Single Gene Testing Research Articles

Differences in set-based tests for sparse alternatives when testing sets of outcomes compared to sets of explanatory factors in genetic association studies.

Set-based association tests are widely popular in genetic association settings for their ability to aggregate weak signals and reduce multiple testing burdens. In particular, a class of set-based tests including the Higher Criticism, Berk-Jones, and other statistics have recently been popularized for reaching a so-called detection boundary when signals are rare and weak. Such tests have been applied in two subtly different settings: (a) associating a genetic variant set with a single phenotype and (b) associating a single genetic variant with a phenotype set. A significant issue in practice is the choice of test, especially when deciding between innovated and generalized type methods for detection boundary tests. Conflicting guidance is present in the literature. This work describes how correlation structures generate marked differences in relative operating characteristics for settings (a) and (b). The implications for study design are significant. We also develop novel power bounds that facilitate the aforementioned calculations and allow for analysis of individual testing settings. In more concrete terms, our investigation is motivated by translational expression quantitative trait loci (eQTL) studies in lung cancer. These studies involve both testing for groups of variants associated with a single gene expression (multiple explanatory factors) and testing whether a single variant is associated with a group of gene expressions (multiple outcomes). Results are supported by a collection of simulation studies and illustrated through lung cancer eQTL examples.

Wilms tumor (nephroblastoma) – clinical and genetic aspects

Nephroblastoma (Wilms tumor – WT) is the most common kidney tumor among the pediatric population, fifth among malignant neoplasms and third among solid tumors. The most common type of WT is sporadic and unilateral. WT occurs either as an isolated, nonsyndromic WT or as syndromic one belonging to the spectrum of a variety of genetic syndromes. Molecular genetic testing should be considered in nonsyndromic WT and include a multigene panel or whole exome sequencing (WES); in syndromic cases single-gene testing, DNA methylation panel and chromosomal microarray. Outcomes of treatment in WT patients remain very good, but there are still subgroups with poor prognosis and increased relapse rates, especially in the blastemic and disseminated anaplasia types. WT survivors have increased risk of chronic kidney disease (CKD). They need further follow-up, not only by oncologists but also by nephrologists, to preserve kidney function or slow down CKD progression.

Genetic testing outcome disparities in minority racial and ethnic sub-populations within a hereditary breast and ovarian cancer program serving a diverse, urban-based population (191)

Genetic testing outcome disparities in minority racial and ethnic sub-populations within a hereditary breast and ovarian cancer program serving a diverse, urban-based population (191)

Genetic counselors' experience with reimbursement and patient out-of-pocket cost for multi-cancer gene panel testing for hereditary cancer syndromes.

Multi-cancer gene panels for hereditary cancer syndromes (hereditary cancer panels, HCPs) are widely available, and some laboratories have programs that limit patients' out-of-pocket (OOP) cost share. However, little is known about practices by cancer genetic counselors for discussing and ordering an HCP and how insurance reimbursement and patient out-of-pocket share impact these practices. We conducted a survey of cancer genetic counselors based in the United States through the National Society of Genetic Counselors to assess the impact of reimbursement and patient OOP share on ordering of an HCP and hereditary cancer genetic counseling. Data analyses were conducted using chi-square and t tests. We received 135 responses (16% response rate). We found that the vast majority of respondents (94%, 127/135) ordered an HCP for patients rather than single-gene tests to assess hereditary cancer predisposition. Two-thirds of respondents reported that their institution had no protocol related to discussing HCPs with patients. Most respondents (84%, 114/135) indicated clinical indications and patients' requests as important in selecting and ordering HCPs, while 42%, 57/135, considered reimbursement and patient OOP share factors important. We found statistically significant differences in reporting of insurance as a frequently used payment method for HCPs and in-person genetic counseling (84% versus 59%, respectively, p< 0.0001). Perceived patient willingness to pay more than $100 was significantly higher for HCPs than for genetic counseling(41% versus 22%, respectively, p< 0.01). In sum, genetic counselors' widespread selection and ordering of HCPs is driven more by clinical indications and patient preferences than payment considerations. Respondents perceived that testing is more often reimbursed by insurance than genetic counseling, and patients are more willing to pay for an HCP than for genetic counseling. Policy efforts should address this incongruence in reimbursement and patient OOP share. Patient-centered communication should educate patients on the benefit of genetic counseling.

