Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates

Nat Commun. 2017 May 11;8:15086. doi: 10.1038/ncomms15086.

Abstract

The requirement for bone-marrow aspirates for genomic profiling of multiple myeloma poses an obstacle to enrolment and retention of patients in clinical trials. We evaluated whether circulating cell-free DNA (cfDNA) analysis is comparable to molecular profiling of myeloma using bone-marrow tumour cells. We report here a hybrid-capture-based Liquid Biopsy Sequencing (LB-Seq) method used to sequence all protein-coding exons of KRAS, NRAS, BRAF, EGFR and PIK3CA in 64 cfDNA specimens from 53 myeloma patients to >20,000 × median coverage. This method includes a variant filtering algorithm that enables detection of tumour-derived fragments present in cfDNA at allele frequencies as low as 0.25% (median 3.2%, range 0.25-46%). Using LB-Seq analysis of 48 cfDNA specimens with matched bone-marrow data, we detect 49/51 likely somatic mutations, with subclonal hierarchies reflecting tumour profiling (96% concordance), and four additional mutations likely missed by bone-marrow testing (>98% specificity). Overall, LB-Seq is a high fidelity adjunct to genetic profiling of bone-marrow in multiple myeloma.

Publication types

  • Clinical Trial, Phase II
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Biomarkers, Tumor / blood
  • Biomarkers, Tumor / genetics*
  • Biopsy / ethics
  • Bone Marrow Cells / metabolism*
  • Bone Marrow Cells / pathology
  • Circulating Tumor DNA / blood
  • Circulating Tumor DNA / genetics*
  • Class I Phosphatidylinositol 3-Kinases / blood
  • Class I Phosphatidylinositol 3-Kinases / genetics
  • ErbB Receptors / blood
  • ErbB Receptors / genetics
  • GTP Phosphohydrolases / blood
  • GTP Phosphohydrolases / genetics
  • Gene Frequency
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Membrane Proteins / blood
  • Membrane Proteins / genetics
  • Multiple Myeloma / blood
  • Multiple Myeloma / diagnosis*
  • Multiple Myeloma / genetics*
  • Multiple Myeloma / pathology
  • Mutation*
  • Proto-Oncogene Proteins B-raf / blood
  • Proto-Oncogene Proteins B-raf / genetics
  • Proto-Oncogene Proteins p21(ras) / blood
  • Proto-Oncogene Proteins p21(ras) / genetics
  • Sensitivity and Specificity
  • Sequence Analysis, DNA

Substances

  • Biomarkers, Tumor
  • Circulating Tumor DNA
  • KRAS protein, human
  • Membrane Proteins
  • Class I Phosphatidylinositol 3-Kinases
  • PIK3CA protein, human
  • EGFR protein, human
  • ErbB Receptors
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf
  • GTP Phosphohydrolases
  • NRAS protein, human
  • Proto-Oncogene Proteins p21(ras)