Single Gene Testing Research Articles

A Cross-sectional Study of Regret in Cancer Patients After Sharing Test Results for Pathogenic Germline Variants of Hereditary Cancers With Relatives.

Research on whole genome/exome sequencing is increasing worldwide. However, challenges are emerging in relation to receiving germline pathogenic variant results and sharing them with relatives. The aim of this study was to investigate the occurrence of and reasoning related to regret among patients with cancer who shared single-gene testing results and whole exome sequencing with family members. This was a single-center, cross-sectional study. The Decision Regret Scale was administered, and descriptive questionnaires were used with 21 patients with cancer. Eight patients were classified as having no regret, 9 patients were classified as having mild regret, and 4 patients were classified as having moderate to strong regret. Reasons patients felt that sharing was the right decision included the following: to allow relatives and children to take preventive measures, the need for both parties to be aware of and ready for the hereditary transmission of cancer, and the need to be able to discuss the situation with others. On the other hand, some patients did not think it was a good decision to share the information because of the associated anxiety. Regret over sharing test results for pathogenic germline variants of hereditary cancers with relatives tended to be low. The main reason was that patients believed that they were able to benefit others by sharing. Healthcare professionals need to understand the postsharing perceptions and experiences of patients and support them throughout the sharing process.

Cost-Effectiveness of Next-Generation Sequencing Versus Single-Gene Testing for the Molecular Diagnosis of Patients With Metastatic Non-Small-Cell Lung Cancer From the Perspective of Spanish Reference Centers.

The aim of this study was to assess the cost-effectiveness of using next-generation sequencing (NGS) versus single-gene testing (SgT) for the detection of genetic molecular subtypes and oncogenic markers in patients with advanced non-small-cell lung cancer (NSCLC) in the setting of Spanish reference centers. A joint model combining decision tree with partitioned survival models was developed. A two-round consensus panel was performed to describe clinical practice of Spanish reference centers, providing data on testing rate, prevalence of alterations, turnaround times, and treatment pathways. Treatment efficacy data and utility values were obtained from the literature. Only direct costs (euros, 2022), obtained from Spanish databases, were included. A lifetime horizon was considered, so a 3% discount rate for future costs and outcomes was considered. Both deterministic and probabilistic sensitivity analyses were performed to assess uncertainty. A target population of 9,734 patients with advanced NSCLC was estimated. If NGS was used instead of SgT, 1,873 more alterations would be detected and 82 more patients could potentially be enrolled in clinical trials. In the long term, using NGS would provide 1,188 additional quality-adjusted life-years (QALYs) in the target population compared with SgT. On the other hand, the incremental cost of NGS versus SgT in the target population was €21,048,580 euros for a lifetime horizon (€1,333,288 for diagnosis phase only). The obtained incremental cost-utility ratios were €25,895 per QALY gained, below the standard cost-effectiveness thresholds. Using NGS in Spanish reference centers for the molecular diagnosis of patients with metastatic NSCLC would be a cost-effective strategy over SgT.

Budget Impact Analysis of Comprehensive Genomic Profiling in Advanced Non–Small Cell Lung Cancer in Taiwan

ObjectivesThe concept of precision oncology using genetic testing has become popular for cancer treatment in recent years. This research aimed to evaluate the financial impact of comprehensive genomic profiling (CGP) in patients with advanced non–small cell lung cancer before receiving any systemic treatments, compared with current practice using single-gene testing, in the hope that the findings can inform the National Health Insurance Administration the decision regarding CGP reimbursement. MethodsA budget impact analysis model was developed comparing the sum of gene testing costs, the first-line and subsequent systemic treatment costs, and other medical costs between the current practice of traditional molecular testing and the new test strategy of CGP. The evaluation time horizon is 5 years from the perspective of the National Health Insurance Administration. Outcome endpoints were incremental budget impact and life-year gained. ResultsThis research indicated CGP reimbursement would benefit 1072 to 1318 more patients receiving target therapies than the current practice and consequently had incremental 232 to 1844 life-years gained from 2022 to 2026. The new test strategy also led to higher gene testing cost and systemic treatment cost. Nevertheless, less medical resource utilization and better patient outcome were demonstrated. The incremental budget impact ranged from US dollar 19 to US dollar 27 million in the 5-year period. ConclusionThis research shows that CGP could pave the way for personalized healthcare with moderate increase of National Health Insurance budget.