A genetic basis is identified in 74% cases of paediatric hyperCKaemia without weakness presenting to a tertiary paediatric neuromuscular centre

Paediatric hyperCKaemia without weakness presents a clinical conundrum. Invasive investigations with low diagnostic yields, including muscle biopsy, may be considered unjustifiable. Improved access to genome-wide genetic testing has shifted first-line investigations towards genetic studies in neuromuscular disease. This research aims to provide an evidence-based diagnostic approach to paediatric hyperCKaemia without weakness, a current gap in the literature. We identified 47 individuals (10-months to 16-years-old; 34 males, 13 females) from 43 families presenting with hyperCKaemia on two or more occasions, without weakness, from The Children's Hospital at Westmead Neuromuscular Clinic Database. Clinical features, investigations and outcomes were analysed via retrospective chart review. Genetic testing has been performed in 34/43. Genetic variants explaining hyperCKaemia were identified in 25/34 (74%) using multiplex ligation-dependent probe amplification, massive parallel sequencing, single gene testing and exome sequencing. Pathogenic/likely pathogenic variants were identified in 19 neuromuscular disease genes and six metabolic myopathy genes. Individuals with metabolic diagnoses had higher peak creatine kinase levels that sometimes normalized. Conversely, creatine kinase levels remained persistently elevated those with neuromuscular diagnoses. In summary, a genetic cause is found in most paediatric patients with hyperCKaemia without weakness informing clinical management and counselling. Thus, we propose a diagnostic algorithm for this cohort.

STXBP1 Stop-Loss Mutation Associated with Complex Early Onset Movement Disorder without Epilepsy.

STXBP1 Stop-Loss Mutation Associated with Complex Early Onset Movement Disorder without Epilepsy.

Audit of Molecular Mechanisms of Primary and Secondary Resistance to Various Generations of Tyrosine Kinase Inhibitors in Known Epidermal Growth Factor Receptor-Mutant Non-small Cell Lung Cancer Patients in a Tertiary Centre

AimsPresently, three generations of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are approved against oncogene addicted EGFR-mutant non-small cell lung cancer (NSCLC). Patients with actionable EGFR mutations invariably develop resistance. This resistance can be intrinsic (primary) or acquired (secondary). Materials and methodsThis was a retrospective study carried out between January 2016 and April 2021 analysing 486 samples of NSCLC for primary and secondary resistance to first- (erlotinib, gefitinb), second- (afatinib) and/or third-generation (osimertinib) TKIs in EGFR-mutant NSCLCs by next generation sequencing (NGS). Tissue NGS was carried out using the Thermofischer Ion Torrent™ Oncomine™ Focus 52 gene assay; liquid biopsy NGS was carried out using the Oncomine Lung Cell-Free Total Nucleic Acid assay. All cases were previously tested for a single EGFR gene with the Therascreen® EGFR RGQ PCR kit. ResultsThe results were divided into four groups: (i) group 1: primary resistance to first- and/or second-generation TKIs. This group, with 21 cases, showed EGFR exon 20 insertions, dual, complex mutations and variant of unknown significance, de novo MET gene amplification besides other mutations. (ii) Group 2: primary resistance to third-generation TKIs. This group showed two cases, with one showing dual EGFR mutation (L858R and E709A) and EGFR gene amplification. (iii) Group 3: secondary resistance to first- and second-generation TKIs. This group had 27 cases, which were previously reported negative for EGFR T790M by single gene testing. Significant findings were MET gene amplification in four cases, with one also showing MET exon 14 skipping mutation. Three cases showed small cell change and one showed loss of primary mutation. (iv) Group 4: secondary resistance to third-generation TKIs. The latter group was further subgrouped into group 4A: secondary resistance to osimertinib (third-generation TKI) when offered as second-line therapy after first- and second-generation TKIs on detection of T790M mutation. This group had 15 cases. EGFR T790M mutation was lost in 10 (10/15; 67%) cases and was retained in five cases. Patients with T790M loss experienced early resistance (6.9 months versus 12.6 months mean, P = 0.0024) compared with cases that retained T790M. Two cases gained MET amplification as the resistance mechanisms. Other mutations that were found when EGFR T790M was lost were in FGFR3, KRAS, PIK3CA, CTNNB1, BRAF genes. One case had EML4-ALK translocation. Two cases showed driver EGFR deletion 19, retained T790M and C797S mutation in Cis form. Group 4B: secondary resistance to osimertinib (when given as first-line therapy) in EGFR-mutant NSCLC. This group had three cases. The duration of osimertinib treatment ranged from 11 to 17 months. Two patients showed additional C797S mutation along with primary EGFR mutation. ConclusionThis study shows the wide spectrum of primary and secondary EGFR resistance mechanisms to first, second and third generation of TKIs and helps us to identify newer therapeutic targets that could carry forward the initial advantage offered by EGFR TKIs.

