one infant had a positive result indicating a diagnosis via two different testing modalities at our institution); “Negative” includes benign/likely benign variants and results indicating carrier status or that are nondiagnostic (e.g. Robertsonian translocation without aneuploidy, secondary findings from ES, carrier of one pathogenic variant for a recessive condition).
Test could have more than one category of result (e.g. one pathogenic variant and one VUS).
Includes targeted mutation analysis and sequencing of select exons.
Includes sequencing and deletion/duplication panels, which are often combined as a single test. Gene tests ordered as a panel but that resulted individually were counted as separate single gene tests.
Additionally, one patient had research single gene sequencing with a positive result.
Candidate novel disease genes.