Cost Savings of Expedited Care with Upfront Next-Generation Sequencing Testing versus Single-Gene Testing among Patients with Metastatic Non-Small Cell Lung Cancer Based on Current Canadian Practices.

This study assessed the total costs of testing, including the estimated costs of delaying care, associated with next-generation sequencing (NGS) versus single-gene testing strategies among patients with newly diagnosed metastatic non-small cell lung cancer (mNSCLC) from a Canadian public payer perspective. A decision tree model considered testing for genomic alterations using tissue biopsy NGS or single-gene strategies following Canadian guideline recommendations. Inputs included prevalence of mNSCLC, the proportion that tested positive for each genomic alteration, rebiopsy rates, time to test results, testing/medical costs, and costs of delaying care based on literature, public data, and expert opinion. Among 1,000,000 hypothetical publicly insured adult Canadians (382 with mNSCLC), the proportion of patients that tested positive for a genomic alteration with an approved targeted therapy was 38.0% for NGS and 26.1% for single-gene strategies. The estimated mean time to appropriate targeted therapy initiation was 5.1 weeks for NGS and 9.2 weeks for single-gene strategies. Based on literature, each week of delayed care cost CAD 406, translating to total mean per-patient costs of CAD 3480 for NGS and CAD 5632 for single-gene strategies. NGS testing with mNSCLC in current Canadian practice resulted in more patients with an identified mutation, shorter time to appropriate targeted therapy initiation, and lower total testing costs compared to single-gene strategies.

Clinical and laboratory genetic counselor attitudes on the reporting of variants of uncertain significance for multigene cancer panels.

Research suggests variants of uncertain significance (VUSs) present a variety of challenges for genetic counselors (GCs), nongenetics clinicians, and patients. Multigene cancer panels reveal more VUSs than single gene testing as a result of the increase in the number of genes being tested. This study surveyed 87 clinical cancer GCs involved with direct patient care and 19 laboratory GCs who provide guidance to clinicians regarding genetic test results about their attitudes on various options for the reporting of VUSs by laboratories for broad multigene cancer panels. Independent samples t-tests were utilized to compare the two groups. Based on a six-point Likert-type scale (1=Strongly Disagree to 6=Strongly Agree), clinical cancer GCs (M=5.4; SD=0.8) and laboratory GCs (M=5.2; SD=0.9) agreed overall that VUSs should be reported (p=0.44; Cohen's d=0.21). When asked about specific reporting options, both clinical cancer GCs (M=1.9; SD=1.1) and laboratory GCs (M=2.1; SD=1.4) disagreed that VUSs should be reported only for genes related to the indication for testing (p=0.50; Cohen's d=0.17). Overall, most GCs felt clinicians should not choose whether VUSs should be reported on genetic test results, with clinical cancer GCs (M=1.9; SD=1.3) feeling more strongly against it than laboratory GCs (M=3.1; SD=1.4; p=0.002; Cohen's d=0.88). Generally, GCs were more in favor of VUSs not being reported for population-based screening, with laboratory GCs (M=4.7; SD=0.8) agreeing more with that practice than clinical cancer GCs (M=3.7; SD=1.4; p=0.001; Cohen's d=0.80). Both clinical cancer GCs (M=4.1; SD=1.2) and laboratory GCs (M=3.9; SD=1.2) agreed additional guidelines on how to approach VUSs in clinical practice should be developed (p=0.54; Cohen's d=0.17). While most GCs supported the reporting of VUSs overall, our analyses suggest clinical cancer and laboratory GCs may have different attitudes toward specific VUS-related reporting options. Further research is needed to elucidate GC preferences to help inform best practices for the reporting of VUSs. The development of additional standardized guidelines on how to approach VUSs would further support clinical practice.

Discordance between germline genetic findings and abnormal tumor immunohistochemistry staining of mismatch repair proteins in individuals with suspected Lynch syndrome.