Unclassified white matter disorders: A diagnostic journey requiring close collaboration between clinical and laboratory services

BackgroundNext generation sequencing studies have revealed an ever-increasing number of causes for genetic disorders of central nervous system white matter. A substantial number of disorders are identifiable from their specific pattern of biochemical and/or imaging findings for which single gene testing may be indicated. Beyond this group, the causes of genetic white matter disorders are unclear and a broader approach to genomic testing is recommended. AimThis study aimed to identify the genetic causes for a group of individuals with unclassified white matter disorders with suspected genetic aetiology and highlight the investigations required when the initial testing is non-diagnostic. MethodsTwenty-six individuals from 22 families with unclassified white matter disorders underwent deep phenotyping and genome sequencing performed on trio, or larger, family groups. Functional studies and transcriptomics were used to resolve variants of uncertain significance with potential clinical relevance. ResultsCausative or candidate variants were identified in 15/22 (68.2%) families. Six of the 15 implicated genes had been previously associated with white matter disease (COL4A1, NDUFV1, SLC17A5, TUBB4A, BOLA3, DARS2). Patients with variants in the latter two presented with an atypical phenotype. The other nine genes had not been specifically associated with white matter disease at the time of diagnosis and included genes associated with monogenic syndromes, developmental disorders, and developmental and epileptic encephalopathies (STAG2, LSS, FIG4, GLS, PMPCA, SPTBN1, AGO2, SCN2A, SCN8A). Consequently, only 46% of the diagnoses would have been made via a current leukodystrophy gene panel test. DiscussionThese results confirm the importance of broad genomic testing for patients with white matter disorders. The high diagnostic yield reflects the integration of deep phenotyping, whole genome sequencing, trio analysis, functional studies, and transcriptomic analyses. ConclusionsGenetic white matter disorders are genetically and phenotypically heterogeneous. Deep phenotyping together with a range of genomic technologies underpin the identification of causes of unclassified white matter disease. A molecular diagnosis is essential for prognostication, appropriate management, and accurate reproductive counseling.

Economic Evaluation of Multiple-Pharmacogenes Testing for the Prevention of Adverse Drug Reactions in People Living with HIV.

