Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies

Abstract

Despite its wide-ranging benefits, whole-transcriptome or RNA exome profiling is challenging to implement in a clinical diagnostic setting. The Unified Assay is a comprehensive workflow wherein exome-enriched RNA-sequencing (RNA-Seq) assays are performed on clinical samples and analyzed by a series of advanced machine learning-based classifiers. Gene expression signatures and rare and/or novel genomic events, including fusions, mitochondrial variants, and loss of heterozygosity were assessed using RNA-Seq data generated from 120,313 clinical samples across three clinical indications (thyroid cancer, lung cancer, and interstitial lung disease). Since its implementation, the data derived from the Unified Assay have allowed significantly more patients to avoid unnecessary diagnostic surgery and have played an important role in guiding follow-up decisions regarding treatment. Collectively, data from the Unified Assay show the utility of RNA-Seq and RNA expression signatures in the clinical laboratory, and their importance to the future of precision medicine.

Combined Afirma Genomic Sequencing Classifier and TERT promoter mutation detection in molecular assessment of Bethesda III–VI thyroid nodules

“…The Afirma GSC is run on an RNA exome (RNA-seq) platform; also referred to as the Veracyte unified assay. 4 The Afirma GSC was validated in adults on fresh thyroid nodule FNA samples shipped in FNAprotect, and consequently, its use for alternative samples such as those retrieved from slide scraping, has not been validated. Submitted samples are initially tested for RNA quantity and quality and adequate samples with at least 15 ng of RNA input are then processed.…”

“…Each sample is sequenced for 26,268 genes, providing data on gene and exon expression, mitochondrial expression, loss of heterozygosity, and detection of expressed gene variants and fusions. 4 While the actual number of genes per Afirma GSC classifier varies, no less than 10,196 genes are analyzed when the test is performed. As a result of this and other work, molecular testing for ITN to improve diagnostic accuracy and support clinical decision-making has been endorsed by the American Thyroid Association and the National Comprehensive Cancer Network Guidelines in Oncology (NCCN guidelines).…”

“…The Afirma GSC uses next generation RNA sequencing (RNA‐seq) and whole exome sequencing combined with machine learning algorithms to create classifiers that provide clinically meaningful diagnostic and prognostic information from thyroid nodule aspirates. Each sample is sequenced for 26,268 genes, providing data on gene and exon expression, mitochondrial expression, loss of heterozygosity, and detection of expressed gene variants and fusions 4 . While the actual number of genes per Afirma GSC classifier varies, no less than 10,196 genes are analyzed when the test is performed.…”