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e-Posters

47P - Comprehensive molecular analysis of tissue samples from cancer patients: Evaluation of a novel all-in-one NGS strategy for diagnosis and theranostic

Date

06 Oct 2021

Session

e-Posters

Presenters

Julie Dardare

Citation

Annals of Oncology (2021) 32 (suppl_6): S1345-S1371. 10.1016/annonc/annonc740

Authors

J. Dardare1, A. Witz2, M. Husson3, J. Merlin2, P. Gilson2, A. Harlé2

Author affiliations

  • 1 Université de Lorraine CNRS UMR 7039 CRAN, Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy/FR
  • 2 Université de Lorraine CNRS UMR 7039 CRAN, Service de Biopathologie, Institut de Cancérologie de Lorraine, 54519 - Vandoeuvre les Nancy/FR
  • 3 Institut de Cancérologie de Lorraine - Alexis Vautrin, 54519 - Vandoeuvre-les-Nancy/FR
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Abstract 47P

Background

DNAseq, RNAseq and determination of microsatellite instability (MSI) are now routine analyses in precision medicine for management of cancer patients. Analyzing DNA/RNA requires reliable assays often performed in two separate runs. Faced with limited quantity of total nucleic acids (TNA) extracted from FFPE this can be challenging. Sequential approaches (i.e. DNAseq followed by RNAseq) increase the turnaround time and cost, delaying treatment. Here, we evaluated a novel NGS approach developed by Invitae (San Francisco, USA). Using TNA from FFPE tissue, we detected SNVs, indels, MSI and structural rearrangements in one single NGS run.

Methods

24 samples from patients with various cancers were included, previously characterized using conventional methods: DNAseq, RNAseq, PCR, IHC or FISH. The study was approved by ICL ethical and scientific committee- all patients gave their consent. FFPE samples were qualified, selected followed by tumor cell content evaluation by a pathologist. After microdissection, TNAs were extracted and libraries were prepared using a parallel VariantPlex (DNA) and FusionPlex (RNA) kit from Invitae. Kits were designed to detect known and novel fusions in gene targets commonly encountered in solid tumors, MSI, and variants using a panel of 156 cancer-relevant target genes (71 DNA, 136 RNA).

Results

Among 9 previous SNVs/indels and 11 MSI samples identified by orthogonal methods, NGS approach confirmed all (100%). Among 12 fusions, 11 were detected by NGS (91.7%). Single ROS1 fusion scored low (1+) using IHC. Further analyses are conducted to determine whether the ROS1 fusion is false positive by IHC, or false negative by NGS.

Conclusions

Novel, all-in-one NGS approach from Invitae shows promising results by comprehensively detecting SNVs, indels, MSI and structural variants. Analyses of DNA and RNA using the novel NGS strategy improves the overall turn-around-time and cost-effectiveness. This can potentially aid clinicians and patients to take timely decisions regarding treatment modalities.

Legal entity responsible for the study

Institut de Cancérologie de Lorraine.

Funding

Invitae.

Disclosure

J-L. Merlin: Financial Interests, Personal, Invited Speaker: AstraZeneca; Financial Interests, Personal, Invited Speaker: BMS; Financial Interests, Personal, Invited Speaker: GSK; Financial Interests, Personal, Invited Speaker: Merck Serono; Financial Interests, Personal, Invited Speaker: Pfizer; Financial Interests, Personal, Invited Speaker: Novartis; Financial Interests, Personal, Invited Speaker: Roche; Financial Interests, Personal, Invited Speaker: MSD; Financial Interests, Personal, Invited Speaker: Amgen; Financial Interests, Personal, Invited Speaker: Sanofi; Financial Interests, Personal, Invited Speaker: Servier. P. Gilson: Non-Financial Interests, Personal, Training: AstraZeneca; Non-Financial Interests, Personal, Training: BMS; Non-Financial Interests, Personal, Training: Pfizer. A. Harlé: Financial Interests, Personal, Invited Speaker: GSK; Financial Interests, Personal, Advisory Board: GSK; Financial Interests, Personal, Advisory Board: Sophia Genetics; Financial Interests, Personal, Invited Speaker: AstraZeneca; Non-Financial Interests, Personal, Invited Speaker: AstraZeneca; Financial Interests, Personal, Invited Speaker: Amgen; Non-Financial Interests, Personal, Invited Speaker: Biocartis; Financial Interests, Personal, Invited Speaker: BioRad; Financial Interests, Personal, Invited Speaker: BMS; Non-Financial Interests, Personal, Invited Speaker: Illumina; Financial Interests, Personal, Invited Speaker: Merck Serono; Financial Interests, Personal, Invited Speaker: Novartis; Financial Interests, Personal, Invited Speaker: Pfizer; Financial Interests, Personal, Invited Speaker: Roche; Financial Interests, Personal, Invited Speaker: Sysmex Inostics; Financial Interests, Personal, Invited Speaker: Sanofi; Financial Interests, Personal, Invited Speaker: Tesaro. All other authors have declared no conflicts of interest.

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