2026 NPOP Complete_Disease_Coverage_Attachment.docx

Complete Disease Coverage Status NPOP Precision Oncology Program - All Malignancies With Detailed Missing Tests Coverage Summary:

Solid Tumors: 7 EXCELLENT, 13 PARTIAL,7 MAJOR GAPS Hematologic: ALL MAJOR GAPS Color Key:

Complete Disease List with Detailed Missing Tests

SOLID TUMOR MALIGNANCIES

• FISH for EWSR1::FLI1 fusion

• RT-PCR for EWSR1::FLI1 fusion

• ER, PR, HER2 (If HER2 is IHC2+, then reflex to HER2 FISH)

• HER2 FISH (if HER2 IHC is 2+)

• MammaPrint

• ER, PR, HER2 (If HER2 is IHC2+, then reflex to HER2 FISH) MMR

• ESR1 mutation testing (repeat testing is recommended)

• ER, PR, HER2 (If HER2 is IHC2+, then reflex to HER2 FISH) PD-L1, 22C3 Clone with CPS Score (pembrolizumab) MMR

• IDH 1 R132 mutation, ATRX, and H3 K27M

• IDH1 R132 mutation, ATRX

• 1p/19q FISH for codeletion CDKN2A/B homozygous loss

• TERT promoter mutation testing

• EGFR for amplification Chromosomes 7 and 10 for gain 7/loss 10

• Chromosomal microarray (aka Oncoscan FFPE)

• MGMT promoter methylation testing

• CDKN2A/B homozygous loss

• TERT promoter mutation testing

• Chromosomal microarray (aka Oncoscan FFPE)

• HPV

• PD-L1 clone 22C3 with CPS

• MLH1, MSH2, MSH6, PMS2

• Microsatellite instability (MSI) status by PCR

• MLH1 promoter hypermethylation testing (in the setting of loss of MLH1 or PMS2 expression by IHC). Hypermethylation suggests somatic mutation. Unmethylated calls for Germline Lynch testing.

• MMR IHC (MLH1, MSH2, MSH6, PMS2)

• MSI testing by PCR (GLA discontinued)

• PD-L1 IHC (clone 22C3 with CPS score)

• HER2 IHC

• HER2 FISH

• Claudin 18.2 IHC 1,000

• MMR testing by IHC (to be performed with or without MSI by PCR)

• MSI testing by PCR (to be performed with or without MMR by IHC)

• MMR testing by IHC

• MLH1, MSH2, MSH6, PMS2

• Microsatellite instability (MSI) status by PCR

• MMR IHC for Stage I (MLH1, MSH2, MSH6, PMS2) - Stage II-IV covered by CGP

• MSI testing by PCR (GLA discontinued)

• BRAF V600E IHC (if MLH1/PMS2 loss)

• BRAF V600E mutation testing (if MLH1/PMS2 loss)

• MLH1 promoter hypermethylation testing

• HER2 FISH (if 2+ on IHC)

• KIT PCR, with reflex to PDGFRA PCR

• MMR IHC (MLH1, MSH2, MSH6, PMS2)

• MSI testing by PCR (GLA discontinued)

• HER2 IHC

• HER2 FISH

• PD-L1 IHC (clone 22C3 with CPS score)

• Claudin 18.2 IHC

• MMR IHC for Stage I-III (MLH1, MSH2, MSH6, PMS2) - covered by CGP when CGP ordered

• MSI testing by PCR (GLA discontinued)

• BRAF V600E IHC (if MLH1/PMS2 loss)

• BRAF V600E mutation testing (if MLH1/PMS2 loss)

• MLH1 promoter hypermethylation testing 1,000

• MLH1, MSH2, MSH6, PMS2

• Microsatellite instability (MSI) status by PCR

• MLH1, MSH2, MSH6, PMS2

• TP53

• ER, PR

• Microsatellite instability (MSI) status by PCR**

• MLH1 promoter hypermethylation testing (in the setting of loss of MLH1 or PMS2 expression by IHC). Hypermethylation suggests somatic mutation. Unmethylated calls for Germline Lynch testing.

• HER2 IHC with reflex to FISH if 2+ on IHC (for trastuzumab) for serous endometrial or carcinosarcoma

• HER2 FISH if 2+ on IHC

• HPV

• HER2

• PD-L1 clone 22C3 with CPS

• MLH1, MSH2, MSH6, PMS2

• TP53

• Microsatellite instability (MSI) status by PCR (if CGP not performed)

• MLH1 promoter hypermethylation testing (in the setting of loss of MLH1 or PMS2 expression by IHC) hypermethylation suggests somatic mutation. Unmethylated calls for Germline Lynch testing.

