Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting

Blood. 2016 Jun 16;127(24):3004-14. doi: 10.1182/blood-2015-08-664649. Epub 2016 Mar 10.

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.

Publication types

  • Evaluation Study

MeSH terms

  • Chromosome Aberrations
  • Clinical Laboratory Techniques / methods
  • DNA Fingerprinting / methods*
  • DNA Mutational Analysis / methods
  • DNA, Neoplasm / analysis
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic
  • Genomics / methods*
  • Hematologic Neoplasms / genetics*
  • Hematologic Neoplasms / metabolism*
  • Hematologic Neoplasms / pathology
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mutation
  • Polymorphism, Genetic
  • RNA, Neoplasm / analysis
  • Sensitivity and Specificity
  • Systems Integration

Substances

  • DNA, Neoplasm
  • RNA, Neoplasm