Clinical RNA sequencing clarifies variants of uncertain significance identified by prior testing

• Published in: Genetics in Medicine Open Vol. 2; p. 101886
• Main Authors: Marquez, Jonathan, Cech, Jennifer N., Paschal, Cate R., Dingmann, Bri, Scott, Anna I., Thies, Jenny M., Mills, Maria R., Albert, Catherine M., Beck, Anita E., Beckman, Erika, Bonkowski, Emily S., Earl, Dawn L., Lam, Christina T., Mefford, Heather C., Merritt, J. Lawrence, Nelson, Zoe, Ohlsen, Timothy J.D., Taylor, Mallory R., Perlman, Seth J., Rudzinski, Erin R., Sikes, Megan C., Waligorski, Natalie, Wenger, Tara L., Adam, Margaret P., Mirzaa, Ghayda M., Bennett, James T., Glass, Ian A., Sternen, Darci L., Miller, Danny E.
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 2024
• Subjects: Clinical genetic testing; Germline testing; RNA sequencing; Splice variants; Variant of uncertain significance; Germline testing; RNA sequencing; Clinical genetic testing; Splice variants; Variant of uncertain significance
• ISSN: 2949-7744; 2949-7744
• DOI: 10.1016/j.gimo.2024.101886

Sequencing-based genetic testing often identifies variants of uncertain significance (VUS) or fails to detect pathogenic variants altogether. We evaluated the utility of RNA sequencing (RNA-seq) to clarify VUS or identify missing variants in a clinical setting. Over a 2-year period, genetics providers at a single institution referred 26 cases for clinical RNA-seq. Cases had either no candidate variant identified by prior testing or a VUS suspected to impact splicing or expression. A committee reviewed each submission to ensure that it met study criteria. Among 26 cases, 8 could not be sequenced because of poor expression in an accessible tissue, 2 did not meet inclusion criteria, 3 were solved before collection, and 4 families declined participation or did not complete sample collection. For the 9 cases sequenced, the clinical laboratory reported 2 positive, 4 negative, and 3 “indeterminate.” For all 3 indeterminate cases, original RNA-seq data were manually evaluated and deemed explanatory. Clinical RNA-seq can clarify VUS, especially splice variants, but laboratory-specific interpretation guidelines may lead to indeterminate results. Identifying individuals likely to benefit from RNA-seq and providing appropriate counseling poses unique challenges.