Clinical impact of genomic testing in B-cell neoplasms
| Entity . | Genetic alteration: test . | Diagnostic use . | Clinical impact . | Future assays . |
|---|---|---|---|---|
| B-cell neoplasms | IG gene rearrangement: PCR-based assays with fragment analysis or HTS | Useful in certain circumstances to demonstrate monoclonality of B-cell lymphoproliferations to establish a diagnosis; mandatory in certain entities (eg, pediatric-type FL) | WGS for the detection of CNAs and SVs WTS to detect microenvironment signatures | |
| Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) | IGHV mutation status∗: IGHV sequencing | Prognostic and predictive. IGHV gene mutational status remains stable through the disease course and only needs to be performed once | Determining BcR stereotypy and IGLV3-21R110 mutation status for risk stratification; tracking of resistance mutations (BTK, PLCG2, and BCL2; supplemental Table 3) WGS for mutations, CNAs, SVs, and complex karyotype determination MRD testing using HTS to guide therapy decisions | |
| del(11q), +12, del(13q), del(17p)∗: FISH | Prognostic and del(17p) is predictive. FISH testing should be performed before each new course of therapy | |||
| TP53 mutations∗: HTS | Prognostic and predictive. TP53 sequencing should be performed before each new course of therapy unless already demonstrated | |||
| Detection of complex karyotype (≥5 abnormalities): cytogenetics∗ or SNP arrays | Prognostic | |||
| Hairy cell leukemia | BRAF V600E mutation: sequencing or IHC | Useful to support the diagnosis on biopsy samples and in cases with uncommon presentations463 | ||
| Follicularlymphoma (FL) | BCL2 rearrangement†: FISH (or cytogenetics) | Consider if BCL2 IHC is negative. Further workup of BCL2-R–negative FL shown in scenario 1B in Table 3 | ||
| EZH2 mutation†: HTS | EZH2 mutation is predictive of response to EZH2 inhibition.81 Tazemetostat is approved by the FDA for use in patients with EZH2-mutated FL (detected by an FDA-approved test) who have received at least 2 prior lines of systemic therapy (and all adult patients, including with wt EZH2 with relapsed/refractory disease and no other satisfactory alternative treatment options) | |||
| Marginal zone lymphomas (MZL) | BCL2 and CCND1 rearrangements: FISH†, MYD88 L265 mutation†: AS-PCR or HTS | Detection prompts considering a diagnosis of other entities; see scenarios 1 and 2 in Table 3 and supplemental Figure 3 | ||
| Extranodal MZL of mucosa associated lymphoid tissue (MALT lymphoma) | MALT1, BCL10, FOXP1 rearrangements†: FISH +3, +1888: cytogenetics and FISH | Detection is useful in certain circumstances to support the diagnosis | ||
| t(11;18) BIRC3::MALT1∗: FISH in H pylori–positive gastric MALT lymphoma | MALT1 rearrangements are associated with lack of antibiotic response in H pylori–positive gastric MALT lymphoma91 | |||
| SplenicMZL | del(7q)†, +3, +1888: cytogenetics and FISH KLF2, NOTCH2 mutations88: HTS | Detection is useful in certain circumstances to support the diagnosis | ||
| NodalMZL | +3, +1888: cytogenetics and FISH KLF2, NOTCH2, PTPRP88 mutations: HTS | Detection is useful in certain circumstances to support the diagnosis | ||
| Mantle cell lymphoma | CCND1 rearrangement†: FISH | Consider if CCND1 IHC is negative | MRD testing using HTS to guide treatment decisions WTS or targeted gene expression panel for proliferation and signatures of nnMCL vs cMCL | |
| CCND2 and CCND3 rearrangement†: FISH | Consider in CCND1-R–negative tumors | |||
| TP53 mutation∗: HTS‡ | Prognostic and guide management111 | |||
| Multiple myeloma (MM) MM-NOS MM with recurrent genetic abnormality MM with CCND family translocation MM with MAF family translocation MM with NSD2 translocation MM with hyperdiploidy | t(4;14) NSD2::IGH; t(14;16) IGH::MAF; t(11;14) CCND1::IGH;∗,§ gain of odd numbered chromosomes: FISH on bone marrow plasma cells (CD138-positive selected sample strongly recommended)∗ | Diagnostic of the ICC subtypes of MM | t(11;14) predictive of response to venetoclax134 | WGS for subtype assignment, risk stratification, and decision making MRD using HTS for decision making |
