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Table 2 Results of Routine Pathologic Evaluation, Tumor Tissue Analysis und Analysis of cfDNA

From: Molecular tumor analysis and liquid biopsy: a feasibility investigation analyzing circulating tumor DNA in patients with central nervous system lymphomas

Nr. Routine Pathologic Evaluation Tumor Tissue – NGS Panel Analysis cfDNA - Plasma cfDNA – CSF
  Histopathologic Diagnosis Tumor cells in CSF Number of somatic mutations a Selected Mutation for Assay (missense) MAF (TC) Tumor cfDNA MAF Tumor cfDNA MAF
1 Primary B-Cell Lymphoma no 24 EP400-c.7792G > A (Chr.12) 0.32b (50%) nod n.a.d nod n.a. d
2 Primary B-Cell Lymphoma no 1 MDM2-c.4G > A (Chr.12) 0.34b (50%) nod n.a. d nod n.a. d
3 Primary B-Cell Lymphoma no 20 TP53-c.845G > A (Chr.17) 0.44 (90%) yes 0.04 yes 0.49
4 Primary B-Cell Lymphoma yes 26 BCL10-c.677G > C (Chr.1) 0.47 (90%) yes 0.004 yes 0.47
5 Primary B-Cell Lymphoma yes 32 ETV6-c.1196G > A (Chr.12) 0.52b,c (50%) yes 0.02 yes 0.99 b,c
6 Unspecific Hypervascularity/No malignancy no 0 n.a. n.a. n.a. n.a. n.a. n.a.
  1. a2 independent somatic mutations within the same gene are counted as 2 mutations. Complex somatic aberrations on the same allele are counted as 1 mutation
  2. bLoss of wt allele
  3. cAdditional duplication of the mutated allele
  4. dIsolation of cfDNA failed in these samples, probably due to the isolation kit (see text)
  5. Nomenclature of the mutations is according to NM_015409.4 (EP400), NM_002392.5 (MDM2), NM_001126114.2 (TP53), NM_003921.4 (BCL10), NM_001987.4 (ETV6)
  6. TC tumor content (calculated based on the NAFs of various somatic mutations and single nucleotide variants both present in tumor and reference tissue)
  7. MAF mutant allele frequency = the frequency with which the mutated allele occurs in the sequencing (1 equals 100%). The observed frequencies are influenced by the tumor content and do not correlate directly with the mutation frequency in the tumor (real frequency = tumor content x MAF). The MAF is also influenced by copy number aberrations