PurposePharmacogenetics (PGx) testing is one of the methods for determining whether individuals are at risk of adverse drug reactions (ADRs). It has been reported that multiple-PGx testing, a sequencing technology, has a higher predictive value than single-PGx testing. Therefore, this study aimed to determine the most cost-effective PGx testing strategies for preventing drug-induced serious ADRs in human immunodeficiency virus (HIV)-infected patients.Patients and MethodsPotential strategies, including 1) single-PGx esting (ie, HLA-B*57:01 testing before prescribing abacavir, HLA-B*13:01 testing before prescribing co-trimoxazole and dapsone, and NAT2 testing before prescribing isoniazid) and 2) multiple-PGx testing as a combination of four single-gene PGx tests in one panel, were all compared to no PGx testing (current practice). To evaluate total cost in Thai baht (THB) and quality-adjusted life years (QALYs) for each strategy-based approach to a societal perspective, a hybrid decision tree and Markov model was constructed. Incremental cost-effectiveness ratios (ICERs) were estimated. Uncertainty, threshold, and scenario analyses were all performed.ResultsBefore prescribing HIV therapy, providing single or multiple-PGx testing might save roughly 68 serious ADRs per year, and the number needed to screen (NNS) to avoid one serious ADR was 40. Consequently, approximately 35% and 40% of the cost of ADR treatment could be avoided by the implementation of single- and multiple-PGx testing, respectively. Compared with no PGx testing strategy, the ICERs were 146,319 THB/QALY gained for single-PGx testing and 152,014 THB/QALY gained for multiple-PGx testing. Moreover, the probability of multiple-PGx testing being cost-effective was 45% at the Thai willingness to pay threshold of 160,000 THB per QALY. Threshold analyses showed that multiple-PGx testing remained cost-effective under the range of cost, sensitivity at 0.95–1.00 and specificity at 0.98–1.00.ConclusionSingle and multiple-PGx testing might be cost-effective options for reducing the incidence of drug-induced serious ADRs in people living with HIV.

Cost-Effectiveness of Parallel Versus Sequential Testing of Genetic Aberrations for Stage IV Non-Small-Cell Lung Cancer in the Netherlands.

PURPOSEA large number of targeted treatment options for stage IV nonsquamous non–small-cell lung cancer with specific genetic aberrations in tumor DNA is available. It is therefore important to optimize diagnostic testing strategies, such that patients receive adequate personalized treatment that improves survival and quality of life. The aim of this study is to assess the efficacy (including diagnostic costs, turnaround time (TAT), unsuccessful tests, percentages of correct findings, therapeutic costs, and therapeutic effectiveness) of parallel next generation sequencing (NGS)–based versus sequential single-gene–based testing strategies routinely used in patients with metastasized non–small-cell lung cancer in the Netherlands.METHODSA diagnostic microsimulation model was developed to simulate 100,000 patients with prevalence of genetic aberrations, extracted from real-world data from the Dutch Pathology Registry. These simulated patients were modeled to undergo different testing strategies composed of multiple tests with different test characteristics including single-gene and panel tests, test accuracy, the probability of an unsuccessful test, and TAT. Diagnostic outcomes were linked to a previously developed treatment model, to predict average long-term survival, quality-adjusted life-years (QALYs), costs, and cost-effectiveness of parallel versus sequential testing.RESULTSNGS-based parallel testing for all actionable genetic aberrations is on average €266 cheaper than single-gene–based sequential testing, and detects additional relevant targetable genetic aberrations in 20.5% of the cases, given a TAT of maximally 2 weeks. Therapeutic costs increased by €8,358, and 0.12 QALYs were gained, leading to an incremental cost-effectiveness ratio of €69,614/QALY for parallel versus sequential testing.CONCLUSIONNGS-based parallel testing is diagnostically superior over single-gene–based sequential testing, as it is cheaper and more effective than sequential testing. Parallel testing remains cost-effective with an incremental cost-effectiveness ratio of 69,614 €/QALY upon inclusion of therapeutic costs and long-term outcomes.

Search for a time- and cost-saving genetic testing strategy for maturity-onset diabetes of the young.

