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Implementation Challenges and Disparities in Molecular Testing for Patients with Stage IV NSCLC: Perspectives from an Urban Safety-Net Hospital

Published:November 11, 2022DOI:https://doi.org/10.1016/j.cllc.2022.11.002

      Abstract

      The advent of next-generation sequencing (NGS), including both tissue assays and circulating tumor DNA (ct-DNA), has been pivotal in improving outcomes for patients with non-small cell lung cancer (NSCLC). Although molecular testing is standard of care for advanced NSCLC, challenges still exist in its implementation. This Perspective examines barriers to the widespread implementation of NGS from the vantage point of a single urban safety-net institution, with a particular focus on examining racial disparities in NGS completion. We conducted a review of patients at our institution from January 2015 through January 2022 and examined molecular testing patterns before and after the publication of updated molecular testing guidelines from the International Association for the Study of Lung Cancer (IASLC), Association for Molecular Pathology (AMP), and College of American Pathologists (CAP) in March of 2018. While NGS increased over time, we found that 43% of patients in the March 2018 through January 2022 group still did not receive NGS, and the most common reasons for the absence of testing included a lack of physician ordering and insufficient tissue on biopsy. We did not note any racial disparities in completion or time-to-adoption of NGS. Patients with squamous cell carcinoma (SCC) histology were noted to receive liquid NGS markedly less often than patients with non-squamous histology in the March 2018 through January 2022 period. Based on our own data and a review of findings from colleagues in the field, we advocate for additional physician educational programming, increased use of ct-DNA biopsy, automated (reflexive) NGS tissue testing on receipt of biopsy, and consideration for the broader molecular profiling of patients with SCC histology.

      Keywords

      Introduction

      Biomarker testing initially emerged in lung cancer guidelines in 2011, when the National Comprehensive Cancer Network (NCCN) first recommended testing for EGFR mutations based on the demonstrated superiority of EGFR tyrosine kinase inhibitors (TKIs) compared to chemotherapy in patients with such mutations
      • Beasley MB
      • Milton DT.
      ASCO provisional clinical opinion: epidermal growth factor receptor mutation testing in practice.
      . That same year, Ellis et al. published consensus guidelines from a panel of Canadian pathologists and medical oncologists recommending routine molecular testing for EGFR mutations in NSCLC
      • Ellis PM
      • Blais N
      • Soulieres D
      • et al.
      A systematic review and Canadian consensus recommendations on the use of biomarkers in the treatment of non-small cell lung cancer.
      . Since that time, the number of actionable biomarkers (including mutations, fusions, and rearrangements) which have approved therapies with high response rates as compared to conventional chemotherapy has rapidly expanded. In 2013, the CAP, IASLC, and AMP issued a joint statement recommending all patients with advanced NSCLC receive molecular testing, including for EGFR mutations, ALK rearrangements, and ROS1 fusions
      • Lindeman NI
      • Cagle PT
      • Beasley MB
      • et al.
      Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.
      ; the American Society of Clinical Oncology (ASCO) endorsed and broadened this recommendation to include BRAF mutation testing
      • Kalemkerian GP
      • Narula N
      • Kennedy EB
      • et al.
      Molecular testing guideline for the selection of patients with lung cancer for treatment with targeted tyrosine kinase inhibitors: American Society of Clinical Oncology endorsement of the College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology clinical practice guideline update.
      .
      This core group of biomarkers is often referred to as a limited molecular panel in contrast to its more expansive peer, the comprehensive molecular panel, which is accomplished via next-generation sequencing (NGS). NGS is a DNA sequencing technology that can rapidly and precisely detect small base substitutions, insertions, and deletions, as well as large exon deletions and chromosomal rearrangements, as opposed to the traditional fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) microarrays which are limited in their individual scopes
      • Behjati S
      • Tarpey PS.
      What is next generation sequencing?.
      . As the development of novel therapeutic agents and recognition of targets continues to expand, the value of NGS has increased in tandem.
      In March of 2018, the IASLC, AMP, and CAP issued updated guidelines that broadened molecular testing recommendations to include the biomarkers ERBB2, MET, KRAS, and RET, which are tested on NGS panels
      • Lindeman NI
      • Cagle PT
      • Aisner DL
      • et al.
      Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology.
      . Within the category of NGS, both tissue testing and peripheral blood-based (liquid) biopsies (utilizing ct-DNA) are available. Current NCCN guidelines indicate tissue testing remains preferred, though liquid biopsies may be an option for either co-testing along with tissue or in the case that tissue is not readily accessible