Tumor immunohistochemical staining (IHC) of DNA mismatch repair (MMR) proteins is often used to guide germline genetic testing and variant classification for patients with suspected Lynch syndrome. This analysis examined the spectrum of germline findings in a cohort of individuals showing abnormal tumor IHC. We assessed individuals with reported abnormal IHC findings and referred for testing with a six-gene syndrome-specific panel (n=703). Pathogenic variants (PVs) and variants of uncertain significance (VUS) in MMR genes were designated expected/unexpected relative to IHC results. The PV positive rate was 23.2% (163/703; 95% confidence interval [CI], 20.1%-26.5%); 8.0% (13/163; 95% CI, 4.3%-13.3%) of PV carriers had a PV in an unexpected MMR gene. Overall, 121 individuals carried VUS in MMR genes expected to be mutated based on IHC results. Based on independent evidence, in 47.1% (57/121; 95% CI, 38.0%-56.4%) of these individuals the VUSs were later reclassified as benign and in 14.0% (17/121; 95% CI, 8.4%-21.5%) of these individuals the VUSs were reclassified as pathogenic. Among patients with abnormal IHC findings, IHC-guided single-gene genetic testing may miss 8% of individuals with Lynch syndrome. In addition, in patients with VUS identified in MMR genes predicted to be mutated by IHC, extreme caution must be taken when the IHC results are considered in variant classification.

Utilisation of exome sequencing for muscular disorders in Thai paediatric patients: diagnostic yield and mutational spectrum

Muscular dystrophies and congenital myopathies are heterogeneous groups of inherited muscular disorders. An accurate diagnosis is challenging due to their complex clinical presentations and genetic heterogeneity. This study aimed to determine the utilisation of exome sequencing (ES) for Thai paediatric patients with muscular disorders. Of 176 paediatric patients suspected of genetic/inherited myopathies, 133 patients received a molecular diagnosis after performing conventional investigations, single gene testing, and gene panels. The remaining 43 patients from 42 families could be classified into three groups: Group 1, MLPA-negative Duchenne muscular dystrophy (DMD) with 9 patients (9/43; 21%), Group 2, other muscular dystrophies (MD) with 18 patients (18/43; 42%) and Group 3, congenital myopathies (CM) with 16 patients (16/43; 37%). All underwent exome sequencing which could identify pathogenic variants in 8/9 (89%), 14/18 (78%), and 8/16 (50%), for each Group, respectively. Overall, the diagnostic yield of ES was 70% (30/43) and 36 pathogenic/likely pathogenic variants in 14 genes were identified. 18 variants have never been previously reported. Molecular diagnoses provided by ES changed management in 22/30 (73%) of the patients. Our study demonstrates the clinical utility and implications of ES in inherited myopathies.

Modeling Costs and Life-Years Gained by Population-Wide Next-Generation Sequencing or Single-Gene Testing in Nonsquamous Non-Small-Cell Lung Cancer in the United States.

Many patients with actionable driver oncogenes (ADOs) are never identified and thus never receive targeted treatment. This study evaluated the economic impact and the potential life-years gained (LYG) that can be attributed to the extent of next-generation sequencing (NGS) testing in the United States compared with single-gene testing (SGT) in patients with metastatic nonsquamous non-small-cell lung cancer in the United States. A model was developed to evaluate incremental rates of SGT or NSG testing on the basis of LYG and cost per LYG. ADOs included for NGS included EGFR, ALK, ROS1, BRAF, RET, MET, and NTRK. SGT included EGFR and ALK. Assumptions were made for expected incidence of ADOs. Survival distributions were fit to published trial averages of median and 5-year overall survival. Treatment costs were estimated from drug cost averages. Reimbursement costs were based on data from the Center for Medicare and Medicaid Services. Each incremental 10% increase in NGS testing produces an average of 2,627.4 additional LYG, with an average cost savings per LYG of $75 US dollars (USD). Replacing SGT at the current rate of 80% with NGS testing would result in an average additional 21,09.6 LYG and reduce cost per LYG by an average of $599 USD. If 100% of eligible patients were tested with NGS and each identified patient had matched treatment, the total average cost per LYG would be $16,641.57 USD. On the basis of current evidence, population-level simulations demonstrate that clinically relevant gains in survival with non-negligible reduction in costs are obtainable from widespread adoption of NGS testing and appropriate treatment matching for patients with advanced nonsquamous non-small-cell lung cancer.