AimsCorrect genetic diagnosis of maturity-onset diabetes of the young (MODY) is beneficial for person’s diabetes management compared to no genetic testing. Aim of the present study was a search for optimal time- and cost-saving strategies by comparing two approaches of genetic testing of participants with clinical suspicion of MODY.MethodsA total of 121 consecutive probands referred for suspicion of MODY (Group A) were screened using targeted NGS (tNGS), while the other 112 consecutive probands (Group B) underwent a single gene test based on phenotype, and in cases of negative findings, tNGS was conducted. The study was performed in two subsequent years. The genetic results, time until reporting of the final results and financial expenses were compared between the groups.ResultsMODY was confirmed in 30.6% and 40.2% probands from Groups A and B, respectively; GCK-MODY was predominant (72.2% in Group A and 77.8% in Group B). The median number of days until results reporting was 184 days (IQR 122–258) in Group A and 91 days (44–174) in Group B (p < 0.00001). Mean costs per person were higher for Group A (639 ± 30 USD) than for Group B (584 ± 296 USD; p = 0.044).ConclusionsThe two-step approach represented a better strategy for genetic investigation of MODY concerning time and costs compared to direct tNGS. Although a single-gene investigation clarified the diabetes aetiology in the majority of cases, tNGS could reveal rare causes of MODY and expose possible limitations of both standard genetic techniques and clinical evaluation.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00592-022-01915-x.

Upfront Next Generation Sequencing in Non-Small Cell Lung Cancer.

In advanced non-small cell lung cancer (NSCLC), patients with actionable genomic alterations may derive additional clinical benefit from targeted treatment compared to cytotoxic chemotherapy. Current guidelines recommend extensive testing with next generation sequencing (NGS) panels. We investigated the impact of using a targeted NGS panel (TruSight Tumor 15, Illumina) as reflex testing for NSCLC samples at a single institution. Molecular analysis examined 15 genes for hotspot mutation variants, including AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GNAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET and TP53 genes. Between February 2017 and October 2020, 1460 samples from 1395 patients were analyzed. 1201 patients (86.1%) had at least one variant identified, most frequently TP53 (47.5%), KRAS (32.2%) or EGFR (24.2%). Among these, 994 patients (71.3%) had clinically relevant variants eligible for treatment with approved therapies or clinical trial enrollment. The incremental cost of NGS beyond single gene testing (EGFR, ALK) was CAD $233 per case. Reflex upfront NGS identified at least one actionable variant in more than 70% of patients with NSCLC, with minimal increase in testing cost. Implementation of NGS panels remains essential as treatment paradigms continue to evolve.

Diagnostic Value and Cost-Effectiveness of Next-Generation Sequencing–Based Testing for Treatment of Patients with Advanced/Metastatic Non-Squamous Non–Small-Cell Lung Cancer in the United States

The study evaluated the diagnostic value and cost-effectiveness of next-generation sequencing (NGS)-based testing versus various combinations of single-gene tests (SGTs) for selection of first-line treatment for patients with advanced/metastatic non-squamous non-small-cell lung cancer in the United States. A dynamic decision analysis model was developed comparing NGS versus SGT from a payer perspective. Inputs were obtained from published sources and included diagnostic performance, biomarker-positive disease rates, biomarker-directed recommendations for treatment, and survival outcomes. Costs were reported in 2020 US dollars. In the base case, NGS improved the detection of actionable biomarkers by 74.4%, increased the proportion of patients receiving biomarker-driven therapy by 11.9%, and decreased the proportion of patients with biomarker-positive disease receiving non-biomarker-driven first-line treatment by 40.5%. The incremental cost-effectiveness ratio per life-year gained of NGS testing versus SGT was $7224 (excluding post-diagnostic costs); the incremental cost-effectiveness ratio for NGS-directed therapy was $148,786 versus SGT-directed therapy. Sensitivity analyses confirmed the robustness of these findings; survival outcomes and targeted therapy costs had the greatest impact on results. Testing strategies with NGS are more comprehensive in the detection of actionable biomarkers and can improve the proportion of patients receiving biomarker-driven therapies. NGS testing may provide a cost-effective strategy for advanced/metastatic non-squamous non-small-cell lung cancer; however, the value of NGS-directed therapy varies by the willingness-to-pay threshold of the decision-maker.

Effectiveness of nationwide insurance coverage for next-generation sequencing in advanced colorectal cancer: A real-world data study.

