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Precision Diagnosis, Classification & Advanced Treatment

What Test to Order

What Test Should I Order?

Based on the Clinical Indications for Molecular Testing


Solid Tumors

Molecular Profiling Indications


Recommended Tests


Hematologic Tumors

Molecular Profiling Indications


Recommended Tests

Solid Tumors


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Non-small cell lung cancer (NSCLC)

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification

EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, PD-L1, (category 1)

-KRAS (especially G12C), NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, RET, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1

Fusions: CD74–NRG1, SLC3A2–NRG1, EZR–ERBB4, TRIM24–BRAF, and KIAA1468–RET

NCCN Recommendation: EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, PD-L1, (category 1)

-KRAS (especially G12C), NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, RET

Prognosis

EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, PD-L1, (category 1)

-KRAS (especially G12C), NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, RET, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1

Fusions: CD74–NRG1, SLC3A2–NRG1, EZR–ERBB4, TRIM24–BRAF, and KIAA1468–RET

Prognosis is based on predicting response to specific therapy
Selecting therapy

EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, PD-L1, (category 1)

-KRAS (especially G12C), NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, RET, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1

Fusions: CD74–NRG1, SLC3A2–NRG1, EZR–ERBB4, TRIM24–BRAF, and KIAA1468–RET

Targeted mutations: EGFR, BRAF, KRAS(G12C), TMB, PIK3CA, PTEN, AKT1

Targetable fusions: ALK, RET, ROS1, NTRK1, NRG1, ERBB4, BRAF, FGFR

Follow-up and minimal residual disease (MRD) Mutations: EGFR, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1

Plasma-based testing should be considered at progression on EGFR TKIs for the T790M mutation.

-Minimal residual disease and relapse

Colorectal cancer

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification MSI, BRAF, KRAS, NRNA, PD-L1, (category 1)
-HRAS, EGFR amplification, NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Lynch: MSH6, PMS2, MLH1, EPCAM and MSH2.
FAP: APC and MUTYH
Cowden/PTEN
Peutz-Jeghers syndrome: STK11
Juvenile polyposis syndrome: SMAD4, BMPR1A
NCCN Recommendation:
MSI, BRAF, KRAS, NRNA, PD-L1, (category 1)
-HRAS, EGFR amplification, NTRK 1/2/3, ERBB2 mut/amplification,
Lynch: MSH6, PMS2, MLH1, EPCAM and MSH2
FAP: APC and MUTYH
Cowden/PTEN
Peutz-Jeghers syndrome: STK11
Juvenile polyposis syndrome: SMAD4, BMPR1A
Prognosis MSI, BRAF, KRAS, NRNA, PD-L1, (category 1)
-HRAS, EGFR amplification, NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Lynch: MSH6, PMS2, MLH1, EPCAM and MSH2.
FAP: APC and MUTYH
Cowden/PTEN
Peutz-Jeghers syndrome: STK11
Juvenile polyposis syndrome: SMAD4, BMPR1A
Prognosis is based on predicting response to specific therapy
Selecting therapy MSI, BRAF, KRAS, NRNA, PD-L1, (category 1)
-HRAS, EGFR amplification, NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Lynch: MSH6, PMS2, MLH1, EPCAM and MSH2.
FAP: APC and MUTYH
Cowden/PTEN
Peutz-Jeghers Syndrome: STK11
Juvenile polyposis syndrome: SMAD4, BMPR1A
Targeted mutations: KRAS (G12C), lack of RAS/REAF mutations
BRAF mutation
TMB, MSI
PIK3CA, PTEN, AKT1
Follow-up and Minimal Residual Disease (MRD) MSI, BRAF, KRAS, NRNA, PD-L1, (category 1)
-HRAS, EGFR amplification, NTRK 1/2/3, ERBB2 mut/amplification, MET amplification, TMB, TP53, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, PIK3CA, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Lynch: MSH6, PMS2, MLH1, EPCAM and MSH2.
FAP: APC and MUTYH
Cowden/PTEN
Peutz-Jeghers syndrome: STK11
Juvenile polyposis syndrome: SMAD4, BMPR1A
Detecting mutations

Breast cancer

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification ERBB2 (HER2) amplification, Mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1, TMB, MSI
Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53
NCCN guideline:
TMB, HER2, BRCA1/2, ATM, MSI, PIK3CA, NTRK1/2/3
Prognosis ERBB2 (HER2) amplification, mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53
Selecting therapy ERBB2 (HER2) amplification, Mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53
NCCN guideline:
TMB, HER2, BRCA1/2, ATM, MSI, PIK3CA, NTRK1/2/3
ESR1 resistant to both AIs and tamoxifen.
Follow-up and minimal residual disease (MRD) ERBB2 (HER2) amplification, mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1
Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53
Detecting mutations

