ABSTRACT
The spectrum of somatic alterations in hematologic malignancies includes substitutions, insertions/deletions (indels), copy number alterations (CNAs), and a wide range of gene fusions; no current clinically available single assay captures the different types of alterations. We developed a novel next-generation sequencing-based assay to identify all classes of genomic alterations using archived formalin-fixed paraffin-embedded blood and bone marrow samples with high accuracy in a clinically relevant time frame, which is performed in our Clinical Laboratory Improvement Amendments-certified College of American Pathologists-accredited laboratory. Targeted capture of DNA/RNA and next-generation sequencing reliably identifies substitutions, indels, CNAs, and gene fusions, with similar accuracy to lower-throughput assays that focus on specific genes and types of genomic alterations. Profiling of 3696 samples identified recurrent somatic alterations that impact diagnosis, prognosis, and therapy selection. This comprehensive genomic profiling approach has proved effective in detecting all types of genomic alterations, including fusion transcripts, which increases the ability to identify clinically relevant genomic alterations with therapeutic relevance.
Subject(s)
DNA Fingerprinting/methods , Gene Expression Profiling/methods , Genomics/methods , Hematologic Neoplasms/genetics , Hematologic Neoplasms/metabolism , Chromosome Aberrations , Clinical Laboratory Techniques/methods , DNA Mutational Analysis/methods , DNA, Neoplasm/analysis , Gene Expression Regulation, Neoplastic , Hematologic Neoplasms/pathology , High-Throughput Nucleotide Sequencing , Humans , Mutation , Polymorphism, Genetic , RNA, Neoplasm/analysis , Sensitivity and Specificity , Systems IntegrationABSTRACT
Cure rates of children and adults with acute myeloid leukaemia (AML) remain unsatisfactory partly due to chemotherapy resistance. We investigated the genetic basis of AML in 107 primary cases by sequencing 670 genes mutated in haematological malignancies. SETBP1, ASXL1 and RELN mutations were significantly associated with primary chemoresistance. We identified genomic alterations not previously described in AML, together with distinct genes that were significantly overexpressed in therapy-resistant AML. Defined gene mutations were sufficient to explain primary induction failure in only a minority of cases. Thus, additional genetic or molecular mechanisms must cause primary chemoresistance in paediatric and adult AML.
Subject(s)
Drug Resistance, Neoplasm/genetics , Genomics/methods , Leukemia, Myeloid, Acute/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Carrier Proteins/genetics , Cell Adhesion Molecules, Neuronal/genetics , Child , Child, Preschool , Extracellular Matrix Proteins/genetics , Female , Gene Expression Profiling , Gene Expression Regulation, Leukemic , Humans , Infant , Male , Middle Aged , Mutation , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , Pregnancy , Reelin Protein , Remission Induction/methods , Repressor Proteins/genetics , Serine Endopeptidases/genetics , Treatment Failure , Young AdultABSTRACT
We sought to define the genomic landscape of diffuse large B-cell lymphoma (DLBCL) by using formalin-fixed paraffin-embedded (FFPE) biopsy specimens. We used targeted sequencing of genes altered in hematologic malignancies, including DNA coding sequence for 405 genes, noncoding sequence for 31 genes, and RNA coding sequence for 265 genes (FoundationOne-Heme). Short variants, rearrangements, and copy number alterations were determined. We studied 198 samples (114 de novo, 58 previously treated, and 26 large-cell transformation from follicular lymphoma). Median number of GAs per case was 6, with 97% of patients harboring at least one alteration. Recurrent GAs were detected in genes with established roles in DLBCL pathogenesis (e.g. MYD88, CREBBP, CD79B, EZH2), as well as notable differences compared to prior studies such as inactivating mutations in TET2 (5%). Less common GAs identified potential targets for approved or investigational therapies, including BRAF, CD274 (PD-L1), IDH2, and JAK1/2. TP53 mutations were more frequently observed in relapsed/refractory DLBCL, and predicted for lack of response to first-line chemotherapy, identifying a subset of patients that could be prioritized for novel therapies. Overall, 90% (n = 169) of the patients harbored a GA which could be explored for therapeutic intervention, with 54% (n = 107) harboring more than one putative target.