Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

TLDR

The study evaluates an integrated clinical test that uses whole‑genome, whole‑exome, and RNA‑seq sequencing to detect diverse somatic and germline mutations in 78 pediatric cancer patients. The analysis pipeline cross‑validates variants across the three sequencing platforms, eliminating confirmatory testing and enabling rapid, comprehensive reporting. Three‑platform sequencing achieved 97–99% PPV for SNVs, 99% for indels, 91% for structural variants, detected 240 pathogenic variants with 98% sensitivity versus 78% for WES+RNA‑seq, underscoring the necessity of WGS in pediatric oncology.

Abstract

Abstract To evaluate the potential of an integrated clinical test to detect diverse classes of somatic and germline mutations relevant to pediatric oncology, we performed three-platform whole-genome (WGS), whole exome (WES) and transcriptome (RNA-Seq) sequencing of tumors and normal tissue from 78 pediatric cancer patients in a CLIA-certified, CAP-accredited laboratory. Our analysis pipeline achieves high accuracy by cross-validating variants between sequencing types, thereby removing the need for confirmatory testing, and facilitates comprehensive reporting in a clinically-relevant timeframe. Three-platform sequencing has a positive predictive value of 97–99, 99, and 91% for somatic SNVs, indels and structural variations, respectively, based on independent experimental verification of 15,225 variants. We report 240 pathogenic variants across all cases, including 84 of 86 known from previous diagnostic testing (98% sensitivity). Combined WES and RNA-Seq, the current standard for precision oncology, achieved only 78% sensitivity. These results emphasize the critical need for incorporating WGS in pediatric oncology testing.