Sarcoma

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification   PAX3, FOXO1, PAX 7, PAX3, AFX, NCOA1, NCOA2, INO80D, MYOD1,  EWSR1, WT1, FLI1, ERG, FEV, ETV1, E1AF, ZSG, FUS, CIC, DUX4, BCOR, CCNB, MYOD1, PIK3CA, RAS, TSC1, TSC2, TFE3, MDM2, CDK4, HMGA2, SAS, GLI, DDIT3, ASPL, TFE3, ATF1, CREB1, ATF1, CREB1, ETV6, NTRK3, COL1A1, PDGFB, CTNNB1, APC, YWHAE, NUTM2,  ZC3H7B, WWTR1, CAMTA1, YAP1, TFE3, ALK, ROS1, NTRK3, TPM3, TPM4, CLTC, RANBP2, CARS, ATIC, SMARCB (INI1), NR4A3, TAF2N, NR4A3, TCF12, NR4A3, TFG-NR4A3, KIT, PDGFRA, SDH, FUS, CREB3L2, FUS-CREB3L1, NF1, CDKN2A, EED, SUZ12, HEY1, NCOA2, NAB2, STAT6, SS18, SSX1, SSX2, SSX4, CSF1, TP53, PTEN, IDH1/2 NCCN guideline:
Alveolar RMS:  PAX3-FOXO1, PAX 7-FOXO1, PAX3-AFX, PAX3-NCOA1, PAX3-NCOA2, PAX3-INO80D, MYOD1 mutations
Desmoplastic small round cell: EWSR1-WT1
Ewing Sarcoma: EWSR1-FLI1, EWSR1-ERG, EWSR1-FEV, EWSR1-ETV1, EWSR1-E1AF, EWSR1-ZSG, FUS-ERG
Undifferentiated round cell: CIC-DUX4, BCOR-CCNB
Embryonal RMS:  MYOD1, PIK3CA, RAS mutations
PEComa: Loss of TSC1, TSC2, or TFE3 fusion
Atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDLS)/ Dedifferentiated liposarcoma: Amplification of region 12q14-15, including MDM2, CDK4, HMGA2, SAS, GLI
Myxoid/round cell liposarcoma: FUS-DDIT3EWSR1-DDIT3
Alveolar soft part sarcoma: ASPL-TFE3
Angiomatoid fibrous histiocytoma: EWSR1-ATF1EWSR1-CREB1FUS-ATF1
Clear cell sarcoma: EWSR1-ATF1EWSR1-CREB1
Congenital/infantile fibrosarcoma: ETV6-NTRK3
Dermatofibrosarcoma protuberans: COL1A1-PDGFB
Desmoid fibromatosis: CTNNB1 or APC mutations
High-grade endometrial stromal sarcoma: YWHAE-NUTM2 ZC3H7B-BCOR
Epithelioid hemangioendothelioma: WWTR1-CAMTA1YAP1 – TFE3
Inflammatory myofibroblastic tumors: ALK, ROS1 and NTRK3, TPM3-ALK5TPM4-ALK5CLTC-ALK5RANBP2-ALK5CARS-ALK5ATIC-ALK5
Epithelioid sarcoma/Extrarenal rhabdoid tumor: SMARCB (INI1) deletion
Extraskeletal myxoid chondrosarcoma: EWSR1-NR4A3 TAF2N-NR4A3 TCF12-NR4A3 TFG-NR4A3
GIST/CARmey-Sratakis syndrome: KIT or PDGFRA Germline SDH subunit mutations
Low-grade fibromyxoid sarcoma: FUS-CREB3L2FUS-CREB3L1
Malignant peripheral nerve sheath tumor:  NF1, CDKN2A, EED, SUZ12
Mesenchymal chondrosarcoma: HEY1 – NCOA2
Solitary fibrous tumor: NAB2 – STAT6
Synovial sarcoma: SS18-SSX1SS18-SSX2SS18-SSX4
Tenosynovial giant cell tumor/pigmented villonodular synovitis (TGCT/PVNS): CSF1
Prognosis   PAX3, FOXO1, PAX 7, PAX3, AFX, NCOA1, NCOA2, INO80D, MYOD1,  EWSR1, WT1, FLI1, ERG, FEV, ETV1, E1AF, ZSG, FUS, CIC, DUX4, BCOR, CCNB, MYOD1, PIK3CA, RAS, TSC1, TSC2, TFE3, MDM2, CDK4, HMGA2, SAS, GLI, DDIT3, ASPL, TFE3, ATF1, CREB1, ATF1, CREB1, ETV6, NTRK3, COL1A1, PDGFB, CTNNB1, APC, YWHAE, NUTM2, ZC3H7B, WWTR1, CAMTA1, YAP1, TFE3, ALK, ROS1, NTRK3, TPM3, TPM4, CLTC, RANBP2, CARS, ATIC, SMARCB (INI1), NR4A3, TAF2N, NR4A3, TCF12, NR4A3, TFG-NR4A3, KIT, PDGFRA, SDH, FUS, CREB3L2, FUS-CREB3L1, NF1, CDKN2A, EED, SUZ12, HEY1, NCOA2, NAB2, STAT6, SS18, SSX1, SSX2, SSX4, CSF1, IDH1/2 See diagnostics
Selecting therapy   PAX3, FOXO1, PAX 7, PAX3, AFX, , NCOA1, NCOA2, INO80D, MYOD1,  EWSR1, WT1, FLI1, ERG, FEV, , ETV1, E1AF, ZSG, FUS, CIC, DUX4, BCOR, CCNB, MYOD1, PIK3CA, RAS, TSC1, TSC2, TFE3, MDM2, CDK4, HMGA2, SAS, GLI, DDIT3, ASPL, TFE3, , ATF1, CREB1, ATF1, CREB1, ETV6, NTRK3, COL1A1, PDGFB, CTNNB1, APC, YWHAE, NUTM2, ZC3H7B, WWTR1, CAMTA1, YAP1, TFE3, ALK, ROS1, NTRK3, TPM3, TPM4, CLTC, RANBP2, CARS, ATIC, SMARCB (INI1), NR4A3, TAF2N, NR4A3, TCF12, NR4A3, TFG-NR4A3, KIT, PDGFRA, SDH, FUS, CREB3L2, FUS-CREB3L1, NF1, CDKN2A, EED, SUZ12, HEY1, NCOA2, NAB2, STAT6, SS18, SSX1, SSX2, SSX4, CSF1, IDH1/2 IDH1/2 in chondrosarcoma
NCCN guideline:
See diagnostics.
Follow-up and minimal residual disease (MRD)   PAX3, FOXO1, PAX 7, PAX3, AFX, NCOA1, NCOA2, INO80D, MYOD1,  EWSR1, WT1, FLI1, ERG, FEV, ETV1, E1AF, ZSG, FUS, CIC, DUX4, BCOR, CCNB, MYOD1, PIK3CA, RAS, TSC1, TSC2, TFE3, MDM2, CDK4, HMGA2, SAS, GLI, DDIT3, ASPL, TFE3, ATF1, CREB1, ATF1, CREB1, ETV6, NTRK3, COL1A1, PDGFB, CTNNB1, APC, YWHAE, NUTM2, ZC3H7B, WWTR1, CAMTA1, YAP1, TFE3, ALK, ROS1, NTRK3, TPM3, TPM4, CLTC, RANBP2, CARS, ATIC, SMARCB (INI1), NR4A3, TAF2N, NR4A3, TCF12, NR4A3, TFG-NR4A3, KIT, PDGFRA, SDH, FUS, CREB3L2, FUS-CREB3L1, NF1, CDKN2A, EED, SUZ12, HEY1, NCOA2, NAB2, STAT6, SS18, SSX1, SSX2, SSX4, CSF1, IDH1/2 Detecting mutations

