Table 2.
AMP/TSCA Performance on 1° and 2° ITDs
| MGH cohort (AMP) | NGS ITDs in total | Same size as 1° CE (total 1° CE ITDs) | Same size as 2° CE (total 2° CE ITDs) | Other size | Unknown size |
|---|---|---|---|---|---|
| Custom FLT3-ITD | 80 | 42 (42) | 17 (17) | 21 | 0 |
| Clinical NGS calls | 22 | 15 (42) | 3 (17) | 4 | 0 |
| Novoalign unfiltered | 39 | 23 (42) | 8 (17) | 8 | 0 |
| BWH cohort (TSCA) | |||||
| Custom FLT3-ITD | 72 | 48 (54) | 17 (20) | 3 | 4 |
| Clinical NGS calls | 53 | 34 (54) | 3 (20) | 12 | 4 |
| AML cohort (TSCA) | Same size as 1° HC (total 1° HC ITDs) | Same size as 2° HC (total 2° HC ITDs) | |||
|---|---|---|---|---|---|
| Custom FLT3-ITD | 7 | 5 (5) | 2 (2) | 0 | 0 |
| Clinical NGS calls | 5 | 3 (5) | 2 (2) | 0 | 0 |
The sensitivity of the custom FLT3-ITD algorithm and clinical standard pipelines within clinical NGS panels (AMP and TSCA) to detect ITDs of the same size as CE or HC was the highest (100%) when applying the custom algorithm to the MGH AMP data. The ability to detect the primary ITD is particularly important because it contributes the most to an assessment of overall allelic ratio.
1°, Primary; 2°, secondary; AML, acute myeloid leukemia; AMP, anchored multiplex PCR; BWH, Brigham and Women's Hospital; CE, capillary electrophoresis; HC, hybrid-capture; ITD, internal tandem duplication; MGH, Massachusetts General Hospital; NGS, next-generation sequencing; TSCA, TruSeq Custom Amplicon.