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. 2017 Jul 18;8(29):48157-48168.
doi: 10.18632/oncotarget.18325.

Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma

Maxime Fontanilles  1   2 , Florent Marguet  3   4 , Élodie Bohers  2 , Pierre-Julien Viailly  2 , Sydney Dubois  2 , Philippe Bertrand  2 , Vincent Camus  1   2 , Sylvain Mareschal  2 , Philippe Ruminy  2 , Catherine Maingonnat  2 , Stéphane Lepretre  1 , Elena-Liana Veresezan  5 , Stéphane Derrey  6 , Hervé Tilly  1   2 , Jean-Michel Picquenot  5 , Annie Laquerrière  3   4 , Fabrice Jardin  1   2
Affiliations

Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma

Maxime Fontanilles et al. Oncotarget. .

Abstract

Purpose: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS).

Patients and methods: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®). First, patient-specific targeted sequencing of identified somatic mutations in tDNA was performed. Then, a second sequencing targeting MYD88 c.T778C was performed and compared to plasma samples from 25 age-matched control patients suffering from other types of cancer.

Results: According to the patient-specific targeted sequencing, eight patients (32% [95% CI 15-54%]) had detectable somatic mutations in cfDNA. Considering MYD88 sequencing, six patients had the specific c.T778C alteration detected in plasma. Using a control group, the sensitivity was 24% [9-45%] and the specificity was 100%. Tumor volume or deep brain structure involvement did not influence the detection of somatic mutations in plasma.

Conclusion: This pilot study provided evidence that somatic mutations can be detected by NGS in the cfDNA of a subset of patients suffering from PCNSL.

Keywords: circulating cell-free tumor DNA; liquid biopsy; next-generation sequencing; primary central nervous system lymphoma; somatic mutation.

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Conflict of interest statement

CONFLICTS OF INTEREST

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1. Mutational profile of tumor genomic alterations per patient (n=25)
The alterations are function-altering variants (SNV, insertion or deletion) and copy number variants (copy gain, heterozygous or homozygous deletion) detected per patient on the horizontal axis and per gene on the vertical axis for the entire PCNSL cohort. MYD88 and CDKN2A were the most commonly affected genes with regard to SNV and heterozygous or homozygous deletions, respectively.
Figure 2
Figure 2. The incidence of somatic mutations in PCNSL identified by Lymphopanel sequencing, and in the matched ctDNA according to the targeted panel sequencing
Mutation frequencies are expressed per gene in this stacked histogram. Black bars represent altered genes for PCNSL, dark gray bars represent the absolute proportion in the ctDNA, and light gray bars represent the relative proportion in the ctDNA.
Figure 3
Figure 3. Two representative examples of the mutant allele frequencies (MAF) identified in tumor and matched plasma ctDNA
The MAF corresponds to the proportion of mutated reads compared to all reads for one specific genomic location. The absence of a histogram bar indicates that no mutation was identified.
Figure 4
Figure 4. Two representative case-control examples of the detection of MYD88 c.T778C in plasma samples by NGS
See this image and copyright information in PMC

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