Table 3.
Utility of genomic testing in selected diagnostic settings
| Diagnostic scenario | Genomic testing |
|---|---|
| Scenario 1: Small B-cell lymphomas | |
| 1A: CD5-positivesmall B-cell lymphoma: SLL/CLL; MCL; CD5-positive MZLs | Demonstration of CCND1, CCND2, or CCND3 rearrangement establishes the diagnosis of MCL; demonstration of BCL2 rearrangement is rare in SLL/CLL and favors FL. Overlapping and heterogeneous mutational landscapes; mutations in the following genes have the most discriminant value: ATM, BIRC3, MEF2B (favor MCL); BRAF, KLF2, NOTCH2, and PTPRD (favor MZLs), NOTCH1, SF3B1, XPO1 (favor SLL/CLL) |
| 1B: CD5-negative, CD10-negative,BCL2-R–negative small B-cell lymphoma: MZLs (including pediatric type); BCL2-R–negative, CD23-positive follicle center lymphoma; FL (without BCL2-R); hairy cell leukemia (tumor presentation) | Demonstration of BCL6 rearrangement or 1p36 deletion favors FL. Overlapping and heterogeneous mutational landscapes; mutations in the following genes have the most discriminant value: KLF2, NOTCH2, PTPRD, CARD11, IRF8, MAP2K1 (favor MZLs and pediatric-type MZL); CREBBP, EZH2, TNFRSF14 (in FLs), STAT6 (favor BCL2-R–negative, CD23-positive follicle center lymphoma); BRAF (in virtually all hairy cell leukemias, also in some MZLs) |
| 1C: Cutaneous involvement by follicular B-cell lymphoma: primary cutaneous follicle center lymphoma; systemic FL | Demonstration of BCL2 rearrangement favors systemic FL but does not exclude primary cutaneous follicle center lymphoma. Mutational landscapes overlap with less frequent incidence of mutations in BCL2, CREBBP, EP300, EZH2, KMT2D more frequent mutations in TNFAIP3, and similar occurrences of TNFRSF14 mutations or 1p36 deletions in primary cutaneous vs systemic cases |
| Scenario 2: B-cell neoplasms with plasmacytic differentiation and plasma cell neoplasms | |
| 2A: Small B-cell lymphoma with plasmacytic differentiation: LPL; nodal MZLs; splenic MZL; extranodal MZL (MALT lymphoma); FL | Demonstration of BCL2 rearrangement supports the diagnosis of FL. Demonstration of trisomies of chromosomes 3 and 18 or del(7q) supports the diagnosis of MZL. Translocations of MALT1, FOXP1, and BCL10 are specific for MALT lymphomas. MYD88L265P mutation is highly suggestive of LPL but not entirely specific because it is also found in a subset of other small B-cell lymphomas. Coexisting CXCR4 mutation further increases the specificity for LPL. Overlapping and heterogeneous mutational landscapes; mutations in the following genes have the most discriminant value: MYD88 and CXCR4 (favor LPL); BRAF, KLF2, NOTCH2, PTPRD, TNFAIP3 (favor MZLs); CREBBP, EZH2, TNFRSF14 (favor FL) |
| 2B: Bone marrow withIgM-secretingneoplasm: IgM MGUS, plasma cell type; IgM MGUS, NOS; LPL; IgM plasmacytoma; IgM plasma cell myeloma | Demonstration of translocations of CCND or MAF family genes or NSD2 indicates a plasma cell neoplasm. Mutational landscapes are distinct with MYD88L265P mutation present in most LPL and MGUS, NOS; other discriminant mutations involve ARID1A, CD79B, CXCR4, KMT2D (in lymphoplasmacytic neoplasms) and BRAF, DIS3, KRAS, NRAS, TENT5C, and TRAF3 (in plasma cell neoplasms). Genomic testing does not resolve the differential diagnosis of MGUS vs lymphoma or myeloma |
| 2C: Small B-cell lymphoma, with spleen, bone marrow, or blood involvement: splenic MZL; hairy cell leukemia; splenic diffuse red pulp small B-cell lymphoma; hairy cell leukemia variant; MCL | Demonstration of CCND1 rearrangement establishes the diagnosis of MCL. Detection of del(7q) is not discriminant in this context. Mutational landscapes are distinct with BRAFV600E mutation being a highly diagnostically sensitive marker for hairy cell leukemia, although not entirely specific; other mutations supportive of diagnosis in this context include MAP2K1 mutations (favor hairy cell leukemia variant); those in KLF2 and NOTCH2 (favor splenic MZL); and those in BCOR and CCND3 (favor splenic diffuse red pulp small B-cell lymphoma) |
