Author of

• 20164

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  P1.15 - SCLC/Neuroendocrine Tumors (ID 701)

  • Event: WCLC 2017
  • Type: Poster Session with Presenters Present
  • Track: SCLC/Neuroendocrine Tumors
  • Presentations: 1
  • Moderators:
  • Coordinates: 10/16/2017, 09:30 - 16:00, Exhibit Hall (Hall B + C)

  • 22796

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    P1.15-011 - Longitudinal Mutation Monitoring in Plasma Without Matching Tumor Tissue by Deep Sequencing in Small Cell Lung Cancer (SCLC) (ID 9622)

    09:30 - 09:30  |  Author(s): F.J. Herth
    • Abstract

    Background:
    SCLC is a devastating cancer with poor overall survival. Mutation profiles and treatment regimens differ significantly from non-small cell lung cancer (NSCLC). Here we demonstrate feasibility of monitoring patients with SCLC by deep sequencing from only 2 ml of plasma, without prior knowledge of the tumor tissue mutations relative to CT imaging.
    
    Method:
    Cell free DNA (cfDNA) was isolated from 64 longitudinal plasma samples (2ml) from 23 subjects with advanced SCLC using the cobas® cfDNA Sample Preparation Kit. The AVENIO ctDNA Surveillance kit (RUO, Roche, Pleasanton, CA, USA) with 197 genes detects SNVs, fusions, CNVs and InDels, and was used for sequencing the cfDNAs. Library preparation with 10-50ng cfDNA yielded a mean pre-capture library yield of 1,728ng. Mean % reads on-target was 65% with a mean deduped coverage of 3,397 fold. CT scans were reviewed to assess disease burden.
    
    Result:
    47 longitudinal plasma samples from 8 subjects were successfully analyzed without access to matched tumor tissue. Sixteen subjects with only one baseline plasma sample were excluded from further analysis. Subjects had 3-10 longitudinal plasma samples. Somatic variants were detected with allele frequency (AF) of >0.5% to 30% and 60-90% if they were present in cfDNA from at least three different time points. Germline variants were identified and removed if AFs were 40-60%, and >90%. All variants with frequencies >1% in ExAC were removed. Somatic variants were identified in TP53 (5), APC (2), NPAP1 (2), MKRN3 (2), BRAF, NFE2L2, CDKN2A, TIAM1, LRRTM1, NYP2, FAM135B, FAM71B, PIK3CG, KEAP1, DCAF12L1, PCDH15, EGFLAM. Tracking somatic variants in the longitudinal plasma samples allowed monitoring of treatment response at the molecular level for 6 of 8 subjects. In one subject with 10 longitudinal plasma samples mutations in five different genes were tracked at 1-3% AF before rising to 5- 20% at month 8 and 12-55% at month 9. Molecular progression was detected 1 month earlier than clinical progression by CT. Another subject had a TP53 splice mutation over 10 time points and through 3 lines of treatment and AF correlated with clinical response as measured by imaging.
    
    Conclusion:
    Subjects with advanced SCLC and mixed SCLC/NSCLC can be monitored at the mutation level using molecular barcoded duplex sequencing in longitudinal plasma samples. 2ml of plasma yielded sufficient cfDNA for testing with the Surveillance kit. Somatic mutation monitoring is possible without matching tumor tissue samples where longitudinal mutation profiles correlate with clinical response by CT imaging.