Brain tumors

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification IDH1/2 (grade II & IIIastrocytoma), MGMT methylation, Codeletion of 1p, 19q/t(1;19), ATRX deletion/Mutation (tumor should not be diagnosed as Oligodendroma if IDH+ and 1p/19q+), TERT mutation/Expression, H3F3A mutation (Midline glioma), BRAF/ BRAF-KIAA1549 (fusion/mutation), RELA-C11orf95 fusion (ependydoma), WNT, TP53, CTNNB1, APC (Medulloblastoma classification, 6q-, EGFR amplification/mutation NCCN guidelines:
With the use of genetic and molecular testing, histologically similar CNS neoplasms can be differentiated more accurately in terms of prognosis and, in some instances, response to different therapies
Prognosis IDH1/2 (grade II & IIIastrocytoma), MGMT methylation, Codeletion of 1p, 19q/t(1;19), ATRX deletion/Mutation (tumor should not be diagnosed as Oligodendroma if IDH+ and 1p/19q+), TERT mutation/Expression, H3F3A mutation (Midline glioma), BRAF/ BRAF-KIAA1549 (fusion/mutation), RELA-C11orf95 fusion (ependydoma), WNT, TP53, CTNNB1, APC (Medulloblastoma classification, 6q-, EGFR amplification/mutation See diagnostics
Selecting therapy IDH1/2 (grade II & IIIastrocytoma), MGMT methylation, codeletion of 1p, 19q/t(1;19), ATRX deletion/mutation (tumor should not be diagnosed as Oligodendroma if IDH+ and 1p/19q+), TERT mutation/Expression, H3F3A mutation (Midline glioma), BRAF/ BRAF-KIAA1549 (fusion/mutation), RELA-C11orf95 fusion (ependydoma), WNT, TP53, CTNNB1, APC (Medulloblastoma classification, 6q-, EGFR amplification/mutation NCCN guidelines:
There are no identified targeted agents with demonstrated efficacy in glioblastoma. However, the panel encourages molecular testing of tumor because if a driver mutation is detected, it may be reasonable to treat with a targeted therapy on a compassionate use basis and/or the patient may have more treatment options in the context of a clinical trial. Molecular testing also has a valuable role in improving diagnostic accuracy and prognostic stratification that may inform treatment selection
Follow-up and minimal residual disease (MRD) IDH1/2 (grade II & IIIastrocytoma), MGMT methylation, Codeletion of 1p, 19q/t(1;19), ATRX deletion/Mutation (tumor should not be diagnosed as Oligodendroma if IDH+ and 1p/19q+), TERT mutation/Expression, H3F3A mutation (Midline glioma), BRAF/ BRAF-KIAA1549 (fusion/mutation), RELA-C11orf95 fusion (ependydoma), WNT, TP53, CTNNB1, APC (Medulloblastoma classification, 6q-, EGFR amplification/mutation Detecting mutations

Head & neck cancer

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI  
Prognosis PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI Molecular classification based on gene expression: Classical, mesenchymal, and atypical.
Selecting therapy PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI NCCN guidelines:
Immunotherapy, targeted therapy, and combination immunotherapy + targeted therapy
Follow-up and minimal residual disease (MRD) PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI Detecting mutations

 

Bladder cancer

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification PIK3CA, BRAF, KRAS, MET. NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI NCCN guidelines:
The panel recommends that molecular/genomic testing be performed for stages IVA and IVB bladder cancer and may be considered for stage IIIB. This testing should be performed only in laboratories that are certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA-88) as qualified to perform highly complex molecular pathology testing.186 The NCCN bladder cancer panel recommends that molecular/genomic testing be carried out early, ideally at diagnosis of advanced bladder cancer, in order to facilitate treatment decision-making and to prevent delays in administering later lines of therapy. In addition to determining eligibility for FDA-approved therapies, molecular/genomic testing may be used to screen for clinical trial eligibility.
Prognosis PIK3CA, BRAF, KRAS, MET. NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI NCCN guidelines:
Within each category of disease, more refined methods to determine prognosis and guide management, based on molecular staging, are under development with the goal of optimizing each patient’s likelihood of cure and chance for organ preservation.
Selecting therapy PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI NCCN guidelines:
Immunotherapy, targeted therapy, and combination immunotherapy + targeted therapy
Follow-up and minimal residual disease (MRD) PIK3CA, BRAF, KRAS, MET, NRA, HRAS, PTEN, BRCA1/2, EGFR, ERBB2, NOTCH1, KEAP1, CCND1, SMAD4, KIT, NTRK1/2/3, HPV, TP53, CDKN2A, FBXW7, RB1, TRAF3, FGFR1/2/3/4, TMB, MSI Detecting mutations

Ovarian cancer

Recommended Test:

1)Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2)Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification

ERBB2 (HER2) amplification, Mutation, overexpression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1, TMB, MSI

Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53

NCCN guidelines:

Tumor molecular testing is recommended prior to initiation of therapy for persistent/recurrent disease. Validated molecular testing should be performed in a CLIA-approved facility using the most recent available tumor tissue. Testing recommended to include at least: BRCA1/2, and MSI or dMMR if not previously done. Evaluation of homologous recombination deficiency can be considered. Additional somatic tumor testing can be considered at the physician’s discretion to identify genetic alterations for which FDA-approved tumor-specific or tumor-agnostic targeted therapy options exist.

Prognosis

ERBB2 (HER2) amplification, Mutation, overexpression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1, TMB, MSI

Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53

NCCN guidelines:
Molecular characterization of clear cell, mucinous, or low-grade (grade 1) serous tumors suggests that mutations in these histologies are different from those in higher grade tumors.125-127 Ovarian cancer can be divided into Types 1 and 2 based on these molecular alterations. Data suggest that serous tumors can be categorized as either low grade (most grade 1 serous tumors) or high grade (most grade 2 or 3 serous tumors).87,89-92,128,129 High-grade endometrioid tumors are difficult to distinguish from high-grade serous tumors.
Selecting therapy

ERBB2 (HER2) amplification, Mutation, overexpression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1, TMB, MSI

Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53

NCCN guidelines:

Immunotherapy, targeted therapy, and combination immunotherapy + targeted therapy

Follow-up and minimal residual disease (MRD)

ERBB2 (HER2) amplification, Mutation, overexpression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, STK11, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, PTEN, AKT1, TMB, MSI

Copy number change: CCND1, TOP2A, PPM1D, MYC, AKT1, CDK9, KRAS, MDM2, CDKN2A, RB1, PTEN, and TP53

Detecting mutations and copy number variation.