| t(4;14) NSD2::IGH; t(14;16) IGH::MAF; amp(1q); del(1p), del(17p)∗; TP53 mutations464, For SMM: t(4;14) NSD2::IGH; t(14;16) IGH::MAF; 1q gain/amplification; del(13)145 and MYC rearrangement139: FISH and HTS | Risk stratification at diagnosis and relapse | The adverse prognosis of high-risk genetics is partially overcome by the addition of a proteasome inhibitor131 and/or anti-CD38 MoAb132 to first-line therapy | ||
| Lymphoplasmacytic lymphoma | MYD88 L265 mutation: AS-PCR testing on bone marrow∗ (or other highly sensitive HTS-based method: consider AS-PCR as a reflex test if negative) | Diagnostic. Aids in the differential with small B-cell lymphomas; see scenario 2A in Table 3 | HTS methods for sensitive mutation detection | |
| CXCR4 mutations†: highly sensitive HTS-based method | Predictive of primary resistance to ibrutinib therapy160 | |||
| Diffuse large B-cell lymphoma, NOS Germinal center B-cell subtype Activated B-cell subtype | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required to exclude HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | See “High-grade B-cell lymphoma” | Genetic subtype assignment (eg, LymphGen187) by panel, exome or WGS and BCL2 and BCL6 rearrangement detection and WTS or targeted gene expression panels (DHITsig29/MHG signature199) HTS-based ctDNA testing465 for response-adapted management |
| COO determination: GEP or widely used IHC surrogates∗ | Required to assign DLBCL, NOS gene expression subtypes | Prognostic for outcomes following R-CHOP (GEP)466; predictive of response to treatment at relapse177 | ||
| High-grade B-cell lymphomas (HGBCL) HGBCL with MYC and BCL2 rearrangement (HGBCL-DH-BCL2) HGBCLwithMYCandBCL6rearrangement (HGBCL-DH-BCL6) HGBCL, NOS | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required for the diagnosis of HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | Prognostic and predictive: HGBCL-DH-BCL2 has poor prognosis with R-CHOP and likely benefits from treatment intensification467 | Rearrangement detection and MYC partner determination by HTS HTS analysis of HGBCL, NOS tumors to assign these tumors to definitive disease categories |
| Burkitt lymphoma | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required to exclude HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | ||
| Pediatric lymphomas | ||||
| Pediatric-type FL Pediatric nodal MZL | BCL2 or BCL6 rearrangements†: FISH IRF8, MAP2K1 TNFRSF14 mutations†: HTS B-cell clonality testing | Useful in certain circumstances for diagnosis; see also scenario 3A in Table 3. Of note, pediatric-type FL and pediatric nodal MZL are not readily distinguishable by genomic features | Detection of CNAs and SVs using HTS | |
| Large B-cell lymphoma with11qaberration | 11q aberration: SNP array or FISH | Required for diagnosis of LBCL-11q | ||
| Large B-cell lymphoma withIRF4rearrangement | IRF4 rearrangement: FISH CARD11, IRF4 mutations†: HTS | FISH required for diagnosis of LBCL-IRF4 rearrangement Useful in certain circumstances for diagnosis; see also scenario 3A in Table 3. | ||
| Classic Hodgkin lymphoma | ctDNA for the detection of genetic aberrations in the Hodgkin/Reed-Sternberg cells and for response-adapted therapy Detection of amplification of 9p24.1 by FISH as a favorable biomarker for PD1 inhibitors in relapsed/refractory CHL248 |
| Entity . | Genetic alteration: test . | Diagnostic use . | Clinical impact . | Future assays . |
|---|---|---|---|---|
| B-cell neoplasms | IG gene rearrangement: PCR-based assays with fragment analysis or HTS | Useful in certain circumstances to demonstrate monoclonality of B-cell lymphoproliferations to establish a diagnosis; mandatory in certain entities (eg, pediatric-type FL) | WGS for the detection of CNAs and SVs WTS to detect microenvironment signatures | |
| Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) | IGHV mutation status∗: IGHV sequencing | Prognostic and predictive. IGHV gene mutational status remains stable through the disease course and only needs to be performed once | Determining BcR stereotypy and IGLV3-21R110 mutation status for risk stratification; tracking of resistance mutations (BTK, PLCG2, and BCL2; supplemental Table 3) WGS for mutations, CNAs, SVs, and complex karyotype determination MRD testing using HTS to guide therapy decisions | |
| del(11q), +12, del(13q), del(17p)∗: FISH | Prognostic and del(17p) is predictive. FISH testing should be performed before each new course of therapy | |||
| TP53 mutations∗: HTS | Prognostic and predictive. TP53 sequencing should be performed before each new course of therapy unless already demonstrated | |||
| Detection of complex karyotype (≥5 abnormalities): cytogenetics∗ or SNP arrays | Prognostic | |||
| Hairy cell leukemia | BRAF V600E mutation: sequencing or IHC | Useful to support the diagnosis on biopsy samples and in cases with uncommon presentations463 | ||
| Follicularlymphoma (FL) | BCL2 rearrangement†: FISH (or cytogenetics) | Consider if BCL2 IHC is negative. Further workup of BCL2-R–negative FL shown in scenario 1B in Table 3 | ||
| EZH2 mutation†: HTS | EZH2 mutation is predictive of response to EZH2 inhibition.81 Tazemetostat is approved by the FDA for use in patients with EZH2-mutated FL (detected by an FDA-approved test) who have received at least 2 prior lines of systemic therapy (and all adult patients, including with wt EZH2 with relapsed/refractory disease and no other satisfactory alternative treatment options) | |||
| Marginal zone lymphomas (MZL) | BCL2 and CCND1 rearrangements: FISH†, MYD88 L265 mutation†: AS-PCR or HTS | Detection prompts considering a diagnosis of other entities; see scenarios 1 and 2 in Table 3 and supplemental Figure 3 | ||
| Extranodal MZL of mucosa associated lymphoid tissue (MALT lymphoma) | MALT1, BCL10, FOXP1 rearrangements†: FISH +3, +1888: cytogenetics and FISH | Detection is useful in certain circumstances to support the diagnosis | ||
| t(11;18) BIRC3::MALT1∗: FISH in H pylori–positive gastric MALT lymphoma | MALT1 rearrangements are associated with lack of antibiotic response in H pylori–positive gastric MALT lymphoma91 | |||
| SplenicMZL | del(7q)†, +3, +1888: cytogenetics and FISH KLF2, NOTCH2 mutations88: HTS | Detection is useful in certain circumstances to support the diagnosis | ||
| NodalMZL | +3, +1888: cytogenetics and FISH KLF2, NOTCH2, PTPRP88 mutations: HTS | Detection is useful in certain circumstances to support the diagnosis | ||
| Mantle cell lymphoma | CCND1 rearrangement†: FISH | Consider if CCND1 IHC is negative | MRD testing using HTS to guide treatment decisions WTS or targeted gene expression panel for proliferation and signatures of nnMCL vs cMCL | |
| CCND2 and CCND3 rearrangement†: FISH | Consider in CCND1-R–negative tumors | |||
| TP53 mutation∗: HTS‡ | Prognostic and guide management111 | |||
| Multiple myeloma (MM) MM-NOS MM with recurrent genetic abnormality MM with CCND family translocation MM with MAF family translocation MM with NSD2 translocation MM with hyperdiploidy | t(4;14) NSD2::IGH; t(14;16) IGH::MAF; t(11;14) CCND1::IGH;∗,§ gain of odd numbered chromosomes: FISH on bone marrow plasma cells (CD138-positive selected sample strongly recommended)∗ | Diagnostic of the ICC subtypes of MM | t(11;14) predictive of response to venetoclax134 | WGS for subtype assignment, risk stratification, and decision making MRD using HTS for decision making |
| t(4;14) NSD2::IGH; t(14;16) IGH::MAF; amp(1q); del(1p), del(17p)∗; TP53 mutations464, For SMM: t(4;14) NSD2::IGH; t(14;16) IGH::MAF; 1q gain/amplification; del(13)145 and MYC rearrangement139: FISH and HTS | Risk stratification at diagnosis and relapse | The adverse prognosis of high-risk genetics is partially overcome by the addition of a proteasome inhibitor131 and/or anti-CD38 MoAb132 to first-line therapy | ||
| Lymphoplasmacytic lymphoma | MYD88 L265 mutation: AS-PCR testing on bone marrow∗ (or other highly sensitive HTS-based method: consider AS-PCR as a reflex test if negative) | Diagnostic. Aids in the differential with small B-cell lymphomas; see scenario 2A in Table 3 | HTS methods for sensitive mutation detection | |