Retrospective Assessment of Complementary Liquid Biopsy on Tissue Single-Gene Testing for Tumor Genotyping in Advanced NSCLC.

Biomarker testing is key for non-small cell lung cancer (NSCLC) management and plasma based next-generation sequencing (NGS) is increasingly characterized as a non-invasive alternative. This study aimed to evaluate the value of complementary circulating tumor DNA (ctDNA) NGS on tissue single-gene testing (SGT). Ninety-one advanced stage NSCLC patients with tumor genotyping by tissue SGT (3 genes) followed by ctDNA (38 genes amplicon panel) were included. ctDNA was positive in 47% (n = 43) and identified a targetable biomarker in 19 patients (21%). The likelihood of positivity on ctDNA was higher if patients had extra-thoracic disease (59%) or were not under active treatment (59%). When compared to SGT, ctDNA provided additional information in 41% but missed a known alteration in 8%. Therapeutic change for targeted therapy based on ctDNA occurred in five patients (5%), while seven patients with missed alterations on ctDNA had EGFR mutations or ALK fusions. The median turnaround time of ctDNA was 10 days (range 6-25), shorter (p = 0.002) than the cumulative delays for the tissue testing trajectory until biomarker availability (13 d; range 7-1737). Overall, the results from this study recapitulate the potential and limitations of ctDNA when used complementarily to tissue testing with limited biomarker coverage.

The Use of Next-Generation Sequencing in Pharmacogenomics.

Next-generation sequencing (NGS) methods have become more commonly performed in clinical and research laboratories. This review summarizes the current laboratory NGS-based diagnostic approaches in pharmacogenomics including targeted multi-gene panel sequencing, whole-exome sequencing (WES), and whole-genome sequencing (WGS). Clinical laboratories perform multiple non-uniform types of pharmacogenetic panels, which can reduce the overall number of single-gene tests to be more cost-efficient. Compared to the targeted multi-gene panels, which are not typically designed to detect novel variants, WES and WGS have a greater potential to identify secondary pharmacogenomic findings, which might be predictive for the pharmacotherapy outcome of different patient settings. WGS overcomes the limitations of WES enabling a more accurate exome-sequencing at appropriate coverage and the sequencing of non-coding regions. Different NGS-based study designs with different test strategies and study populations, varying sample sizes, and distinct analytical and interpretation procedures lead to different identification results of pharmacogenomic variants. The rapid progress in gene sequencing technologies will overcome the clinical and laboratory challenges of WES and WGS. Further high throughput NGS-based pharmacogenomics studies in different populations and patient settings are necessary to expand knowledge about rare functional variants and to enhance translation in clinical practice.

Renal Genetics Clinic: 3-Year Experience in the Cleveland Clinic

There has been an increasing demand for the expertise provided by a renal genetics clinic. Such programs are limited in the United States and typically operate in a genomics research setting. Here we report a 3-year, real-world, single-center renal genetics clinic experience. Retrospective cohort. Outpatient cases referred to the renal genetics clinic of the Cleveland Clinic between January 2019 and March 2022 were reviewed. Clinical and laboratory characteristics were analyzed. All genetic testing was performed in clinical labs. 309 new patients referred from 15 specialties were evaluated, including 118 males and 191 females aged 35.1±20.3 years. Glomerular diseases were the leading presentation followed by cystic kidney diseases, electrolyte disorders, congenital anomalies of kidneys and urinary tract, nephrolithiasis, and tubulointerstitial kidney diseases. Dysmorphic features were noted in 27 (8.7%) patients. Genetic testing was recommended in 292 (94.5%) patients including chromosomal microarray (8.9%), single-gene tests (19.5%), multigene panels (77.3%), and exome sequencing (17.5%). 80.5% of patients received insurance coverage for genetic testing. 45% (115/256) of patients had positive results, 25% (64/256) had variants of unknown significance, and 22.3% (57/256) had negative results. 43 distinct monogenic disorders were diagnosed. Family history of kidney disease was present in 52.8% of patients and associated with positive genetic findings (OR, 2.28; 95% CI, 1.40-3.74). 69% of patients with positive results received a new diagnosis and/or a change in the diagnosis. Among these, 39.7% (31/78) of patients received a significant change in disease management. Retrospective and single-center study. The renal genetics clinic plays important roles in the diagnosis and management of patients with genetic kidney diseases. Multigene panels are the most frequently used testing modality with a high diagnostic yield. Family history of kidney disease is a strong indication for renal genetics clinic referral.