Gastric cancer

Recommended Test:

1) Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2) Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification

CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, over expression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1, TMB

NCCN guideline:

Next-generation sequencing (NGS) offers the opportunity to assess numerous mutations simultaneously, along with other molecular events such as amplification, deletions, tumor mutation burden, and microsatellite instability status. When limited diagnostic tissue is available for testing and the patient is unable to undergo additional procedures, NGS can be considered instead of sequential testing for single biomarkers.

Prognosis

CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, Mutation, overexpression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1, TMB

NCCN guideline:

HER2, inherited susceptibility, MSI, TMB

Selecting therapy

CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, over expression

MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1, TMB

NCCN guideline:

MSI, TMB, RAS/RAF:

Immunotherapy, targeted therapy, and combination immunotherapy + targeted therapy

Follow-up and minimal residual disease (MRD)

CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, overexpression

BRCA1, BRCA2, ATM, TP53, PIK3CA,

BRAF, KRAS, NRNA, PD-L1,

EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1

Detecting mutations

Prostate cancer

Recommended Test:

1) Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2) Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification TMPRSS2-ERG, CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, Mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
NCCN guideline:
Consider cancer predisposition next-generation sequencing (NGS) panel testing, which includes BRCA1, BRCA2, ATM, PALB2, CHEK2, MLH1, MSH2, MSH6, and PMS2.  Additional genes may be appropriate depending on clinical context. For example, HOXB13
 
 
Prognosis TMPRSS2-ERG, CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
Detecting mutations and copy number variation for stratification predicting response
Selecting therapy TMPRSS2-ERG, CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, over expression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
Immunotherapy, PARP inhibitors
Follow-up and minimal residual disease (MRD) TMPRSS2-ERG, CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, overexpression
MSI, BRCA1, BRCA2, ATM, TP53, PIK3CA,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, NTRK 1/2/3, FGFR1/2/3/4, ERBB3, MET amplification, TMB, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1

Gastrointestinal stromal tumor (GIST)

Recommended Test:

1) Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2) Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification KIT (exons: 9,11,13,17), PDGFRA, NF1, KRAS, NRAS, HRAS, BRAF, SDHB, SDHC, CDKN2A, CDKN2B, RB1, TP53, CUL1, ATM Detecting mutations and copy number variation
 
 
Prognosis KIT (exons: 9,11,13,17), PDGFRA, NF1, KRAS, NRAS, HRAS, BRAF, SDHB, SDHC, CDKN2A, CDKN2B, RB1, TP53, CUL1, ATM Heinrich et al (https://doi.org/10.1186/s13569-019-0112-7)
Selecting therapy KIT (exons: 9,11,13,17), PDGFRA, NF1, KRAS, NRAS, HRAS, BRAF, SDHB, SDHC, CDKN2A, CDKN2B, RB1, TP53, CUL1, ATM Kinase inhibitors
Follow-up and minimal residual disease (MRD) KIT (exons: 9,11,13,17), PDGFRA, NF1, KRAS, NRAS, HRAS, BRAF, SDHB, SDHC, CDKN2A, CDKN2B, RB1, TP53, CUL1, ATM  

Cancer of unknown primary (CUP)

Recommended Test:

1) Solid Tumor Profile PLUS™ (FFPE block or unstained slides)

2) Solid Tumor Monitoring Profile™ (Liquid Biopsy) (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification GEP (AI), MSI, TMB, fusions: ALK, ROS1, RET, TMPRSS2-ERG, NTRK1/2/3, FGFR1/2/3/4 mutations: CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH,APC, ERBB2 (HER2) amplification, mutation, over expression
BRCA1, BRCA2, ATM, TP53, PIK3CA, HRAS,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, ERBB3, MET amplification, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
NCCN guideline:
Since the identification of clinically relevant genomic alterations has the potential to influence therapy options, use of standardized comprehensive NGS assays may help identify novel treatment paradigms to address the limited treatment options and poor prognoses of patients with CUP
 
 
Prognosis GEP (AI), MSI, TMB, fusions: ALK, ROS1, RET, TMPRSS2-ERG, NTRK1/2/3, FGFR1/2/3/4 mutations: CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH,APC, ERBB2 (HER2) amplification, mutation, over expression
BRCA1, BRCA2, ATM, TP53, PIK3CA, HRAS,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, ERBB3, MET amplification, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
Detecting mutations and copy number variation for stratification predicting response
Selecting therapy GEP (AI), MSI, TMB, fusions: ALK, ROS1, RET, TMPRSS2-ERG, NTRK1/2/3, FGFR1/2/3/4 mutations: CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, overexpression
BRCA1, BRCA2, ATM, TP53, PIK3CA, HRAS,
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, ERBB3, MET amplification, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
Immunotherapy, Targeted therapy
Follow-up and minimal residual disease (MRD) CDH1 (Hereditary diffuse gastric cancer), SMAD4 (Juvenile polyposis syndrome), STK11 (Peutz-Jeghers syndrome), PTEN (Cowden), PMS2, MSH2, EPCAM, MLH1, MSH6, (Lynch), MUTYH, APC, ERBB2 (HER2) amplification, mutation, over expression
BRCA1, BRCA2, ATM, TP53, PIK3CA, HRAS
BRAF, KRAS, NRNA, PD-L1,
EGFR amplification, ERBB3, MET amplification, KEAP1, NF1, SETD2, RBM10, ARID1A, SMARCA4, RB1, CDKN2A, AKT1
 

Hematology

Myelodysplastic syndrome (MDS)

