Assessment of Diagnostic Outcomes of RNA Genetic Testing for Hereditary Cancer

Abstract

IMPORTANCE Performing DNA genetic testing (DGT) for hereditary cancer genes is now a wellaccepted clinical practice; however, the interpretation of DNA variation remains a challenge for laboratories and clinicians. Adding RNA genetic testing (RGT) enhances DGT by clarifying the clinical actionability of hereditary cancer gene variants, thus improving clinicians' ability to accurately apply strategies for cancer risk reduction and treatment. OBJECTIVE To evaluate whether RGT is associated with improvement in the diagnostic outcome of DGT and in the delivery of personalized cancer risk management for patients with hereditary cancer predisposition. DESIGN, SETTING, AND PARTICIPANTS Diagnostic study in which patients and/or families with inconclusive variants detected by DGT in genes associated with hereditary breast and ovarian cancer, Lynch syndrome, and hereditary diffuse gastric cancer sent blood samples for RGT from March 2016 to April 2018. Clinicians who ordered genetic testing and received a reclassification report for these variants were surveyed to assess whether RGT-related variant reclassifications changed clinical management of these patients. To quantify the potential number of tested individuals who could benefit from RGT, a cohort of 307 812 patients who underwent DGT for hereditary cancer were separately queried to identify variants predicted to affect splicing. Data analysis was conducted from March 2016 and September 2018. MAIN OUTCOMES AND MEASURES Variant reclassification outcomes following RGT, clinical management changes associated with RGT-related variant reclassifications, and the proportion of patients who would likely be affected by a concurrent DGT and RGT multigene panel testing approach. Author affiliations and article information are listed at the end of this article. Open Access. This is an open access article distributed under the terms of the CC-BY-NC-ND License.

Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation

“…Methods that enable quantification of the proportion of aberrantly spliced transcripts arising from a variant allele, such as recently developed RNA massively parallel sequencing assays (Farber-Katz et al, 2018;Karam et al, 2019), will aid in the interpretation of cases that demonstrate expression of naturally occurring alternatively spliced transcripts and greatly improve the contribution of splicing assays to classification of sequence variants once methods for quantifying transcript expression are routinely instituted. These assays will further increase the use and utility of splicing assay data in variant classification by fulfilling the requirement of quantifying the splicing defect to ensure no full-length transcript is expressed, as currently documented in the InSiGHT MMR gene classification rules (Thompson et al, 2014).…”

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing

“…Transcriptome sequencing (RNA-seq) is emerging as another tool in the genetic diagnostic toolbox, leading to a reported 7.5-36% improvement in the diagnostic rate depending on the sampled tissue and clinical phenotype (4)(5)(6)(7)(8), and aiding in the prioritization and resolution of variants of uncertain significance (9,10). The approach to RNA-seq analysis varies but generally focuses on differences in splicing and the expression levels of genes.…”

“…The approach to RNA-seq analysis varies but generally focuses on differences in splicing and the expression levels of genes. A traditional analytic approach relies on the time-consuming identification of candidate variants first in the ES/GS data that are then manually reviewed in the transcriptome to determine any functional consequences (8)(9)(10). While effective, there are several limitations to this strategy.…”

Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

“…In a recent study, RNA genetic test results facilitated classification of 88% of the cancer gene splicing variants selected for analysis as either pathogenic or benign, and was predicted to impact 1 in 43 individuals if performed simultaneously with DNA testing. 9 Thus, a substantial proportion of patients currently receiving DNA testing are likely to benefit from the addition of RNA genetic testing. Several studies have also identified pathogenic deep-intronic variants across a range of hereditary cancer conditions, including hereditary breast and ovarian cancer (HBOC), 10,11 Lynch syndrome, 12,13 familial adenomatous polyposis, 14 neurofibromatosis, 15 and Li-Fraumeni syndrome.…”