3602 Background: Next-generation sequencing (NGS) has been covered by Korean national health insurance since March 2017 for patients with advanced colorectal cancer (CRC). We explored the clinical and socioeconomic impact of NGS compared with that of a single gene test (SGT) alone. Methods: From the nationwide database, we identified patients who 1) are diagnosed with advanced CRC classified as a distant disease using Summary Stage between March 1, 2017, and December 31, 2018; 2) had NGS or SGT within 2 months after diagnosis of advanced CRC. Multivariate logistic regression with covariates including age, sex, Charlson comorbidity index, insurance type, year of diagnosis, and region and type of hospital with the initial diagnosis was conducted to identify factors affecting the performance of NGS. We conducted 1:3 propensity score matching to minimize the impact of confounding factors. The median overall survival and the adjusted hazard ratio (aHR) were estimated using the Kaplan-Meier method and the Cox proportional hazard model, respectively. We calculated the total medical cost, and per patient per year (PPPY) cost adjusted for the survival period. Results: Among 5,029 patients with advanced CRC, 655 patients were identified as NGS group and 1,995 as SGT group after matching. Old age, low household income, rural location, and non-tertiary hospital were all characteristics that reduced the likelihood of obtaining an NGS test. The NGS group showed significantly favorable survival compared to the SGT group (median survival 29.2 vs. 24.9 months, P =.031; adjusted hazard ratio [HR] 0.86, P =.034). The total medical cost was lower in the NGS group ($55,445) than the SGT group ($57,989), and the PPPY cost was also lower in the NGS group ($44,879 and $49,734, respectively). Conclusions: We found that some socioeconomic factors such as age, insurance type, region, and hospital type may hamper the implementation of NGS. Also, lowering the barrier of NGS tests by reimbursing NGS in a specific clinical setting may have survival and cost-benefit in patients with advanced CRC.

Effectiveness of nationwide insurance coverage for next-generation sequencing in advanced non–small cell lung cancer: A real-world data study.

9134 Background: Next-generation sequencing (NGS) has been covered by Korean national health insurance since March 2017 for patients with advanced non-small cell lung cancer (NSCLC). We explored the clinical and socioeconomic impact of NGS compared with that of a single gene test (SGT) alone. Methods: From the nationwide database, we identified patients who 1) are diagnosed with advanced NSCLC classified as a distant disease using Summary Stage between March 1, 2017, and December 31, 2018; 2) had NGS or SGT within 2 months after diagnosis of advanced NSCLC. Patients with squamous cell carcinoma were excluded. We conducted multivariate logistic regression to identify factors (e.g., age, sex, Charlson comorbidity index, insurance type, year of diagnosis, and region and type of hospital with the initial diagnosis) affecting the performance of NGS. Further, we divided the cohort into subgroups based on whether patients received treatment targeting epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutations (group A) or not (group B). We conducted 1:5 propensity score matching for each group to minimize the impact of confounding factors. The median overall survival and the adjusted hazard ratio (aHR) for death were estimated using the Kaplan-Meier method and the Cox proportional hazard model, respectively. We calculated the total medical cost, and per patient per year (PPPY) cost adjusted for the survival period. Results: Among 10,247 patients with advanced NSCLC, 768 patients were identified as group A and 1,596 as group B after matching. Old age, low household income, and rural region were factors negatively impacting on having NGS tests. In Group A, we did not find a significant difference in survival outcome between the NGS cohort and the SGT cohort (median survival 31.6 vs. 27.5 months, P =.331; aHR 0.80, P =.204). In contrast, significantly favorable survival was observed for the NGS group in Group B (median survival 14.1 vs. 9.5 months, P =.023; aHR 0.80, P =.009). Although the total medical cost was higher in the NGS group ($39,145) than the SGT group ($36,207) for Group B, the PPPY cost was lower in the NGS group ($57,502 and $63,293, respectively). Conclusions: Socioeconomic factors hampering the implementation of NGS were identified. Lowering the barrier by covering the NGS cost publicly in a specific clinical setting may have survival and cost-benefit in patients with advanced NSCLC.

The Use of Next-generation Sequencing in the Diagnosis of Rare Inherited Anaemias: A Joint BSH/EHA Good Practice Paper.

The Use of Next-generation Sequencing in the Diagnosis of Rare Inherited Anaemias: A Joint BSH/EHA Good Practice Paper.

