Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology

Abstract

Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. Molecular analyses resulted in a median number of 2.5 (gene panel) to 3.5 (WES/WGS ± TS) treatment recommendations per patient. Our results showed that approximately half of the therapy recommendations (TRs) of both sequencing programs were identical, while approximately one-third of the TRs in WES/WGS ± TS relied on biomarkers not covered by the panel. Eight of 10 molecularly informed therapy implementations were supported by the panel, the remaining two were based on biomarkers absent from the panel, highlighting the potential additional clinical benefit of WGS and TS.

Fig. 1. Study flow chart.

Extracted tumor DNA and RNA, as well as normal tissue DNA from 20 patients with one hematologic and 18 different advanced solid cancer diagnoses, were originally sequenced as participants in the MASTER program and discussed in the molecular tumor board (MTB) from 10/2015 to 12/2020 (MASTER 1). Aliquots of the same tumor DNA and RNA, as well as normal tissue DNA were then used for panel sequencing (annotation 06–10/2022). To harmonize and update WES/WGS ± TS data, MASTER 1 sequencing data was reanalyzed with the current bioinformatics pipeline of the MASTER program in 06/2023 (MASTER 2). Both panel sequencing and MASTER 2 data were evaluated by physicians trained in precision oncology with access to the patients’ medical history up to the MTB of MASTER 1 (evaluation panel: 06/2022–03/2023, evaluation MASTER 2: 06–08/2023). Therapy recommendations (TRs) and their underlying biomarkers (BMs) derived from the panel were then compared to TRs and underlying BMs from MASTER 1 (comparison 1) and MASTER 2 (comparison 2).

Fig. 2. Oncoplot depicting biomarkers of different alteration types used for therapy recommendations (black frame) or their presence (no frame) in both whole-exome/whole-genome ± transcriptome sequencing (WES/WGS ± TS) analyses MASTER 1 (M1) and MASTER 2 (M2) as well as panel sequencing (P) of all 20 study patients.

Deletions of NF1 (patient 9), CDKN2A/B (patients 3, 13, 14, 17, 20), and STK11 (patient 19) as well as gains of NTRK3 (patient 1) and PIM1 (patient 3) were all found in a retrospective analysis of panel sequencing data and therefore could not be used as therapy recommendation rationales in P. PVRL4 (patients 2 and 16), TACSTD2 (patients 2 and 7), MTAP (patients 3 and 17), FOLR1 and MSLN (both patient 13) are newer genes of interest in WGS/TS and were all retrospectively analyzed for M1; therefore, they were not available as biomarkers for physicians assessing M1. (MSI microsatellite instability, TMB tumor mutational burden, grid lines: no data available, blue: SNV/Indel [single nucleotide variation/small insertion or deletion], orange: CNV [copy number variation], dark green: DNA structural variant, light green: RNA fusion, pink: RNA expression, dark brown: multiple alteration types of one gene).

Fig. 3. Venn diagrams depicting the sum and categorization of therapy recommendations (TRs) and underlying biomarkers (BMs) in absolute numbers.

a Comparison 1: original whole-exome/whole-genome ± transcriptome sequencing (WES/WGS ± TS, MASTER 1) versus panel sequencing. b Comparison 2: reanalyzed WES/WGS ± TS (MASTER 2) versus panel sequencing. (exp data: RNA expression data, HRD Homologous recombination deficiency, SBS Single-base substitution).

Fig. 4. Head-to-head comparison of the most important findings of therapy recommendations (TRs) from the original whole-exome/whole-genome ± transcriptome sequencing (WES/WGS ± TS, MASTER 1), the reanalysis WES/WGS ± TS (MASTER 2), and the panel sequencing.

a Distribution of identical and different TRs in comparison 1 (MASTER 1 versus panel) and comparison 2 (MASTER 2 versus panel), and their underlying biomarkers (BMs). b TRs in MASTER 1 and MASTER 2 based on BMs not covered by the panel. c TRs in MASTER 1 and MASTER 2 based on copy number variations retrospectively detected in the panel by bin count analysis. d TRs based on identical BMs, which were not used as a TR rationale in the comparative analysis. (exp data: RNA expression data, HRD homologous recombination deficiency, SBS single-base substitution).