CO157 The Clinical and Economic Impact of Nationwide Insurance Coverage for Next-Generation Sequencing in Advanced Ovarian Cancer: A Retrospective Observational Study Using the Nationwide Database in South Korea

ext-generation sequencing (NGS) has been covered by Korean national health insurance since March 2017 for patients with cancer. This study compared the clinical and economic impact of NGS with that of single gene tests (SGTs).

Budget impact analysis of next-generation sequencing versus sequential single-gene testing in Japanese patients with advanced non-small-cell lung cancer

BackgroundIdentification of genomic alterations (e.g., EGFR, ALK, ROS1, BRAF, NTRK, and MET) is essential for initiating targeted therapy in patients with advanced non-small-cell lung cancer (aNSCLC). This study estimated the budget impact of using the sequential single-gene (SSG) test, which tests for each mutation one at a time, versus next-generation sequencing (NGS), which tests for all mutations at the same time, among newly diagnosed patients with aNSCLC from a Japanese healthcare payer’s perspective. MethodsA budget impact model (BIM) was used to determine the expected budget impact associated with NGS for newly diagnosed aNSCLC in Japan over a 3-year period. The BIM compared the total costs (biopsy, testing, and treatment) and average turnaround time of “future NGS” and “current NGS” versus SSG testing. ResultsThe adoption of current NGS over SSG testing had a budget impact of –0.24%, but adoption of future NGS over SSG testing had a budget impact of +4.33% across a 3-year time horizon on the Japanese budget for aNSCLC treatment. The adoption of current or future NGS over SSG testing would shorten the average turnaround time for testing. ConclusionsThe adoption of current NGS over SSG testing would slightly decrease the yearly costs. However, the adoption of future or current NGS over SSG testing would shorten the average turnaround time, enabling faster identification of genomic alterations and earlier initiation of treatment for aNSCLC patients in Japan.

Challenges of genetic diagnosis of inborn errors of metabolism in a major tertiary care center in Lebanon.

Background: Inborn errors of metabolism are rare genetic disorders; however, these are prevalent in countries with high consanguinity rates, like Lebanon. Patients are suspected, based on a combination of clinical and biochemical features; however, the final confirmation relies on genetic testing. Using next generation sequencing, as a new genetic investigational tool, carries several challenges for the physician, the geneticist, and the families. Methods: In this retrospective study, we analyzed the clinical, biochemical, and genetic profile of inborn errors of metabolism suspected patients, seen at a major tertiary care center in Lebanon, between 2015 and 2018. Genetic testing was performed using next generation sequencing. Genotype-phenotype correlation and diagnostic yield of each testing modality were studied. Results: Out of 211 patients genetically tested, 126 were suspected to have an inborn error of metabolism. The diagnostic yield of next generation sequencing reached 64.3%. Single gene testing was requested in 53%, whole exome sequencing in 36% and gene panels in 10%. Aminoacid disorders were mostly diagnosed followed by storage disorders, organic acidemias and mitochondrial diseases. Targeted testing was performed in 77% of aminoacid and organic acid disorders and half of suspected storage disorders. Single gene sequencing was positive in 75%, whereas whole exome sequencing diagnostic yield for complex cases, like mitochondrial disorders, reached 49%. Good clinical and biochemical correlation allowed the interpretation of variants of unknown significance and negative mutations as well as therapeutic management of most patients. Conclusion: Tailoring the choice of test modality, by next generation sequencing, to the category of suspected inborn errors of metabolism may lead to rapid diagnosis, shortcutting the cost of repeated testing. Whole exome sequencing as a first-tier investigation may be considered mainly for suspected mitochondrial diseases, whereas targeted sequencing can be offered upon suspicion of a specific enzyme deficiency. Timing and modality of gene test remain challenging, in view of the cost incurred by families.