Economic impact of broad panel versus sequential single and narrow panel sequencing in lung cancer patients.

e18718 Background: Recent developments in next-generation sequencing (NGS) technology have revolutionized our understanding of cancer biology and clinical research by improving diagnoses and recognizing mutations for personalized therapies. Sequential single (SS) gene testing and narrow panel sequencing (NPS) are used to select targeted therapies and precision medicine strategies for lung cancer patients. While broad panel sequencing (BPS) can identify more mutations than SS and NPS, it is more expensive. This study aims to assess the long-term cost-effectiveness of BPS vs. SS and NPS in lung cancer patients. Methods: This study will evaluate lung cancer patients undergoing biomarker testing insured by a large commercial and Medicare health plan in the United States between January 1, 2021, and May 31, 2021. The SS and NPS group consists of patients with 50 or fewer genes sequenced; the BPS group consists of those with more than 50 genes sequenced. Our primary clinical endpoint for analysis is the total cost of care defined as the allowed costs paid for all medical and pharmacy claims six months from the first gene sequencing panel. Multivariable regression analysis will assess the influence of explanatory variables on costs. Analysis will be complete February 28, 2022.

A real-world (rw) evidence study quantifying the clinical value of multi-gene testing in early-stage lung adenocarcinoma (LUAD).

8525 Background: Resected early-stage NSCLC has high risk of recurrence, and tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICI), each requiring testing for precision biomarkers, have recently been approved in the adjuvant (adj) setting. We assessed the potential value of multi-gene testing in early NSCLC via enabling timely 1L therapy selection at recurrence and through avoidance of adj ICI in pts with driver alterations unlikely to benefit per current guidelines and the label for atezolizumab in first line (1L) NSCLC. Methods: Using the nationwide (̃280 US cancer clinics) de-identified EHR-derived rw Flatiron Health- Foundation Medicine clinico-genomic database, we selected 6,725 evaluable pts with LUAD who underwent tissue comprehensive genomic profiling (CGP) as part of routine cancer care (01/2011 – 06/2021). We focused on alterations in 4 drivers ( EGFR, ALK, ROS1, RET) and studied prevalence in early-stage specimens versus advanced (adv) specimens, as well as the rate of timely delivery of 1L therapy at recurrence for pts receiving CGP in early disease. We estimated the cost implications of adj ICI in pts with PD-L1+ LUAD and an ALK, ROS1, or RET fusion with a probabilistic decision tree. Results: CGP was performed on 1,490 specimens collected prior to adv disease (stage I 36%, II 27%, IIIA 37%) and ordered prior to adv diagnosis for 981 pts (15% of total, median 10 weeks after initial diagnosis). In specimens collected in early (n = 1,490) or adv (n = 5,130) stage LUAD, CGP identified drivers in EGFR (early/adv: 13%/16%), ALK (2.0%/4.2%), ROS1 (0.7%/1.1%), RET (1.0%/1.1%), and prevalence was similar when limiting to PD-L1+ cases. Studying 596 pts with recurrence and CGP on samples collected prior to recurrence, pts with CGP results obtained before (n = 196) vs after (n = 400) recurrence had less time between recurrence and start of any 1L therapy (median 3.1 vs 5.9 weeks, p &lt; 0.001). In the subset with a targetable driver detected, 32/42 (76%) with CGP before recurrence initiated matched 1L TKI while 43/67 (64%) with CGP after recurrence received matched 1L TKI (p = 0.2). Through avoidance of ICI in PD-L1+ early LUAD with an ALK/ ROS1/ RET driver, we estimate universal CGP (compared to EGFR single-gene testing) could reduce per pt expected costs by $875 (an average incremental $4,050 treatment cost reduction compared to a $3,175 increase in diagnostic cost per pt). Conclusions: CGP of early-stage LUAD can identify EGFR, ALK, ROS1 and RET drivers and enable appropriate selection of precision therapies and timely use of effective 1L therapy at recurrence. Assuming adj ICI maintains the lack of activity in RET/ ROS1 as seen for ALK, CGP could represent a cost-effective approach for avoiding futile adj ICI and reducing the risk of subsequent TKI-associated toxicity. Additional analysis of driver+ pts receiving adj ICI is needed to help balance the risk/benefit for these high risk pts.