| 2D:EBV-negativeplasmablastic neoplasm: plasmablastic lymphoma; plasmablastic MM; ALK-positive DLBCL | Demonstration of translocations of CCND or MAF families or NSD2 indicates an MM; ALK translocations (generally substituted by IHC) define ALK-positive DLBCL. Demonstration of MYC rearrangement while supporting the diagnosis of plasmablastic lymphoma does not exclude plasmablastic MM. Overlapping and heterogeneous mutational landscapes; mutations in the following genes more frequent in plasmablastic lymphoma: EP300, MYC, SOCS1, STAT3, TET2, and TP53 |
| Scenario 3: LBCLs | |
| 3A:Nodal-basedfollicular B-cell lymphoproliferations with a predominance of large cells in the pediatric population: pediatric-type FL; follicular hyperplasia; LBCL-IRF4 rearrangement; in adults: FL grade 3A; FL grade 3B; LBCL-IRF4 rearrangement | Demonstration of monoclonal IG gene rearrangement is useful to establish the diagnosis of lymphoma over reactive hyperplasia, in particular in pediatric conditions. Demonstration of BCL2 rearrangement favors grade 3A over grade 3B FL and excludes pediatric entities. BCL6 rearrangement occurs in both grade 3A and 3B cases, more commonly in 3B, but not in pediatric-type FL Demonstration of IRF4 (or IGH, IGK or IGL) rearrangements is essential for supporting LBCL-IRF4 rearrangement; demonstration of one or several IRF4 mutations in exon 1-2 is a strong indicator of IRF4 rearrangement including cryptic translocation. IRF4 rearrangement can be present in association with other rearrangement(s) (BCL2 or MYC) in DLBCLs, and these do not qualify for LBCL-IRF4. Overlapping and heterogeneous mutational landscapes; mutations in the following genes have the most discriminant value: IRF8 and MAP2K1 (pediatric-type FL; note that the same mutations are found in pediatric nodal MZL); IRF4 and MYC (LBCL-IRF4); CARD11 (LBCL-IRF4 and FL, not in pediatric-type FL); BCL2, CREBBP, EZH2, and KMT2D (FL) |
| 3B: Aggressive mature B-cell lymphomas: BL; LBCL with 11q aberration; HGBCL (NOS; with MYC and BCL2 rearrangements; with MYC and BCL6 rearrangements); DLBCL, NOS | Demonstration or exclusion of MYC, BCL2, and/or BCL6 rearrangements or 11q aberrations, are essential in this differential diagnosis and should be applied according to the algorithm presented in Figure 4. Mutations in ID3 and TCF3 favor BL whereas B2M, CREBBP, EZH2, MYD88L265P, SOCS1, and TNFRSF14 mutations favor other aggressive B-cell entities. Similarly, BCL2 mutations imply the presence of IGH::BCL2, thereby favoring entities other than BL |
| 3C: LBCL involving mediastinum: PMBCL; DLBCL, NOS involving mediastinum; mediastinal gray-zone lymphoma | Demonstration of BCL2 or BCL6 rearrangement favors DLBCL, NOS, as these uncommonly occur in PMBCL; conversely, CIITA rearrangement, CD274 rearrangement or CNV are typical of primary mediastinal lymphomas. Mutations in IL4R, ITPKB, NFKBIE, SOCS1, STAT6, and XPO1 are characteristic of PMBCL, while several genes often mutated in DLBCL, NOS, such as CD79B, CREBBP, KMT2D, MYD88, PIM1, and others, are not altered in PMBCL. Mediastinal gray-zone lymphoma has genomic features closer to PMBCL than to DLBCL, NOS, but distinctive genomic features between mediastinal gray-zone lymphoma and PMBCL are not described. Gene expression–based tests differentiate PMBCL from DLBCL, NOS |
| 3D: Cyclin D1–positive blastoid or pleomorphic B-cell neoplasm: MCL; DLBCL, NOS positive for cyclin D1 expression; DLBCL, NOS with CCND1 rearrangement | Demonstration of CCND1 translocation indicates MCL or DLBCL with CCND1 rearrangement. Demonstration of additional BCL2, BCL6, or MYC rearrangement is common in DLBCL with CCND1 translocation. Blastoid MCL may harbor secondary MYC rearrangement or TP53 mutations. Mutations in ATM, BIRC3, NSD2, and UBR5 support mantle cell lymphoma |
| Scenario 4: T-cell lymphoproliferations | |
| 4A: Hodgkin/Reed-Sternberg(–like) cells in a T-cell background: CHL; nodular lymphocyte-predominant B-cell lymphoma; T-cell/histiocyte-rich LBCL; TFHL; PTCL NOS. | Clonality testing for IG and TR rearrangements is useful in the differential diagnosis because a monoclonal TR rearrangement supports a diagnosis of T-cell lymphoma and argues against CHL or B-cell lymphomas; conversely, monoclonal IG rearrangements may be variably demonstrated in CHL, nodular lymphocyte-predominant B-cell lymphoma, and T-cell/histiocyte-rich LBCL as well as in PTCLs with an associated B-cell component (more often present in TFHLs). Demonstration of mutations in genes commonly mutated in T-cell lymphomas (CARD11, CD28, DNMT3A, IDH2, PLCG1, RHOA, STAT3, and TET2) supports that diagnosis; caution is required when interpreting mutations present only in TET2 and/or DNMT3A, which can be related to CH |
