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 Jd, 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
Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA.
Department of Laboratories, Seattle Children's Hospital, Seattle, WA.
Genet Med Open. 2024;2. doi: 10.1016/j.gimo.2024.101886. Epub 2024 Aug 9.
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 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 prior to collection, and 4 families declined participation or did not complete sample collection. For the 9 cases sequenced, the clinical laboratory reported two positive, four negative, and three "indeterminate." For all three indeterminate cases, original RNA-seq data was 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.
基于测序的基因检测常常会识别出意义未明的变异（VUS），或者完全未能检测到致病变异。我们评估了RNA测序（RNA-seq）在临床环境中澄清VUS或识别缺失变异的效用。
在两年时间里，一家机构的遗传学专家转诊了26例患者进行临床RNA测序。这些病例要么之前的检测未识别出候选变异，要么怀疑存在影响剪接或表达的VUS。一个委员会对每份提交的病例进行审查，以确保其符合研究标准。
在26例病例中，8例因可获取组织中的表达不佳而无法测序，2例不符合纳入标准，3例在样本采集前已得到解决，4个家庭拒绝参与或未完成样本采集。对于测序的9例病例，临床实验室报告了2例阳性、4例阴性和3例“不确定”。对于所有3例不确定病例，对原始RNA测序数据进行了人工评估并认为具有解释性。
临床RNA测序可以澄清VUS，尤其是剪接变异，但实验室特定的解读指南可能会导致不确定的结果。识别可能从RNA测序中受益的个体并提供适当的咨询带来了独特的挑战。