Real-world biomarker testing trends in metastatic non-small cell lung cancer (NSCLC).

e18728 Background: NSCLC is now recognized as not one disease, but many—differentiated by an increasing number of molecular targets. About 50% of patients with advanced nonsquamous NSCLC have a targetable driver mutation. We retrospectively assessed biomarker testing trends in a large community oncology practice to identify evolving real-world testing rates and patterns in the areas of methodology, specimen types, and vendors. Methods: Natural-language processing queries were used to extract data from biomarker testing reports of patients diagnosed with stage IV NSCLC in 2015-2019. Tests were included if done within 1 year of diagnosis and were classified as NGS panels (20+ genes) or targeted single-gene tests. Results: Records of 587 patients were included. Over the 5-year study window, testing rates increased for all 6 mutations analyzed (Table). In 2015, only ALK, ROS1, and EGFR were profiled in our data (n = 20 patients), all using targeted single-gene tests. The use of multigene panels increased steadily over time, constituting the majority by 2019. MET, RET, and NTRK were tested almost exclusively using NGS panels (data beginning in 2016). Tissue-only specimens were used for 93.8% of patients diagnosed in 2015, while tissue plus blood were used in 6.3%. Blood-only samples began appearing in our data in 2016, making up 7% of patients. By 2019, the use of blood tests had increased substantially, to 47% of patients, although tissue-only remained the most common type (54%). While blood testing has become more popular, it is often still performed with tissue tests. The primary testing methods used in 2015-2017 were FISH for ALK and ROS1; NGS for MET, NTRK, and RET; and Sanger or NGS for EGFR. By 2018, NGS had become the predominant test method across all 6 biomarkers. During 2015-2016, several vendors were used for testing, with a very segmented market for ALK and EGFR tests. By 2019, the market had aligned to a few key vendors for the majority of tests. In 2016, the top 5 vendors did 76% of 180 total tests, which increased to 93% of 1880 tests in 2019. Almost all blood testing in our data was performed by a single vendor. Conclusions: Testing rates for ALK, ROS1, and EGFR were more consistent than those for MET, RET, and NTRK throughout the study window, possibly because of earlier availability of tests and treatments for these biomarkers. NGS was more available by the time MET, RET, and NTRK became established as actionable biomarkers, explaining the earlier use of panels. A limitation is that nearly 75% of the data are from the final 2 years. These results, however, represent notable testing trends from a large practice and illustrate the expanding application of molecular testing in community oncology.[Table: see text]

Patient and Clinician Preferences for Genetic and Genomic Testing in Non-Small Cell Lung Cancer: A Discrete Choice Experiment.

Precision (personalised) medicine for non-small cell lung cancer (NSCLC) adopts a molecularly guided approach. Standard-of-care testing in Australia is via sequential single-gene testing which is inefficient and leads to tissue exhaustion. The purpose of this study was to understand preferences around genetic and genomic testing in locally advanced or metastatic NSCLC. A discrete choice experiment (DCE) was conducted in patients with NSCLC (n = 45) and physicians (n = 44). Attributes for the DCE were developed based on qualitative interviews, literature reviews and expert opinion. DCE data were modelled using a mixed multinomial logit model (MMNL). The results showed that the most important attribute for patients and clinicians was the likelihood of an actionable test, followed by the cost. Patients significantly preferred tests with a possibility for reporting on germline findings over those without (β = 0.4626) and those that required no further procedures over tests that required re-biopsy (β = 0.5523). Physician preferences were similar (β = 0.2758 and β = 0.857, respectively). Overall, there was a strong preference for genomic tests that have attribute profiles reflective of comprehensive genomic profiling (CGP) and whole exome sequencing (WES)/whole genome sequencing (WGS), irrespective of high costs. Participants preferred tests that provided actionable outcomes, were affordable, timely, and negated the need for additional biopsy.