OR18-3 Case Series of 16 Patients With 17β-Hydroxysteroid Dehydrogenase Type 3 Deficiency at Five Children's Hospitals in the United States

Abstract Objectives The 17β-hydroxysteroid dehydrogenase type 3 (17βHSD3) enzyme, expressed in the testes, converts androstenedione to testosterone. Deficiency of 17βHSD3 causes a 46,XY difference of sex development (DSD). Until recently, just 12 cases of 17βHSD3 deficiency had been reported in the literature in the United States. We report a series of 16 patients diagnosed at five children's hospitals in the United States. Methods We performed a multi-center chart review of patients with 17βHSD3 deficiency diagnosed based on hormone values and/or sequencing and deletion/duplication analysis of the HSD17B3 gene. Results Sixteen patients were identified, ranging in age at diagnosis from birth to 22.3 years (average age 9.5 years). One patient, assigned female at birth, was diagnosed due to a positive family history of the condition. Three patients underwent testing due to discordance between the sex predicted by prenatal cell-free DNA testing and the external genital appearance on prenatal ultrasound or at birth (two were assigned female, one was assigned male). An additional four patients had non-binary (atypical) appearing external genitalia at birth (two assigned female, two assigned male). Two children assigned female at birth were diagnosed after undescended testes were identified during hernia repair in early childhood. Six patients who were assigned female at birth came to medical attention peri-pubertally due to signs of excess/undesired androgen effects and/or primary amenorrhea. Data on gender identity is limited by the current age of many of the patients, but as of most recent follow-up, one patient assigned male and one assigned female are reported to be exploring their gender identities. Four patients had a prior diagnosis of complete or partial androgen insensitivity syndrome and 8 had a prior diagnosis of 46,XY DSD of unknown etiology. Eleven patients had genetic testing confirming pathogenic or likely pathogenic variants in the HSD17B3 gene (two identified on whole exome, one on a DSD-specific multi-gene panel, and the remaining 8 on single gene testing). Of the patients without genetically confirmed 17βHSD3 deficiency, one had a clinical diagnosis due to a genetically-confirmed diagnosis in a sibling. The remaining four declined or have not completed genetic testing, but had hormonal testing consistent with the diagnosis. Conclusions 17βHSD3 deficiency is likely much more common in the US than previously appreciated, and can present at any age with a range of physical findings. Accurate diagnosis is important, as the broad category of 46,XY DSD encompasses a wide spectrum of gonadal malignancy risk, potential for pubertal hormone function and fertility, and gender identity outcomes. We suggest evaluating for this potential diagnosis with genetic and/or hormonal testing in cases of 46,XY DSD with absent uterus. Presentation: Monday, June 13, 2022 11:30 a.m. - 11:45 a.m.

Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples.

Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. The present study is aimed at assessing the overall accuracy of RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world diagnostics. Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex© Solid tumor kit through the manufacturer's pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)]. The combination of FusionPlex© Solid tumor with ArcherDX® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens. Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.

Comprehensive genetic testing approaches as the basis for personalized management of growth disturbances: current status and perspectives.

The implementation of high-throughput and deep sequencing methods in routine genetic diagnostics has significantly improved the diagnostic yield in patient cohorts with growth disturbances and becomes increasingly important as the prerequisite of personalized medicine. They provide considerable chances to identify even rare and unexpected situations; nevertheless, we must be aware of their limitations. A simple genetic test in the beginning of a testing cascade might also help to identify the genetic cause of specific growth disorders. However, the clinical picture of genetically caused growth disturbance phenotypes can vary widely, and there is a broad clinical overlap between different growth disturbance disorders. As a consequence, the clinical diagnosis and therewith connected the decision on the appropriate genetic test is often a challenge. In fact, the clinician asking for genetic testing has to weigh different aspects in this decision process, including appropriateness (single gene test, stepwise procedure, comprehensive testing), turnaround time as the basis for rapid intervention, and economic considerations. Therefore, a frequent question in that context is ‘what to test when’. In this review, we aim to review genetic testing strategies and their strengths and limitations and to raise awareness for the future implementation of interdisciplinary genome medicine in diagnoses, treatment, and counselling of growth disturbances.

