Table 3.
Test Set Specimens
| Blocka | Diagnosis | Highest Amyloid Protein Above Cutoffb | Other Amyloidogenic Proteinsc | λ/κd | LC-MS/MS Typing |
|---|---|---|---|---|---|
| 1 | ATTR | TTHY (0.06466, 610%) | ATTR | ||
| 2 | ACal | CALCA (0.05698, NA e ) | APOA4 (0.04200) | ACal | |
| IGKC (0.01950) | |||||
| 3 | AL(κ) | IGKC (0.06541, 187%) | 0.1 | AL(κ) | |
| 4 | AL(κ) | IGKC (0.05909, 169%) | 0.1 | AL(κ) | |
| 5 | Amyloid type indeterminate | LAC (0.06485, 414%) | APOA1 (0.01413) | 2.2 | AL(λ) |
| IGKC (0.02995) | |||||
| 6 | AA | SAA1 (0.04145, 345%) | AA type | ||
| 7 | AL(λ) | None | LAC (0.01483, 95%) | 0.9 | AL(λ) |
| 8* | FGN | NA | NA | FGN (DNAJB9 detectedf) | |
| 9* | ALECT2 | LECT2 (0.00274, 762%) | ALECT2 | ||
| 10 | AL(λ) | LAC (0.03176, 203%) | 2.5 | AL(λ) | |
| 11 | AL(λ) | LAC (0.02729, 174%) | 10.7 | AL(λ) | |
| 12* | ATTR | TTHY (0.19490, 1,839%) | IGKC (0.01869) | ATTR | |
| 13* | AL(λ) | None | TTHY (0.00990) | 0.6 | AL (λ) |
| LAC (0.01285, 82%) | |||||
| IGKC (0.02156) | |||||
| 14* | AL(λ) | LAC (0.02488, 159%) | 1.1 | AL(λ) | |
| 15 | AA type | SAA1 (0.02289, 191%) | AA type | ||
| 16 | AL(λ) | None | LAC (0.01038, 66%) | 1.3 | AL (λ) |
| 17 | AA-type | SAA1 (0.073963, 616%) | IGKC (0.01939) | AA type | |
| 18 | AL(λ) | LAC (0.01811, 116%) | 15.5 | AL(λ) | |
| 19 | AL(λ) | LAC (0.03816, 244%) | 4.7 | AL(λ) | |
| 20 | AL(κ) | None | IGKC (0.01968, 56%) | 0.0 | AL(κ) |
| 21 | AL(λ) | None (PEVAC inadequate) | NA | ||
| 22 | AA type | SAA1 (0.03080, 257%) | IGKC (0.03776) | AA type | |
| LAC (0.01012) | |||||
| 23 | AA type | SAA1 (0.14968, 1,247%) | AA type | ||
| 24 | AL(λ) | None | LAC (0.01476, 94%) | 3.1 | AL(λ) |
| SAA1 (0.00734) | |||||
| 25 | FGN | NA | NA | FGN (DNAJB9 detectedf) | |
| 26 | AL(λ) | None | LAC (0.00809, 52%) | 1.6 | AL(λ) |
| 27 | Amyloid type indeterminate | TTHY (0.02464, 232%) | APOA1 (0.017062) | ATTR type | |
| LAC (0.01988) | |||||
| IGKC (0.04088) |
AA, serum protein A type; ACal, calcitonin type; ALECT2, LECT2 type; AL(κ), κ light chain type; AL(λ), λ light chain type; APOA4, apolipoprotein A-IV (UniProt P06727); ATTR, transthyretin type; CALCA, calcitonin gene–related peptide 1 (UniProt P06881); DNAJB9, DnaJ heat shock protein family member B9 (UniProt Q9UBS3); FGN, fibrillary glomerulonephritis; IGKC, immunoglobulin κ constant (UniProt P01837); LAC, λ constant region (UniProt entry P0CG04, P0CG05, P0CG06, P0CF74, or A0M8Q6); LC-MS/MS, liquid chromatography–tandem mass spectrometry; LECT2, leukocyte cell–derived chemotaxin 2; NA, not applicable; SAA1, serum amyloid A-1 (UniProt P0DJI8); PEVAC, serum amyloid P, apolipoprotein E, victronectin, apoliprotein A4, and clusterin; TTHY, transthyretin (Uniprot P02766).
aFive of 27 formalin-fixed, paraffin-embedded blocks were reevaluations (*) of cases included in the training set. All blocks above reflected unique cases/patients.
bAmyloidogenic protein with highest normalized spectral abundance factor (NSAF) relative to its 100% specificity threshold (bolded, if a protein met this criteria). Values in parentheses are the actual NSAF result and its proportion compared to the cutoff, expressed as a percentage: (NSAFResult / NSAFCutoff) * 100%.
cOther amyloidogenic proteins measured with NSAF of at least 50% of its 100% specificity cutoff.
dLess than 0.30 favors κ type; more than 0.30 favors λ type.
eAn ACal case was only encountered in the test set. CALCA protein was not detected in any other samples from the training or test set, and thus the proportion of the NSAF result to a specificity cutoff cannot be calculated.
fNon–Congo red positive but subjected to similar processing for the detection of DNAJB9 and confirmation of FGN. For case 8, average NSAF of DNABJ9 was 0.00367 (5,241% of cutoff). For case 25, DNAJB9 NSAF was 0.0091379839 (13,054% of cutoff).