Germline Variants Incidentally Detected via Tumor-Only Genomic Profiling of Patients With Mesothelioma.

Importance: Patients with mesothelioma often have next-generation sequencing (NGS) of their tumor performed; tumor-only NGS may incidentally identify germline pathogenic or likely pathogenic (P/LP) variants despite not being designed for this purpose. It is unknown how frequently patients with mesothelioma have germline P/LP variants incidentally detected via tumor-only NGS. Objective: To determine the prevalence of incidental germline P/LP variants detected via tumor-only NGS of mesothelioma. Design, Setting, and Participants: A series of 161 unrelated patients with mesothelioma from a high-volume mesothelioma program had tumor-only and germline NGS performed during April 2016 to October 2021. Follow-up ranged from 18 months to 7 years. Tumor and germline assays were compared to determine which P/LP variants identified via tumor-only NGS were of germline origin. Data were analyzed from January to March 2023. Main Outcomes and Measures: The proportion of patients with mesothelioma who had P/LP germline variants incidentally detected via tumor-only NGS. Results: Of 161 patients with mesothelioma, 105 were male (65%), the mean (SD) age was 64.7 (11.2) years, and 156 patients (97%) self-identified as non-Hispanic White. Most (126 patients [78%]) had at least 1 potentially incidental P/LP germline variant. The positive predictive value of a potentially incidental germline P/LP variant on tumor-only NGS was 20%. Overall, 26 patients (16%) carried a P/LP germline variant. Germline P/LP variants were identified in ATM, ATR, BAP1, CHEK2, DDX41, FANCM, HAX1, MRE11A, MSH6, MUTYH, NF1, SAMD9L, and TMEM127. Conclusions and Relevance: In this case series of 161 patients with mesothelioma, 16% had confirmed germline P/LP variants. Given the implications of a hereditary cancer syndrome diagnosis for preventive care and familial counseling, clinical approaches for addressing incidental P/LP germline variants in tumor-only NGS are needed. Tumor-only sequencing should not replace dedicated germline testing. Universal germline testing is likely needed for patients with mesothelioma.

Truncating Variants in RFC1 in Cerebellar Ataxia, Neuropathy, and Vestibular Areflexia Syndrome.

BACKGROUND AND OBJECTIVE: Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease characterized by adult-onset and slowly progressive sensory neuropathy, cerebellar dysfunction, and vestibular impairment. In most cases, the disease is caused by biallelic (AAGGG)n repeat expansions in the second intron of the replication factor complex subunit 1 (RFC1). However, a small number of cases with typical CANVAS do not carry the common biallelic repeat expansion. The objective of this study was to expand the genotypic spectrum of CANVAS by identifying sequence variants in RFC1-coding region associated with this condition. METHODS: Fifteen individuals diagnosed with CANVAS and carrying only 1 heterozygous (AAGGG)n expansion in RFC1 underwent whole-genome sequencing or whole-exome sequencing to test for the presence of a second variant in RFC1 or other unrelated gene. To assess the effect of truncating variants on RFC1 expression, we tested the level of RFC1 transcript and protein on patients' derived cell lines. RESULTS: We identified 7 patients from 5 unrelated families with clinically defined CANVAS carrying a heterozygous (AAGGG)n expansion together with a second truncating variant in trans in RFC1, which included the following: c.1267C>T (p.Arg423Ter), c.1739_1740del (p.Lys580SerfsTer9), c.2191del (p.Gly731GlufsTer6), and c.2876del (p.Pro959GlnfsTer24). Patient fibroblasts containing the c.1267C>T (p.Arg423Ter) or c.2876del (p.Pro959GlnfsTer24) variants demonstrated nonsense-mediated mRNA decay and reduced RFC1 transcript and protein. DISCUSSION: Our report expands the genotype spectrum of RFC1 disease. Full RFC1 sequencing is recommended in cases affected by typical CANVAS and carrying monoallelic (AAGGG)n expansions. In addition, it sheds further light on the pathogenesis of RFC1 CANVAS because it supports the existence of a loss-of-function mechanism underlying this complex neurodegenerative condition.

Understanding and interpretation of a variant of uncertain significance (VUS) genetic test result by pediatric providers who do not specialize in genetics.

The advancement of genetic testing technologies has allowed for better diagnosis and management of patients, but also results in more variants of uncertain significance (VUSs) due to the increased number of genes being analyzed. There are more genetic tests available and more providers who do not specialize in genetics ordering genetic testing, but few studies examining how providers who do not specialize in genetics interpret VUSs. This study surveyed pediatric providers at a midwestern pediatric care center who do not specialize in genetics about their understanding of a mock genetic test report with a VUS result and whether their understanding of the result was associated with experience ordering genetic tests. Participants' preferences about content of the report and steps taken to understand the result were also examined. Of the 51 participants, 33% correctly answered both knowledge questions about the VUS result: one asking them to interpret the result and one asking them how they would explain the result to the patient. There was no association between answering both knowledge questions correctly and types of previous genetic tests ordered (p > .1 for 8 types of genetic tests), having received a genetic test report with a VUS result (p = .58), having referred patients to a genetics professional (p = .74), or feeling comfortable discussing a positive, negative, or VUS genetic test result (p > .4). This suggests that having previous experience ordering genetic tests does not contribute to the participants' knowledge about a variant of uncertain significance. Most participants reported that the amount of information in each section of the mock report was adequate. Participants were likely to reference multiple resources to better understand a VUS result, including published literature (82%), gene-specific databases (67%), and colleagues (63%). While these results cannot be generalized to all institutions, institutions can use the two knowledge questions to determine participants' understanding of genetic test results. This will help healthcare institutions determine methods that will best aide their providers who order genetic testing but do not specialize in genetics in learning more about the genetic testing process and better utilize results to improve patient care.

Reduction of Health Care Costs and Improved Appropriateness of Incoming Test Orders: the Impact of Genetic Counselor Review in an Academic Genetic Testing Laboratory.

The goal of this study was to evaluate the impact of genetic counselor (GC) review of incoming test orders received in an academic diagnostic molecular genetics laboratory. The GC team measured the proportion of orders that could be modified to improve efficiency or sensitivity, tracked provider uptake of GC proposed testing changes, and calculated the health care dollar savings resulting from GC intervention. During this 6-month study, the GC team reviewed 2367 incoming test orders. Of these, 109 orders (4.6%) were flagged for review for potentially inefficient or inappropriate test ordering. These flagged orders corresponded to a total of 51 cases (1-5 orders for each patient), representing 54 individuals and including 3 sibling pairs. The GC team proposed a modification for each flagged case and the ordering providers approved the proposed change for 49 of 51 cases (96.08%). For the 49 modifications, the cost savings totaled $98,750.64, for an average of $2015.32 saved per modification. This study provides evidence of the significant contribution of genetic counselors in a laboratory setting and demonstrates the benefit of laboratories working with ordering providers to identify the best test for their patients. The review of test orders by a genetic counselor both improves genetic test ordering strategies and decreases the amount of health care dollars spent on genetic testing.