• P16 IHC (for HPV status)

• ISH for EBV-encoded RNA (EBER)

• IHC for LMP1

• PD-L1 clone 22C3 with CPS 2,700

• EGFR mutation testing (Stage IB only - all other stages fully covered via CGP)

• BRAF V600E/K PCR

• BRAF V600E mutation

• BRAF V600E/K PCR KIT PCR

• Gene expression profiling for risk stratification

• Chromosomal micro array for risk stratification

• High resolution testing for HLA-A*02:01 for recurrent metastatic uveal melanoma only 4,300

• AR HER2 (for trastuzumab deruxtecan indication)

• HER2 FISH if IHC is 2+ (for trastuzumab alone)

• Genomic sequencing classifier

HEMATOLOGIC MALIGNANCIES

• Leukemia/lymphoma panel

• -5/-5q, -7/-7q, KMT2A, t(8;21) RUNX1::RUNX1T1, t(15;17) PML::RARA, t(16;16) or inv(16) CBFB::MYH11; t(9;22) BCR::ABL1; TP53

• Karyotype

• FLT3 ITD and TKD, IDH1/2, NPM1 (quantitative preferred), CEBPA (optional)

• NGS panel ASXL1, BCOR, CEBPA, EZH2, FLT3, IDH1, IDH2, NPM1, RUNX1, SF3B1, SRSF2, STAG2, TP53, U2AF1, and ZRSR2. Optional genes include: CBL, DDX41, KIT, KRAS, NRAS, and other genes associated with myeloid neoplasms.

• Leukemia/lymphoma panel

• t(15;17) PML::RARA

• Karyotype

• FLT3 ITD and TKD

• NGS panel ASXL1, BCOR, CEBPA, EZH2, FLT3, IDH1, IDH2, NPM1, RUNX1, SF3B1, SRSF2, STAG2, TP53, U2AF1, and ZRSR2. Optional genes include: CBL, DDX41, KIT, KRAS, NRAS, and other genes associated with myeloid neoplasms.

• PML::RARA quantitative PCR

• FISH panel should include probes for chromosomes 13q, 17p, 11q, and 12, t(11;14)

• TP53 sequencing

• IGHV hyper mutation status

• CpG-stimulated karyotype

• FISH panel should include probes for chromosomes 13q, 17p, 11q, and 12

• TP53 (If alteration not detected previously)

• BTK and PLCG2 sequencing (if BTK inhibitor resistant)

• MRD detection by flow cytometry or NGS (if clinically indicated)

• FISH (Bone marrow or peripheral blood) for t(9;22) BCR-ABL1

• Bone marrow karyotype*

• BCR-ABL1 quantitative PCR

• ABL1 kinase domain mutation analysis

• Hans algorithm testing for cell of origin CD10, MUM1, and BCL6

• IHC for BCL2, MYC double expressor status

• MYC, BCL2, BCL6 break apart FISH

• EBER in-situ hybridization (if morphologically concerning)

• Consider Ki67, Cyclin D1 (if pathologist recommended post discussion)

• Consider IHC for CD30 (if considering brentuximab therapy)

• Consider FISH for IRF4 rearrangement (if pathologist recommended post discussion)

• Consider IHC for TdT and CD34 if concerned for lymphoblastic lymphoma

• Consider CD5 and cyclin D1 if concerned for pleomorphic/blastoid mantle cell lymphoma

• Consider 11q abnormalities for Burkitt-like lymphoma

• Reticulin staining on bone marrow biopsy*

• FISH to rule out t(9;22) BCR-ABL1

• Bone marrow karyotype

• MPN reflex test: JAK2 V617F --> CALR (if JAK2 V617F negative) --> MPL (if CALR negative)

• Targeted myeloid NGS panel including ASXL1, BCOR, BCOR1, CBL, CUX1, DNMT3A, ETV6, EZH2, FLT3, IDH1, IDH2, KRAS, NPM1, NRAS, PHF6, RAD21, RUNX1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1, ZRSR2, JAK2, CALR, MPL, SETBP1, ETNK1, PTPN11, and NF1. Optional: DDX41.

• IHC for BCL2 and BCL6

• FISH for t(14;18), BCL6, IRF4 or IGH rearrangements, 1p36

• IHC for BCL2, BCL6, CD10 and MUM1

• FISH for IRF4/MUM1 cryptic rearrangement with IGH

• Expression of CD20, CD22, CD11c, CD200 and co-expression of CD25, CD103, CD123 TRAP, Annexin-A1, cyclin D1, TBX21/T-Bet

• BRAF V600E (If not tested by molecular)

• BRAF V600E (If not tested by IHC)

• Targeted sequencing for MYD88 and CXCR4 mutations

• Cyclin D1 (CCND1), TP53, SOX11, Ki-67

• Translocations t(11;14) Test for deletion 17p

• TP53 mutation

• Leukemia/lymphoma panel on bone marrow

• FISH (-bone marrow or peripheral blood) -- only if karyotype unsatisfactory or logistically difficult to order* MDS panel, including -5/5q; -7/7q; +8; del(20q)

• Bone marrow karyotype

• Targeted myeloid NGS panel required genes include: TP53, KMT2A, FLT3, SF3B1, NPM1, RUNX1, NRAS, ETV6, IDH2, CBL, EZH2, U2AF1, SRSF2, DNMT3A, ASXL1, KRAS; desired but optional genes include: BCOR, BCORL1, CEBPA, ETNK1, GATA2, GNB1, IDH1, NF1, PHF6, PPM1D, PRPF8, PTPN11, SETBP1, STAG2, WT1, DDX41.