Recommended Test:
Hematology Profile™ (Bone marrow or peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis DNMT3A, ASXL1, EZH2, SF3B1, SRSF2, U2AF1, ZRSR2, RUNX1, TP53, STAG2, NRAS, CBL, NF1, JAK2, CALR, MPL, ETV6, GATA2, IDH2, SETBP1, BCOR, FLT3, WT1, NPM1, STAT3 NCCN guidelines: “Bone marrow or peripheral blood cells should be assayed for MDS-associated gene mutations using gene panels that include genes listed on MDS-C. These gene mutations can establish the presence of clonal hematopoiesis, which can help exclude benign causes of cytopenias in cases with non-diagnostic morphology, but do not establish a diagnosis of MDS in the absence of clinical diagnostic criteria”
Distinguishing MDS from CHIP or CCUS  VAF and type of mutated genes  NCCN guidelines:  >10% VAF and >=2 mutations or mutations in spliceosome or RUNX1 or JAK2 are predictor of MDS, MPN, or AML. TET2, DNMT3A, or ASXL1 have less prediction and may imply CHIP or CCUS
 DNMT3A, TET2, ASXL1, RUNX1, PPM1D, and TP53 Mutations in these genes with VAF<10% are more associated with CHIP and CCUS
Distinguishing MDS from LGL STAT3 mutation NCCN guideline: distinguish LGL from MDS
Subclassification (NCCN guidelines) TET2, SRSF2, ASXL1, RUNX1, NRAS, CBL CMML-0/CMML-1/CMML-2
SETBP1, ETNK1 aCML
PTPN11, NF1, NRAS, KRAS, CBL, SETBP1, JAK3 JMML
TET2, NRAS, RUNX1, CBL, SETBP1, ASXL1 MDS/MPN
SF3B1, JAK2, MPL, CALR MDS/MPN-T
CSF3R CNL
Prognosis DNMT3A, ASXL1, EZH2, SF3B1, SRSF2, U2AF1, ZRSR2, RUNX1, TP53, STAG2, NRAS, CBL, NF1, JAK2, CALR, MPL, ETV6, GATA2, IDH2, SETBP1, BCOR, FLT3, WT1, NPM1 NCCN guideline: Mutations in these genes are associated with more aggressive disease
Prognosis IDH1, PHF6, PPM1D, PPM1D, TET2 NCCN guideline: Mutations in these genes have neutral effects on prognosis
Heterogeneity VAF Used for monitoring, evolution into more aggressive disease, and evaluating efficacy of targeted therapy.
Aiding in ruling out hereditary predisposition (Gene mutations associated with hereditary myeloid malignancies). These are used to recommend testing another tissue to rule in or out hereditary predisposition if these genes VAF around 50% and all other mutations are at significantly lower VAF
CEBPA, DDX41, ANKRD, ETV6 AML/MDS and other hematologic neoplasms
GATA2 MONO syndrome
RUNX1 Thrombocytopenia with mild bleeding
SAMD9 MIRAGE syndrome
SAMD9L Ataxia-Pancytopenia
SRP72 Congenital sensorineural deafness.
RPL5, RPL11, RPL15, RPL23, RPL26, RPL27, RPL31, RPL35A, RPS7, RPS10, RPS17, RPS19, RPS24, RPS26, RPS27, RPS28, RPS29, TSR2, GATA1 Diamond-Blackfan anemia
FANCA, FANCB, FANCC, FANCD1/BRCA2, FANCD2, FANCDE, FANCF, FANCG, FANCI, FANCJ/BRIP1/BACH1, FANCL, FANCM, FANCN/PALB2, FANCO/RAD51C, FANCP/SLX4, FANQ/ERCC4, FANCR/RAD51, FANCS/BRCA1, FANCT/UNE2T, FANCU/XRCC2, FANCV/REV7 Fanconi anemia
SBDS, EFL1, DNAJC21 Shwachman-Diamond syndrome
ACD, CTC1, DKC1, NAF1, NHP2, NOP10, PARN, POT1, RTEL1, TERC, TERT, TINF2, USB1, WRAP53 Telomere biology disorders
ELANE, G6PC3, GFI1, HAX1 Congenital neutropenia
GATA1 Down syndrome, acute megakaryocytic leukemia
TP53 AML/MDS in patients with Li-Fraumeni syndrome
EPCAM, MLH1, MSH2, MSH6, PMS2 AML/MDS in constitutional mismatch repair deficiency
BRCA1, BRCA2 AML/MDS in hereditary breast and ovarian cancer
CBL, KRAS, NF1, PTPN11 AML/MDS/CMML/AMML in patients with RASopathies
BLM AML/MDS in Bloom syndrome
Aiding in deciding therapeutic approach FLT3, IDH1/2 Presence of mutation any of these genes will trigger recommendation of ordering the single gene FDA-cleared test for confirmation and potential use of targeted therapy.
TET2 NCCN guidelines: “TET mutations have been shown to impact the response to hypomethylating agents. Patients with mutated TET2 had an 82% response rate to AzaC compared to 45% of patients with wildtype TET2(P = .007).”
Aiding in monitoring VAF Disappearance or emergence of clones that may affect targeted therapy or overall therapeutic approach.
Aiding in selecting potential clinical trials FLT3 inhibitors, KIT inhibitors, PI3K/AKT/mTOR inhibitors, aurora and polo-like kinase inhibitors, CDK4/6
inhibitors, CHK1, WEE1, MPS1 inhibitors, SRC and HCK inhibitors, HDAC inhibitors, IDH1 inhibitors, IDH2 inhibitors, DOT1L inhibitors, BET-bromodomain inhibitors, EVI1 inhibitors, NPM1 inhibitors, hedgehog inhibitors, spliceosome inhibitors.

Acute myeloid leukemia (AML)

Recommended Tests:

1) Hematology Profile™ (Bone marrow or peripheral blood/cfDNA)

2) Order Hematology Profile PLUS™ if chromosomal translocation is expected (Bone marrow or peripheral blood)

3) Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis c-KIT, FLT3-ITD, FLT3-TKD, NPM1, CEBPA, IDH1/IDH2, RUNX1, ASXL1, and TP53 NCCN guidelines: “Several gene mutations are associated with specific prognoses in a subset of patients (category 2A), and may guide treatment decisions (category 2B). Presently, c-KIT, FLT3-ITD, FLT3-TKD, NPM1, CEBPA, IDH1/IDH2, RUNX1, ASXL1, and TP53 are included in this group. All patients should be tested for mutations in these genes, and multiplex gene panels and next-generation sequencing (NGS) analysis can be obtained to develop a more comprehensive prognostic assessment. FLT3 mutation status ideally should be resulted rapidly to allow for addition of FLT3 inhibitor (midostaurin) on day 8 of upfront intensive chemotherapy.”
Aiding in distinguishing de novo from secondary AML AXL1, SF3B1, DNMT3A, TET2, SRSF2, EZH2, BCOR, STAG2 ELN recommendation; “Mutations associated with secondary AML occur in genes encoding SRSF2, SF3B1, U2AF1, and ZRSR2 (splicing factors); ASXL1, EZH2, and BCOR (epigenetic regulators); and STAG2 (a member of the cohesin complex).”
Determining heterogeneity comparing VAF between mutated genes Relevant in selecting targeted therapy, monitoring and understanding clinical course.
Distinguishing between transient myeloproliferative disorder Vs megakaryocytic leukemia in patients with down syndrome GATA1 mutation
Ruling out hereditary predisposition (Gene mutations associated with hereditary myeloid malignancies) See MDS description
Aiding in deciding therapeutic approach KIT NCCN guideline: Potential adding Dasatinib in CBF leukemia with KIT mutation.
FLT3, IDH1/2 Presence of mutation any of these genes will trigger recommendation of ordering the single gene FDA-cleared test for confirmation and potential use of targeted therapy.
TP53 Allo-hematologic stem cell transplant or clinical trials.
Determining molecular response Molecular profiling abnormalities CR is determined by the counting of <5% blasts in bone marrow, but this is not reliable because these blasts can be leukemic of regenerating normal cells.  Molecular profiling helps in confirming CR (Molecular CR). It is not unusual in secondary AML that mutations in genes associated with acute phase (NPM1, FLT3) disappear, but the background MDS disease (TET2, ASXL…) remain.
Monitoring clonal evolution Monitoring VAF relative changes between various genes Clonal evaluation and intensive therapy selection of aggressive subclone is well documented and therapy can be modified and adjusted accordingly.
Aiding in monitoring residual disease Molecular profiling abnormalities NCCN guideline: “NGS-based assays can be used to detect mutated genes through targeted sequencing gene panels though higher sensitivities are observed in PCR- and flow cytometry-based methods compared to conventional NGS.”
Aiding in selecting potential clinical trials FLT3 inhibitors, KIT inhibitors, PI3K/AKT/mTOR inhibitors, aurora and polo-like kinase inhibitors, CDK4/6
inhibitors, CHK1, WEE1, MPS1 inhibitors, SRC and HCK inhibitors, HDAC inhibitors, IDH1 inhibitors, IDH2 inhibitors, DOT1L inhibitors, BET-bromodomain inhibitors, EVI1 inhibitors, NPM1 inhibitors, hedgehog inhibitors, spliceosome inhibitors.

Myeloproliferative neoplasms (MPN)

Recommended Tests:

1) Hematology Profile™ (Bone marrow or peripheral blood/cfDNA)

2) Hematology Profile PLUS™ if chromosomal translocation is expected (Bone marrow or peripheral blood)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis Molecular testing (blood) for JAK2 V617F mutation; if negative, test for CALR and MPL mutations (for patients with ET and MF) and JAK2 exon 12 mutations (for patients with PV) or molecular testing using multi-gene NGS panel that includes JAK2, CALR, and MPL” NCCN Guideline: “Molecular testing (blood)for JAK2 V617F mutation; if negative, test for CALR and MPL mutations (for patients with ET and MF) and JAK2 exon 12 mutations (for patients with PV) or molecular testing using multi-gene NGS panel that includes JAK2, CALR, and MPL”.
Distinguishing MPN from CMML, aCML, and JMML DNMT3A, ASXL1, EZH2, SF3B1, SRSF2, U2AF1, ZRSR2, RUNX1, TP53, STAG2, NRAS, CBL, NF1, JAK2, CALR, MPL, ETV6, GATA2, IDH2, SETBP1, BCOR, FLT3, WT1, NPM1.
Prognosis DNMT3A, ASXL1, EZH2, SF3B1, SRSF2, U2AF1, ZRSR2, RUNX1, TP53, STAG2, NRAS, CBL, NF1, JAK2, CALR, MPL, ETV6, GATA2, IDH2, SETBP1, BCOR, FLT3, WT1, NPM1. NCCN Guideline: “Additional molecular testing using multi-gene NGS panel should be considered to evaluate for higher-risk mutations associated with disease progression in patients with primary PMF.”
Determining prognosis in primary myelofibrosis (NCCN guidelines) Mutated Gene Primary myelofibrosis (PMF)
JAK2 V617F Intermediate prognosis and higher risk of thrombosis compared to patients with CALR mutation
MPL W515L/K Intermediate prognosis and higher risk of thrombosis compared to patients with CALR mutation
CALR Improved survival compared to JAK2 mutation and “triple-negative” PMF-Lower risk of thrombosis compared to JAK2 mutation
CALR Type 1/Type 1-like Improved overall survival compared to CALR type 2/type 2-like and JAK2 V617F mutation”
Triple negative (non-mutated JAK2, MPL, and CALR) Inferior leukemia-free survival compared to patients with JAK2- and/or CALR-mutated PMF Inferior overall survival compared to patients with CALR-mutated PMF
ASXL1 Independently associated with inferior overall survival*and leukemia-free survival
EZH2 Independently associated with inferior overall survival
IDH1/2 Independently associated with inferior leukemia-free survival
SRSF2 Independently associated with inferior overall survival and leukemia-free survival
Combined CALR and ASXL1 status Survival longest for CALR (+) ASXL1 (-) patients (median 10.4 years) and shortest in CALR (-) ASXL1 (+) patients (median 2.3 years) Intermediate survival (median 5.8 years) for CALR (+) ASXL1 (+) or CALR (-) ASXL1 (-) patients
TP53 Associated with leukemic transformation
U2AF1 Q157 Inferior overall survival compared to patients with U2AF1 S34 mutated or U2AF1 unmutated PMF. The effect was most evident in younger patients
Aiding in selecting potential clinical trials JAK2, CALR, MPL, Ph+

Acute lymphoblastic leukemia (ALL)

Recommended Test:

1)Hematology Profile PLUS™ (Bone marrow or peripheral blood)