      National Comprehensive Cancer Network (NCCN). NCCN Clinical Practice Guidelines in Oncology. Non-Small Cell Lung Cancer. Version 1.2022. Accessed January 2, 2022.

      . The most significant limitation of NGS using ct-DNA remains its limited sensitivity as compared to tissue biopsy; one study specifically comparing tissue biopsy-proven EGFR-mutated NSCLC noted NGS via plasma ct-DNA detected only 87% of exon 19 deletions
      • Reckamp K.L.
      • Melnikova V.O.
      • Karlovich C.
      • et al.
      Highly sensitive and quantitative test platform for detection of NSCLC EGFR mutations in urine and plasma.
      . NGS utilizing ct-DNA holds the advantage of limited invasiveness and quicker time to results compared to tissue biopsy
      • Gobbini E
      • Swalduz A
      • Levra MG
      • et al.
      Implementing ctDNA Analysis in the Clinic: Challenges and Opportunities in Non-Small Cell Lung Cancer.
      . Also in 2018, the European Society for Medical Oncology (ESMO) published clinical practice guidelines which advised testing of programmed-death ligand 1 (PD-L1) by immunohistochemistry (IHC) as studies had emerged demonstrating improved outcomes with immune checkpoint inhibitors in patients with PD-L1 expression of at least 1%
      • Wu YL
      • Planchard D
      • Lu S
      • et al.
      Pan-Asian adapted Clinical Practice Guidelines for the management of patients with metastatic non-small cell lung cancer; a CSCO-ESMO initiative endorsed by JSMO, KSMO, MOS, SSO and TOS.
      ,
      • Pennell NA
      • Arcila ME
      • Gandara DR
      • West H.
      Biomarker Testing for Patients With Advanced Non-Small Cell Lung Cancer: Real-World Issues and Tough Choices.
      .
      Literature reporting the impact of these testing recommendations on minority communities has been limited, often by the assessment of only single biomarkers or the inclusion of patients across a wide geographic area where biomarker testing is not comparably available
      • Enewold L
      • Thomas A.
      Real-World Patterns of EGFR Testing and Treatment with Erlotinib for Non-Small Cell Lung Cancer in the United States.
      ,
      • Stein JN
      • Rivera MP
      • Weiner A
      • et al.
      Sociodemographic disparities in the management of advanced lung cancer: a narrative review.
      . Unfortunately, patients from racial and ethnic minority groups in the United States remain underrepresented in lung cancer research
      • Zavala VA
      • Bracci PM
      • Carethers JM
      • et al.
      Cancer health disparities in racial/ethnic minorities in the United States.
      . In a review of cancer-related clinical trials, only 1.08% of participants were identified as black, and no racial/ethnic registration was recorded for 66.95% of participants
      • Guerrero S
      • López-Cortés A
      • Indacochea A
      • et al.
      Analysis of Racial/Ethnic Representation in Select Basic and Applied Cancer Research Studies.
      . In addition, black patients are less likely to be treated with immunotherapy than non-Hispanic whites, even when controlling for insurance status
      • Verma V
      • Haque W
      • Cushman TR
      • et al.
      Racial and Insurance-related Disparities in Delivery of Immunotherapy-type Compounds in the United States.
      . Given these historically documented disparities in the treatment of black patients with NSCLC
      • Hardy D
      • Liu CC
      • Xia R
      • et al.
      Racial disparities and treatment trends in a large cohort of elderly black and white patients with nonsmall cell lung cancer.
      , we sought to identify any disparities in the increasingly critical domain of tumor molecular profiling. Here we analyze molecular testing practices at Boston Medical Center, the largest safety-net hospital in New England, which serves a patient population composed of 65% self-identified racial and ethnic minorities
      Boston Medical Center Enterprise Analytics Clinical Data Warehouse Team
      Boston Medical Center Race and Ethnicity Profiles: Calendar Year.
      . In analyzing the molecular testing practices of our own institution, we also review the barriers to NGS in the broader oncology community and our thoughts on how these barriers may continue to be addressed.