Assessment of BRAF V600E (VE1) immunochemistry for the detection of BRAF V600E mutation in non-small cell lung carcinoma cytology specimens.

Non-small cell lung carcinoma (NSCLC) patients with BRAF V600E-mutated tumors respond to targeted therapy. Testing for BRAF V600E is commonly performed with molecular methods; however, a mutation-specific VE1 antibody clone can provide an alternative testing option using immunohistochemistry (IHC)for practices using single-gene testing and in situations when the specimen is inadequate for molecular testing. This study evaluates the usefulness of VE1 IHC in screening for BRAF V600E mutations in NSCLC cytology specimens. The authors retrospectively identified cytology cases with a diagnosis of NSCLC that had BRAF V600E IHC performed on cell block sections with the monoclonal VE1 antibody clone. The BRAF V600E IHC results were compared with those of molecular testing performed with an amplicon-based next-generation sequencing assay. There were 201 NSCLC cases evaluated. The VE1 IHC was positive in seven of seven BRAF V600E-mutated tumors (100%) and was negative in 158 of 158 nonmutated BRAF V600E tumors (100%). Thirty cases did not undergo molecular testing, primarily because of insufficient tissue or because molecular testing was performed on an alternative specimen. Six cases showed equivocal weak/focal staining: Two cases demonstrated BRAF V600E mutations, and four cases were negative by molecular testing. This study suggests that BRAF V600E IHC can be used reliably to screen NSCLC cytology specimens, and negative results strongly indicate the absence of a BRAF V600E mutation. Having a low threshold for equivocal staining is recommended with molecular confirmation of BRAF V600E for any cases demonstrating weak and/or focal cytoplasmic staining.

O.01 Correlating molecular genetic testing for rare genetic variants with a broad clinicopathologic spectrum of congenital myopathies

Congenital myopathies (CMs) are a group of clinically heterogeneous disorders presenting with a range of overlapping findings, making diagnosis challenging. Despite advances in genetic testing, many cases remain undiagnosed. The Beggs' laboratory CM cohort, which currently totals over 1,100 individuals, constitutes a robust dataset of existing cases. Subjects were ascertained based on clinical presentation and pathologic diagnoses suggestive of CM. We report that over 65% have been solved by a combination of single gene, panel, or genomic sequencing, and/or RNA-Seq. Of 727 solved cases, 610 had mutations in either ACTA1, DNM2, MTM1, NEB, RYR1, SELENON, TPM2, TPM3, or TTN. All these genes are well-known causes of congenital myopathy. While all patients shared a myopathic pattern of weakness and hypotonia, a wide spectrum of clinicopathologic features were appreciated among the cases. The remaining 117 cases had mutations in one of 52 different genes, including a number of rare or novel genes, as well as some more commonly mutated non-CM disease genes in patients who presented atypically for those associated conditions. Among a heterogeneous group of 96 probands with congenital myopathy with nonspecific or no pathology, 31 (32%) had SELENON mutations; 9 (9.4%) had RYR1 mutations and 6 (6.25%) had TTN mutations. This survey of the Beggs' laboratory cohort cases, accumulated over roughly 20 years, emphasizes the crucial and growing role of WES/WGS in establishing a molecular genetic diagnosis of CM, as opposed to disease-based gene panels or single-gene testing, which may miss cases where the presentation does not fit the classical description of the disorder, or where multiple genes may present with overlapping clinicopathologic diagnoses. Moreover, certain syndromes not known to present predominantly with myopathic symptoms may go undiagnosed if genetic testing is done in a more targeted fashion based on specific clinical symptoms or pathologic diagnosis alone.

MA12.05 Economic Impact of Delaying Care with Single-Gene Testing Versus Next-Generation Sequencing in Non-small Cell Lung Cancer

By reducing delays in identifying a broad list of genomic alterations in non-small cell lung cancer (NSCLC), next-generation sequencing (NGS) testing has been found to be cost-effective in the United States compared to single-gene testing strategies. However, evidence is limited in Canada. This study assessed total costs of testing (including estimated costs of delaying care) associated with NGS versus single-gene testing strategies among patients with metastatic NSCLC (mNSCLC) from a Canadian public payer perspective.