2)Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification BCR-ABL1 (190 vs 210), various fusions: t(v;11q23.3) [KMT2A rearranged]; t(12;21)(p13.2;q22.1) [ETV6-RUNX1]; t(1;19)(q23;p13.3) [TCF3-PBX1]; t(5;14)(q31.1;q32.3) [IL3-IGH]; Ph–like; B-lymphoblastic leukemia/lymphoma with iAMP21; early T-cell precursor lymphoblastic leukemia.
Ph-like: ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, or PDGFRB and mutations involving FLT3, IL7R, NTRK, SH2B3, JAK1, JAK3, and JAK2
NCCN guideline: “The Ph-like phenotype is associated with recurrent gene fusions and mutations that activate tyrosine kinase pathways and includes gene fusions involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, or PDGFRB and mutations involving FLT3, IL7R, SH2B3, JAK1, JAK3, and JAK2 (in combination with CRLF2 gene fusions). Testing for these abnormalities at diagnosis may aid in risk stratification.”
Prognosis Good: Cases with trisomy of chromosomes 4, 10, and 17 appear to have the most favorable outcome t(12;21)(p13;q22): ETV6-RUNX1a
Poor: KMT2A rearranged (t[4;11] or others)  t(v;14q32)/IgH t(9;22)(q34;q11.2): BCR-ABL1 (defined as high risk in the pre-TKI era) Complex karyotype (5 or more chromosomal abnormalities) Ph-like ALL; intrachromosomal amplification of chromosome 21
NCCN guideline as cytogenetic risk stratification
Selecting therapy Bosutinib: T315I, V299L, G250E, or F317L
Dasatinib: T315I/A, F317L/V/I/C, or V299L
NilotinibT315I, Y253H, E255K/V, or F359V/C/I or G250E
Ponatinib
ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK1, JAK2, JAK3, PDGFRβ, EBF1, FLT3, IL7R, NTRK3, and SH2B3 genes. A genomic profiling study found kinase-activating alternations in 91% of Ph-like ALL cases,56 suggesting potential for ABL-class tyrosine kinase inhibitors (TKIs) or other targeted therapies to significantly improve patient outcomes in this subgroup
B-ALL with iAMP21 (RUNx1)
Ph-Positive ALL
Ph-like ALL
PH-negative ALL
(COG AALL-0031 regimen, EsPhALL, TKIs combined with hyper-CVAD, TKIs combined with multiagent chemotherapy, TKIs Combined with Vincristine and Dexamethasone, HSC transplant, CAR-T….)
Ph-Like:
ABL1, ABL2, PDGFRB, and CSF1R: Dasatinib
CRLF2, JAK2 , EPOR , TSLP: JAK2 inhibitors
IL2RB:  JAK1/JAK3 inhibitor
TYK2: TYK2 inhibitor
NTRK3: Crizotinib/NTRK inhibitors
PTK2B: FAK inhibitor
Follow-up and minimal residual disease (MRD) ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK1, JAK2, JAK3, PDGFRβ, EBF1, FLT3, IL7R, NTRK3, NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3, BRAF, GATA3, ETV6, RUNX1, IKZF1 NCCN guideline: PCR/NGS methods can detect leukemic cells at a sensitivity threshold of <1 x 10-6 (<0.0001%) bone MNCs. The concordance rate for detecting MRD between these methods is generally high.
Aiding in selecting potential clinical trials Ph+, Ph-like

B-cell lymphoma

Recommended Test:

1)Hematology Profile PLUS™ (Lymph node, fresh tissue, bone marrow and peripheral blood)

2)Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification BCL2, MYC, BCL6, 1p36, IRF4/MUM1, Ki-67, cyclin D1, TNFRSF14, STAT6, t(1;14); t(3;14); t(11;18),TP63 rearrangement, MYD88, ATM, del(17p)/TP53 mutation, +12; del(11q); del(13q);
BRAF, IgvH4-31, IgVH3-21, MYD88, CXCR4
Double expressor
GCB vs ABC
NCCN: MYD88 distinguish between WM and SMZL
Hodgkin Vs T-cell lymphoma, Mantle Vs marginal, AITL vs B-cell,
Double expressor
GCB vs ABC
Prognosis BCL2, MYC, BCL6, 1p36, IRF4/MUM1, Ki-67, cyclin D1, TNFRSF14, STAT6, t(1;14); t(3;14); t(11;18), MYD88, ATM, del(17p)/TP53 mutation, +12; del(11q); del(13q);
BRAF, IgvH4-31, IgVH3-21, MYD88, CXCR4
Double expressor
GCB vs ABC
TP53 mutation/loss
ATM mutation/loss
MYC, NOTCH1, 6q-,
DLBCL subclassification
CLL: SF3B1, NOTCH1, TP53
IgvH mutation status in CLL
Double expressor
GCB vs ABC
Selecting therapy BCL2, MYC, BCL6, 1p36, IRF4/MUM1, Ki-67, cyclin D1, TNFRSF14, STAT6, t(1;14); t(3;14); t(11;18), MYD88, ATM, del(17p)/TP53 mutation, +12; del(11q); del(13q);
Double expressor
GCB vs ABC
NCCN guideline:
Useful in certain circumstances
Brentuximab vedotin for CD30+ disease
Bendamustinek ± rituximab (category 2B)
Ibrutinibm (non-GCB DLBCL)
Lenalidomide ± rituximab (non-GCB DLBCL)
– BTK and PLCG2 mutations
ALK-positive DLBCL
DLBCL with IRF4/MUM1
Follow-up and minimal residual disease (MRD) BCL2, MYC, BCL6, 1p36, IRF4/MUM1, Ki-67, cyclin D1, TNFRSF14, STAT6, t(1;14); t(3;14); t(11;18), MYD88, TP53, ATM Mutation detection (cfDNA) is highly sensitive for MRD

T-cell lymphoma

Recommended Test:

1)Hematology Profile PLUS™ (Lymph node, fresh tissue, bone marrow and peripheral blood)

2)Minimal residual diease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification STAT3, STT5B, ALK expression/fusion, DUSP22, IRF4, TP63 rearrangement, TCL1A, MTCP1-B1, IDH, TET2, DNMT3A, RHOA, CCR4, TP53 Hodgkin Vs T-cell lymphoma, PTCL, BIAA, ALCL, LK-Pos, EATL, MEITL, PTCL-TFH, FTCL, ATIL, TPLL, NKTL, HSTCL, MF/Sezary, large granular lymphocytic leukemia (STAT3 and STAT5B)
 
Prognosis STAT3, STT5B, ALK expression/fusion, DUSP22, IRF4, TP63, TCL1A, MTCP1-B1, IDH, TET2, DNMT3A, RHOA, TP53
inv(14) (q11;q32); t(14;14)(q11;q32); t(X;14)(q28;q11); trisomy 8
Hodgkin Vs T-cell lymphoma, PTCL, BIAA, ALCL, LK-Pos, EATL, MEITL, PTCL-TFH, FTCL, ATIL, TPLL, NKTL, HSTCL, MF/Sezary, large granular lymphocytic leukemia (STAT3 and STAT5B)
 
 
Selecting therapy STAT3, STT5B, ALK expression/fusion, DUSP22, IRF4, TP63 rearrangement, TCL1A, MTCP1-B1, IDH, TET2, DNMT3A, RHOA,
inv(14) (q11;q32); t(14;14) (q11;q32); t(X;14) (q28;q11); trisomy 8
NCCN guideline:
CCR4 gain-of-function mutations have been reported to be predictive of sensitivity to mogamulizumab treatment
Follow-up and minimal residual disease (MRD) STAT3, STT5B, ALK expression/fusion, DUSP22, IRF4, TP63, TCL1A, MTCP1-B1, IDH, TET2, DNMT3A, RHOA, TP53
inv(14) (q11;q32); t(14;14)(q11;q32); t(X;14)(q28;q11); trisomy 8
Mutation detection (cfDNA) is highly sensitive for MRD

