Table 1. A list of sequenced tumor and non-tumor samples with known alterations, clinical annotations and number of replicates.
| Sample ID | Known alteration | Diagnosis | Tumor percentage | Tissue | Detection method | Panel | Nt | Nd |
|---|---|---|---|---|---|---|---|---|
| 1 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 2 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 3 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 4 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 5 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 6 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 7 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 8 | FLT3 indel | AML | 50 | Blood | Sanger sequencea | OPv2.1 | 1 | 0 |
| 9 | KIT deletion | GIST | NA | FFPE | Sanger sequence | OPv2.1 | 1 | 0 |
| 10 | t(2;2) ALK-EML4 | LA | 50 | FF | FISHb | OPv2.1 | 16 | 6 |
| 11 | t(2;2) ALK-EML4 | LA | 60 | FFPE | FISHb | OPv2.1 | 1 | 0 |
| 12 | t(2;2) ALK-EML4 | LA | 100 | Cell line | See reference (33) | OPv2.2 | 2 | 0 |
| 13 | t(2;2) ALK-EML4 | LA | 100 | Cell line | See reference (33) | OPv2.2 | 1 | 0 |
| 14 | t(2;2) ALK-EML4 | LA | 70 | FFPE | FISHb | OPv2.2 | 1 | 0 |
| 15 | t(9;22) BCR-ABL1 | CML | NA | Blood | qRT-PCR | OPv2.2 | 3 | 0 |
| 16 | t(9;22) BCR-ABL1 | ALL | NA | Heme | qRT-PCR | OPv2.1 | 2 | 0 |
| 17 | t(9;22) BCR-ABL1 | CML | NA | Heme | qRT-PCR | OPv2.1 | 1 | 0 |
| 18 | t(9;22) BCR-ABL1 | CML | NA | Heme | qRT-PCR | OPv2.1 | 10 | 6 |
| 19 | t(9;22) BCR-ABL1 | CML | NA | Heme | qRT-PCR | OPv2.1 | 7 | 0 |
| 20 | t(9;22) BCR-ABL1 | CML | NA | Heme | qRT-PCR | OPv2.1 | 6 | 0 |
| 21 | t(9;22) BCR-ABL1 | CML | 50 | Bone Marrow | qRT-PCR | OPv2.2 | 1 | 0 |
| 22 | t(7;16) EGFR translocation | LA | 70 | FFPE | PCR | OPv2.1 | 15 | 6 |
| 23 | t(21;22) ERG-EWSR1 | Ewing's Sarcoma, PNET | >90 | FFPE | FISHc | OPv2.2 | 1 | 0 |
| 24 | t(11;22) FLI1-EWSR1 | Ewing's Sarcoma | 100 | FFPE | FISHc | OPv2.1 | 1 | 0 |
| 25 | t(11;22) WT1-EWSR1 | DSRCT | 90 | FFPE | FISHc | OPv2.1 | 1 | 0 |
| 26 | t(11;22) FLI1-EWSR1 | Ewing's Sarcoma, PNET | >90 | FFPE | karyotype | OPv2.2 | 1 | 0 |
| 27 | t(8;17) FGFR1-ANKRD13B | CML | 90 | MeoH Ac-acid fixed | Karyotype, FISH | OPv2.1 | 1 | 0 |
| 28 | t(4;4) FIP1L1-PDGFRA | CML | NA | MeoH Ac-acid fixed | FISH | OPv2.1 | 1 | 0 |
| 29 | t(16;21) FUS-ERG | AML | 100 | Bone Marrow | Karyotype | OPv2.1 | 1 | 0 |
| 30 | t(14;18) IGH-BCL2 | CAP survey sample | NA | DNA | Qualitative DNA PCR assay | OPv2.1 | 3 | 0 |
| 31 | t(14;18) IGH-BCL2 | FL | NA | Frozen lymph node | Qualitative DNA PCR assay | OPv2.1 | 8 | 0 |
| 32 | t(10;11) KMT2A translocation | AML | NA | MeoH Ac-acid fixed | FISH | OPv2.1 | 1 | 0 |
| 33 | t(11;17) KMT2A translocation | AML | NA | MeoH Ac-acid fixed | FISH | OPv2.1 | 1 | 0 |
| 34 | t(6;11) KMT2A translocation | AML | 50 | Bone Marrow | FISH | OPv2.1 | 1 | 0 |
| 35 | t(9;11) MLLT3-KMT2A | AML | 100 | Cell line | See reference (34) | OPv2.2 | 2 | 0 |
| 36 | t(8;14) MYC-IGH | DLBCL | 70 | FFPE | FISH | OPv2.1 | 1 | 0 |
| 37 | t(15;17) PML-RARA | APML/AML M3 | 50 | Bone Marrow | RT-PCR | OPv2.2 | 1 | 0 |
| 38 | t(15;17) PML-RARA | APML/AML M3 | NA | Bone Marrow | Qualitative DNA PCR assay | OPv2.1 | 10 | 6 |
| 39–118 | Normal ‘controls’ | NA | NA | Blood | NA | OPv2.1 | 80 | 0 |
Nt: total number of replicates; Nd: number of dilution replicates; LA: lung adenocarcinoma; AML: acute myeloid leukemia; GIST: gastrointestinal stromal tumor; NSCLC: non-small cell lung cancer; DSRCT: desmoplastic small round cell tumor; CML: chronic myelogenous leukemia; ALL: acute lymphoblastic leukemia; PNET: primitive neuroectodermal tumor; DLBCL: diffuse large B-cell lymphoma; APML: acute promyelocytic leukemia; FL: follicular B-cell lymphoma; OPv2.1: OncoPanel-clinical; OPv2: OncoPanel v2; FFPE: formalin-fixed paraffin-embedded; FF: fresh frozen; FISH: fluourescence in situ hybridization; qRT-PCR: quantitative real-time PCR; NA: not available.
aNon-CLIA validated assay.
bVysis LSI ALK Dual color, Break Apart Rearrangement Probe (Abbott Molecular) at 2p23.
cLSI EWSR1 Dual Color, Break Apart Rearrangement Probe (Abbott Molecular) at 22q12.