| CXCR4 mutations†: highly sensitive HTS-based method | Predictive of primary resistance to ibrutinib therapy160 | |||
| Diffuse large B-cell lymphoma, NOS Germinal center B-cell subtype Activated B-cell subtype | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required to exclude HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | See “High-grade B-cell lymphoma” | Genetic subtype assignment (eg, LymphGen187) by panel, exome or WGS and BCL2 and BCL6 rearrangement detection and WTS or targeted gene expression panels (DHITsig29/MHG signature199) HTS-based ctDNA testing465 for response-adapted management |
| COO determination: GEP or widely used IHC surrogates∗ | Required to assign DLBCL, NOS gene expression subtypes | Prognostic for outcomes following R-CHOP (GEP)466; predictive of response to treatment at relapse177 | ||
| High-grade B-cell lymphomas (HGBCL) HGBCL with MYC and BCL2 rearrangement (HGBCL-DH-BCL2) HGBCLwithMYCandBCL6rearrangement (HGBCL-DH-BCL6) HGBCL, NOS | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required for the diagnosis of HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | Prognostic and predictive: HGBCL-DH-BCL2 has poor prognosis with R-CHOP and likely benefits from treatment intensification467 | Rearrangement detection and MYC partner determination by HTS HTS analysis of HGBCL, NOS tumors to assign these tumors to definitive disease categories |
| Burkitt lymphoma | MYC, BCL2, and/or BCL6 rearrangement (latter two can be performed concurrently or only if MYC rearrangement is detected): FISH∗ | Required to exclude HGBCL-DH-BCL2 and HGBCL-DH-BCL6 | ||
| Pediatric lymphomas | ||||
| Pediatric-type FL Pediatric nodal MZL | BCL2 or BCL6 rearrangements†: FISH IRF8, MAP2K1 TNFRSF14 mutations†: HTS B-cell clonality testing | Useful in certain circumstances for diagnosis; see also scenario 3A in Table 3. Of note, pediatric-type FL and pediatric nodal MZL are not readily distinguishable by genomic features | Detection of CNAs and SVs using HTS | |
| Large B-cell lymphoma with11qaberration | 11q aberration: SNP array or FISH | Required for diagnosis of LBCL-11q | ||
| Large B-cell lymphoma withIRF4rearrangement | IRF4 rearrangement: FISH CARD11, IRF4 mutations†: HTS | FISH required for diagnosis of LBCL-IRF4 rearrangement Useful in certain circumstances for diagnosis; see also scenario 3A in Table 3. | ||
| Classic Hodgkin lymphoma | ctDNA for the detection of genetic aberrations in the Hodgkin/Reed-Sternberg cells and for response-adapted therapy Detection of amplification of 9p24.1 by FISH as a favorable biomarker for PD1 inhibitors in relapsed/refractory CHL248 |
AS-PCR, allele-specific polymerase chain reaction; BcR, B-cell receptor; BL, Burkitt lymphoma; BTK, Bruton’s tyrosine kinase; CHL, classic Hodgkin lymphoma; cMCL, conventional MCL; CLL, chronic lymphocytic leukemia; COO, cell-of-origin; ctDNA, circulating tumor DNA; DLBCL, diffuse large B-cell lymphoma; FDA, Food and Drug Administration; FL, follicular lymphoma; HGBCL, high-grade B-cell lymphoma; IGHV, immunoglobulin heavy variable; IHC, immunohistochemistry; LBCL-IRF4, large B-cell lymphoma with IRF4 rearrangement; MALT, mucosa-associated lymphoid tissue; MCL, mantle cell lymphoma; MHG, molecular high grade; MM, multiple myeloma; MRD, measurable residual disease; MZL, marginal zone lymphoma; NMZL, nodal MZL; NMM, newly diagnosed multiple myeloma; nnMCL, non-nodal MCL; NOS, not otherwise specified; R-CHOP, rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone; SLL, small lymphocytic lymphoma; SMM, smoldering multiple myeloma; SMZL, splenic MZL; SNP, single nucleotide polymorphism; wt, wild-type.
Required/strongly recommended in the National Comprehensive Cancer Network 2022 guidelines.
Useful in certain circumstances in the National Comprehensive Cancer Network 2022 guidelines.
IHC for TP53 has reported 82% sensitivity for TP53 missense mutations.468
IGH break-apart FISH can be used to screen before the other FISH assays are performed.