| 4B: Expansions of T cells with follicular helper phenotype: reactive TFH cells in benign lymphadenopathies; reactive TFH cells in small B-cell lymphomas; early involvement by TFHL | Demonstration of a monoclonal TR gene rearrangement or somatic mutations in other genes is useful in the distinction between reactive vs neoplastic expansions of TFH cells. Demonstration of mutations in genes commonly mutated in TFHL (most specific: IDH2 and RHOA; others: CARD11, CD28, DNMT3A, PLCG1, and TET2) supports TFHL; caution is required when interpreting mutations present only in TET2 and/or DNMT3A, which can be related to CH and are not per se indicative of a T-cell neoplasm; in cases of reactive TFH expansions, the presence of mutations in genes related to B-cell lymphomas favor MZLs or FLs |
| 4C:EBV-negativecytotoxic T-lymphocytosis in blood, bone marrow, or spleen: T-LGLL; HSTCL; reactive T-cell expansions | Monoclonal TR gene rearrangements or somatic mutations (PIK3CD, SETD2, STAT3, STAT5B, and TNFAIP3) favor neoplasia over reactive expansions. Isochromosome 7q is characteristic of HSTCL. Mutations in the following genes may help differentiating between HSTCL (CD8−/+ Tαβ or Tγδ) and CD8+Tαβ or Tγδ−LGLL: SETD2 (exclusive to HSTCL), STAT3 (less common in HSTCL than in T-LGLL), STAT5B (less common in T-LGLL than in HSTCL) |
| 4D: Intestinal T-cell lymphoproliferations: RCDII; EATL; MEITL; intestinal T-cell lymphoma, NOS; indolent gastrointestinal lymphoproliferative disorders | Demonstration of a monoclonal TR rearrangement is useful in the distinction of (type I refractory) celiac disease and RCDII, as well as for distinguishing indolent clonal T-lymphoproliferative disorders from prominent inflammatory infiltrates. T-cell or NK-cell lymphoproliferations are further supported by somatic mutations or fusions (STAT3, JAK3, JAK2::STAT3, others). Most discriminant mutated genes between EATL and MEITL are JAK1 and STAT3 (more commonly mutated in EATL) and GNAI2, JAK3, SETD2, and STAT5B (more commonly mutated in MEITL) |
| 4E: Lymphoproliferations of large CD30-positiveT cells: ALCL, ALK-positive; ALCL, ALK-negative; BIA-ALCL; PTCL, NOS; primary cutaneous CD30-positive lymphoproliferative disorders; transformed mycosis fungoides; subsets of EATL, or ENKTCL | Demonstration of ALK rearrangement (generally substituted by IHC) defines ALCL, ALK-positive. Demonstration of DUSP22 rearrangement in ALK-negative CD30-positive large-cell lymphoproliferations establishes the diagnosis of ALCL, ALK-negative, over PTCL, NOS, but does not discriminate between primary cutaneous vs systemic ALCL, ALK-negative. VAV1 and TP63 rearrangements occur in small subsets of ALCL, ALK-negative but are not specific for that entity. Demonstration of ALK, DUSP22, or TP63 translocations exclude BIA cases, whereas chromosome 20q loss is characteristic of that entity. Overlapping and heterogeneous mutational landscapes, including mutations in STAT3 and JAK1, are common to several entities |
| Scenario 5: Successive neoplasms | |
| Clonal relationship between successive hematologic neoplasms | Analysis of IG or TR gene rearrangements helps to distinguish between clonally related and clonally unrelated neoplasms and to establish transdifferentiation in cases of secondary histiocytic/dendritic cell neoplasms; interpretation may be ambiguous in cases of clonal evolution; sequencing-based clonality assays provide more precise results in that setting. Analysis of somatic mutations provides information on linear vs divergent evolution and secondary genomic alterations |
Refer to supplemental Figure 1 and supplemental Table 1 for prevalence of genetic aberrations in the major entities.
BIA, breast implant–associated; CHL, classic Hodgkin lymphoma; EATL, enteropathy-associated T-cell lymphoma; EBV, Epstein-Barr virus; MEITL, monomorphic epitheliotropic intestinal T-cell lymphoma; MGUS, monoclonal gammopathy of undetermined significance; PMBCL, primary mediastinal large B-cell lymphoma; PTCL, peripheral T-cell lymphoma; RCDII, type II refractory celiac disease.