Abstract
Background As knowledge of mechanisms that drive the development of cancer grows, there has been corresponding growth in therapies specific to a mechanism. While these therapies show improvements in patient outcomes, they can be expensive and are effective only for a subset of patients. These treatments drive interest in research focused on the assignment of cancer therapies based on aberrations in individual genes or biomarkers that assess the broader mutational landscape, including microsatellite instability (MSI) and tumor mutational burden (TMB).
Methods Here we describe the TruSight™ Oncology 500 (TSO500; Research Use Only) bioinformatics workflow. This tumor-only approach leverages the next-generation sequencing-based assay TSO500 to enable high fidelity determination of DNA variants across 523 cancer-relevant genes, as well as MSI status and TMB in formalin-fixed paraffin-embedded (FFPE) samples.
Results The TSO500 bioinformatic workflow integrates unique molecular identifier (UMI)-based error correction and a dual approach variant filtering strategy that combines statistical modeling of error rates and database annotations to achieve detection of variants with allele frequency approaching 5% with 99.9998% per base specificity and 99% sensitivity in FFPE samples representing a variety of tumor types. TMB determined using the tumor-only workflow of TSO500 correlated well with tumor-normal (N =170, adjusted R2=0.9945) and whole-exome sequencing (N=108, adjusted R2=0.933). Similarly, MSI status determined by TSO500 showed agreement (N=106, 98% agreement) with a MSI-PCR assay.
Conclusion TSO500 is an accurate tumor-only workflow that enables researchers to systematically characterize tumors and identify the next generation of clinical biomarkers.
Competing Interest Statement
All authors are employees and shareholders of Illumina Inc.
List of abbreviations
- MSI
- microsatellite instability
- TMB
- tumor mutational burden
- TSO500
- TruSight™ Oncology 500
- FFPE
- formalin-fixed paraffin-embedded
- UMI
- unique molecular identifier
- NGS
- next-generation sequencing
- IHC
- immunohistochemistry
- PCR
- polymerase chain reaction
- WES
- whole exome sequencing
- NRUMIs
- non-random unique molecular identifiers
- AQ
- variant quality score
- LQ
- likelihood ratio score
- COSMIC
- Catalogue of Somatic Mutations in Cancer
- CNV
- copy number variant
- VAFs
- Variant allele frequencies