Feasibility and clinical utility of comprehensive genomic profiling of hematological malignancies

Abstract

Identification of genetic alterations through next-generation sequencing (NGS) can guide treatment decision-making by providing information on diagnosis, therapy selection, and prognostic stratification in patients with hematological malignancies. Although the utility of NGS-based genomic profiling assays was investigated in hematological malignancies, no assays sufficiently cover driver mutations, including recently discovered ones, as well as fusions and/or pathogenic germline variants. To address these issues, here we have devised an integrated DNA/RNA profiling assay to detect various types of somatic alterations and germline variants at once. Particularly, our assay can successfully identify copy number alterations and structural variations, including immunoglobulin heavy chain translocations, IKZF1 intragenic deletions, and rare fusions. Using this assay, we conducted a prospective study to investigate the feasibility and clinical usefulness of comprehensive genomic profiling for 452 recurrently altered genes in hematological malignancies. In total, 176 patients (with 188 specimens) were analyzed, in which at least one alteration was detected in 171 (97%) patients, with a median number of total alterations of 7 (0-55). Among them, 145 (82%), 86 (49%), and 102 (58%) patients harbored at least one clinically relevant alteration for diagnosis, treatment, and prognosis, respectively. The proportion of patients with clinically relevant alterations was the highest in acute myeloid leukemia, whereas this assay was less informative in T/natural killer-cell lymphoma. These results suggest the clinical utility of NGS-based genomic profiling, particularly for their diagnosis and prognostic prediction, thereby highlighting the promise of precision medicine in hematological malignancies.

Keywords: comprehensive genomic profiling; hematological malignancy; next-generation sequencing; precision medicine; somatic alteration.

FIGURE 1

Overview of the study using comprehensive genomic profiling of patients with hematological malignancies. (A) Schema of the prospective hospital‐based cohort study. (B) Strategy for capturing fusions by targeted RNA sequencing (RNA‐seq). (C) Detection rate of known alterations using cell lines according to alteration type. (D) Representative result of copy number (CN) analysis (top) and zoom‐in view for an IKZF1 deletion (bottom) in SUP‐B15 cell line. (E) Flow diagram showing enrollment, nucleic acid extraction, and sequencing. (F) Distribution of tissues and specimen types in all 188 specimens. (G) Distribution of disease types in 176 patients. ALAL, acute leukemias of ambiguous lineage; ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; BM, bone marrow; B‐NHL, B‐cell non‐Hodgkin lymphoma; BPDCN, blastic plasmacytoid dendritic cell neoplasm; DNA‐seq, DNA sequencing; FFPE, formalin‐fixed, paraffin‐embedded; HL, Hodgkin lymphoma; HSCT, hematopoietic stem cell transplantation; ITD, internal tandem duplication; LBL, lymphoblastic lymphoma; MDS, myelodysplastic syndrome; MM, multiple myeloma; MPN, myeloproliferative neoplasm; PB, peripheral blood; PTD, partial tandem duplication; SNP, single nucleotide polymorphism; SV, structural variation; T/NK‐NHL, T/natural killer‐cell non‐Hodgkin lymphoma

FIGURE 2

Frequencies and types of genetic alterations detected in clinical specimens from patients with hematological malignancies. (A) Number of somatic alterations detected in each patient (n = 176). (B) Number of patients with somatic alterations for each driver gene according to alteration type. Genes altered in ≥5 patients are shown. In case of >1 alteration type detected, they are considered multiple for tumor suppressor or functionally unknown genes, whereas only one major alteration type is counted for oncogenes. CNA, copy number alteration; ITD, internal tandem duplication; PTD, partial tandem duplication; SV, structural variation

FIGURE 3

Detection of activating and fusion‐generating structural variations (SVs) in clinical specimens from patients with hematological malignancies. (A) Distribution of breakpoints and partners of immunoglobulin heavy chain (IGH) translocations in B‐cell non‐Hodgkin lymphoma (B‐NHL; triangle) and multiple myeloma (MM; circle). (B) Distribution of breakpoints and partners of BCL6 SVs. (C) Rare fusions and SVs detected in this study. Red triangles represent SV breakpoints. AA, amino acid; DNA‐seq, DNA sequencing; EGF, epidermal growth factor; Ig, immunoglobulin; PEST, proline, glutamic acid, serine, and threonine; PTP, protein tyrosine phosphatase; Rbp, Recombination signal binding protein; RING, really interesting new gene; RNA‐seq, RNA sequencing; TRAF, tumor necrosis factor receptor‐associated factor

FIGURE 4

Spectrum of altered genes in clinical specimens from patients with hematological malignancies, by disease type. (A–E) Number of somatic alterations in patients diagnosed with (A) acute myeloid leukemia (AML), (B) acute lymphoblastic leukemia (ALL)/lymphoblastic lymphoma (LBL), (C) B‐cell non‐Hodgkin lymphoma (B‐NHL), (D) T/natural killer‐cell non‐Hodgkin lymphoma (T/NK‐NHL), and (E) multiple myeloma (MM). Stars represent the evidence level assigned to genes according to the Japanese Society of Hematology Genome Guideline in each disease type. In case of >1 alteration type detected, they are considered multiple for tumor suppressor or functionally unknown genes, whereas only one major alteration type is counted for oncogenes. CNA, copy number alteration; SV, structural variation

FIGURE 5

Clinical utility of comprehensive genomic profiling in hematological malignancies. Proportion of patients harboring at least one somatic alteration with indicated clinical evidence level according to the Japanese Society of Hematology Genome Guideline in acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL)/lymphoblastic lymphoma (LBL), B‐cell non‐Hodgkin lymphoma (B‐NHL), T/natural killer‐cell non‐Hodgkin lymphoma (T/NK‐NHL), and multiple myeloma (MM), and for all patients