Multiple myeloma (MM)

Recommended Test:

1)Hematology Profile PLUS™ (Bone marrow or peripheral blood)

2)Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification KRAS, NRAS, TP53, FAM46C, DIS3 and BRAF, MYD88, IRF4, TP53, ATM, XBP1, PSMB5, del 13, del 17p13, t(4;14), t(11;14), t(14;16), t(14:20), (4p16 FGFR3/MMSET, 16q23 c-maf, 20q11 mafB, 11q13 CCND1, 6p21 CCND3) 1q21 amplification, 1p deletion MGUS, solitary plasmacytoma, smoldering myeloma, multiple myeloma, monoclonal gammopathy of renal significance.
Prognosis KRAS, NRAS, TP53, FAM46C, DIS3 and BRAF, MYD88, IRF4, TP53, ATM, XBP1, PSMB5, del 13, del 17p13, t(4;14), t(11;14), t(14;16), t(14:20), (4p16 FGFR3/MMSET, 16q23 c-maf, 20q11 mafB, 11q13 CCND1, 6p21 CCND3) 1q21 amplification, 1p deletion Short PFS, OS: t(4;14) or del(17p)
Treating Vs observing in sMM: del(17p13), del(13q), del(1p12), ampl(1q21), t(11;14), t(4;14), and t(14;16)
Selecting therapy XBP1, CRBN, PSMG2, NR3C1, KRAS, NRAS, TP53, FAM46C, DIS3 and BRAF, MYD88, IRF4, TP53, ATM, XBP1, PSMB5, del 13, del 17p13, t(4;14), t(11;14), t(14;16), t(14:20), (4p16 FGFR3/MMSET, 16q23 c-maf, 20q11 mafB, 11q13 CCND1, 6p21 CCND3) 1q21 amplification, 1p deletion Treating Vs observing in sMM: del(17p13), del(13q), del(1p12), ampl(1q21), t(11;14), t(4;14), and t(14;16)
Resistance to bortezomib: XBP1, CRBN, PSMG2, NR3C1
Drug inhibitors: BRAF, MDM2, RAS, TP53
Follow-up and minimal residual disease (MRD) KRAS, NRAS, TP53, FAM46C, DIS3 and BRAF, MYD88, IRF4, TP53, ATM, XBP1, PSMB5, NCCN: MRD negativity in the marrow (next-generation flow [NGF], next-generation sequencing [NGS], or both) and by imaging as defined below, confirmed minimum of 1 year apart. Subsequent evaluations can be used to further specify the duration of negativity (eg, MRD-negative at 5 years).

Hairy cell leukemia (HCL)

Recommended Test:

1)Hematology Profile PLUS™ (Bone marrow or peripheral blood) + IgH Mutation status

2)Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification IGHV4-34, BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8 NCCN guideline:
IGHV4-34 rearrangement behaves more like HCLv, IGHV4-34 HCL typically lacks BRAF V600E mutations.
MAP2K1 mutation in HCLv
Prognosis BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8 NCCN guideline:
IGHV4-34 rearrangement behaves more like HCLv, IGHV4-34 HCL typically lacks BRAF V600E mutations.
MAP2K1 mutation associated with resistance
Selecting therapy BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8, BTK, PCLG2 Drug inhibitors: BRAF, BTK inhibitors
Follow-up and minimal residual disease (MRD) BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8

Chronic myeloid leukemia (CML)

Recommended Test:

1)Hematology profile PLUS™ (Bone marrow or peripheral blood)

2)Minimal residual disease (MRD): Hematology Profile™ (Peripheral blood/cfDNA and BCR-ABL1 by PCR)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification BCR-ABL1 fusion, AB1, DNMT3A, EZH2, RUNX1, TET2, TP53, U2AF1 and ZRSR2.
Prognosis BCR-ABL1 fusion, AB1, DNMT3A, EZH2, RUNX1, TET2, TP53, U2AF1 and ZRSR2. Relevant upon evidence of progression
NCCN guideline:
E255K/V, F359C/V, Y253H, and T315I mutants are most commonly associated with disease progression and relapse.
Selecting therapy BCR-ABL1 fusion, AB1, DNMT3A, EZH2, RUNX1, TET2, TP53, U2AF1 and ZRSR2. NCCN guidelines:
The T315A, F317L/I/V/C, and V299L mutants are resistant to Dasatinib and E255K/V, F359V/C, and Y253H mutants are resistant to nilotinib.
Bosutinib has demonstrated activity in patients with BCR-ABL1 mutants resistant Todasatinib (F317L) and nilotinib (Y253H, E255K/V, and F359C/I/V). However, bosutinib has minimal activity against F317Lmutant while in vitro studies suggest that F317L is highly sensitive to nilotinib. Nilotinib may be preferred over bosutinib in patients with F317Lmutation. T315I, G250E, and V299L mutants are resistant to bosutinib. Ponatinib is active against BCR-ABL1 mutants resistant to Dasatinib or Nilotinib, including E255V, Y253H, and F359V, in addition to T315I.
Follow-up and minimal residual disease (MRD) BCR-ABL1 fusion by PCR

Indeterminate potential (CHIP)

Recommended Test:

Hematology Profile™ (Peripheral blood/cfDNA)

Clinical Indication
Genes/Molecular Abnormality
Remarks
Aiding in establishing diagnosis/stratification TET2, DNMT3A, ASXL1, JAK2, SF3B1, TP53 -Low levels (VAF <10%) in individuals above the age of 50
– Clonal cytopenias of undetermined significance (CCUS): Presence of cytopenia (anemia, low platelets, or white cells)
-19% in individuals with history of cancer treated with myelotoxic chemotherapy
Prognosis TET2, DNMT3A, ASXL1, JAK2, SF3B1, TP53 -VAF: 10-20%
– Progression to myeloid or lymphoid neoplasm:
0.5–1% per year
VAF: 10-20
Selecting therapy TET2, DNMT3A, ASXL1, JAK2, SF3B1, TP53 Monitoring VAF
Follow-up and minimal residual disease (MRD) TET2, DNMT3A, ASXL1, JAK2, SF3B1, TP53 Monitoring VAF