• IHC for CD5, CD10, CD103, CD200, CD11c, CD25, CD23, BCL2, BCL6, cyclin D1, KI-67

• FISH for t(11;14) to differentiate from mantle cell lymphoma

• MYD88 mutation testing to differentiate from lymphoblastic lymphoma

• MYD88 mutation testing to differentiate from lymphoplasmacytic lymphoma. Please note that can be found in 5-10% of MALTs.

• FISH for MALT1 break apart, t(1;14), t(3;14), t(14;18), t(11;18)

• Trisomy 3 and trisomy 18. Please note that they may not be specific

• IHC for IgM, IgG, IgG4, IgA

• Reticulin stain. Consider Trichrome stain if reticulin is moderate or marked.

• Flow cytometry – Leukemia/lymphoma panel

• FISH for t(9;22) BCR::ABL1

• Bone marrow karyotype

• Targeted myeloid NGS panel including ASXL1, BCOR, BCOR1, CBL, CUX1, DNMT3A, ETV6, EZH2, FLT3, IDH1, IDH2, KRAS, NPM1, NRAS, PHF6, RAD21, RUNX1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1, ZRSR2, JAK2, CALR, MPL, SETBP1, ETNK1, PTPN11, and NF1. Optional: DDX41.

• Hans algorithm testing for cell of origin CD10, MUM1, and BCL6

• Consider IHC for CD30 (if considering brentuximab therapy)

• EBER in-situ hybridization

• MYC, BCL2, BCL6 break apart FISH to exclude high grade B-cell lymphoma

• Sufficient T-cell markers to confirm lineage and exclude specific entities

• Consider T-cell clonality if needed for diagnosis

• 1) ALK, CD30 2) T-cell markers to confirm lineage 3) PAX5 to exclude B-cell lineage

• FISH for TP63, DUSP22 rearrangement

• Reticulin staining on bone marrow biopsy*

• FISH (Peripheral blood or Bone marrow) to rule out t(9;22) BCR-ABL1

• Bone marrow karyotype

• JAK2 V617F with reflex to JAK2 sequencing of exons 12 - 15

• Targeted myeloid NGS panel including ASXL1, BCOR, BCOR1, CBL, CUX1, DNMT3A, ETV6, EZH2, FLT3, IDH1, IDH2, KRAS, NPM1, NRAS, PHF6, RAD21, RUNX1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1, ZRSR2, JAK2, CALR, MPL, SETBP1, ETNK1, PTPN11, AND NF1. Optional: DDX41

• FISH panel should be performed on CD138-sorted cells and include 17p (TP53), del 13, 1q21, 1p, and t(11;14). Additional upfront or reflex testing for t(4;14), t(14;16), and t(14;20)

• Flow cytometry

• Karyotyping

• MRD detection by flow cytometry or NGS (if clinically indicated)

Notes:

Coverage column shows: # of test types covered / # with gaps. Missing tests are listed in red in the table above.

Top Test Types Needed (by frequency):

1. IHC/Immunohistochemistry (32 gaps) - 17 diseases

· MMR (MLH1, MSH2, MSH6, PMS2)

· PD-L1 (clone 22C3)

· HER2, ER/PR

· Specialty stains (BCL2, BCL6, CD markers, claudin 18.2)

2. FISH (28 gaps) - 20 diseases

· HER2 FISH for solid tumors

· Chromosome abnormalities for heme (13q, 17p, 11q, etc.)

· Fusion detection (EWSR1, BCR-ABL1, etc.)

3. NGS/Sequencing Panels (25 gaps) - 19 diseases

· Myeloid NGS panels (ASXL1, FLT3, IDH1/2, NPM1, etc.) including rapid leukemia panels

· Single gene sequencing (TP53, IGHV, BTK, PLCG2)

4. PCR-based Tests (15 gaps) - 14 diseases

· MSI testing by PCR

· RT-PCR for fusions

· Quantitative PCR (BCR-ABL1, PML-RARA)

5. Karyotyping/Cytogenetics (11 gaps) - 11 diseases

· Bone marrow karyotype

· Chromosomal microarray

· CpG-stimulated karyotype

6. Flow Cytometry (7 gaps) - 6 diseases

· Leukemia/lymphoma panels

· MRD detection: DNA based, likely will need clonaseq.

· CD138-sorted cell analysis

7. Methylation Testing (3 gaps) - 3 diseases

· MLH1 promoter hypermethylation

· MGMT promoter methylation