      Materials and Methods

      We performed a retrospective review of all patients with stage IV NSCLC diagnosed at Boston Medical Center from January 2015 through January 2022 which included 157 patients total, 69 patients diagnosed from January 2015 through March 2018, and 88 patients diagnosed from April 2018 through January 2022. This research was conducted with an Institutional Review Board (IRB) approval. March of 2018 was used as a dividing timepoint as this was when the IASLC, AMP, and CAP updated molecular testing guidelines were published. Demographic, histologic, and molecular data were abstracted from each case. Gender and race information that was abstracted from the medical record had been provided by patient self-identification at the time of initial appointment. Molecular testing was categorized into “none,” meaning no molecular testing was performed; “limited,” referring to testing only for EGFR and BRAF mutations, ALK rearrangements, ROS1 fusions; and “next-generation sequencing,” which includes NGS via either tissue or ct-DNA liquid biopsy. For those patients who did not undergo NGS tissue testing, charts were reviewed and categorized by reason for lack of testing. At our institution, when a tissue biopsy is obtained, if the biopsy is positive for adenocarcinoma there is an automatic reflex to limited in-house testing for EGFR, BRAF, ALK, and ROS. PD-L1 is a reflexive send-out test. For other histologic subtypes of advanced NSCLC, limited molecular testing must be specifically requested by the oncologist. For all histologic subtypes, NGS testing on both tissue and ct-DNA specimens must be separately requested by the oncologist. When tissue is insufficient for NGS, this is documented in the pathology report. Patients in whom there was no other documented reason for lack of testing (such as insufficient tissue noted on pathology report, or driver mutation detected on initial reflex testing and further molecular testing therefore not indicated) were categorized as not receiving testing due to lack of oncologist ordering. Statistical analysis was performed using Chi-Square tests of independence to compare the completion of different types of molecular testing between time groups (pre-guideline and post-guideline groups) and to compare completion of different types of molecular testing between histologic subgroups within the same period. The null hypothesis for each Chi-Square test was that no association exists between the categorical variables. An alpha value of 0.05 was selected as threshold for statistical significance. An alpha value of less than 0.05 prompted rejection of the null hypothesis and adoption of the alternate hypothesis that a relationship exists between the categorical variables in the specific test. For analysis of racial differences in implementation of NGS, a Chi-Square test of independence was performed comparing the self-identified racial groups and the proportion of each group that underwent NGS testing in the post-guideline period. The null hypothesis was that no association exists between racial group and completion of NGS in the post-guideline period. An alpha value of 0.05 was selected as threshold for statistical significance. The alternate hypothesis was that an association between racial group and completion of NGS exists in the post-guideline period.

      Results

      Patient Characteristics

      Of the 157 patients reviewed in this retrospective study from January 2015 through January 2022, 95 (61%) were male and 62 (39%) were female. Most patients identified as black (68, 43%) or white (52, 33%). The majority of patients were diagnosed with adenocarcinoma (122, 78%) and most were current or former smokers (102, 65%). The most common insurance payer was Medicaid (49, 31%). See Table 1 for a full description of patient characteristics.
      Table 1Characteristics of Patients with Stage IV NSCLC Diagnosed between January 2015 and January 2022 at Boston Medical Center
      CharacteristicNPercentMeanStandard Deviation
      Gender
      Male9561%
      Female6239%
      Race
      Black6843%
      White5233%
      Asian1610%
      Other2113%
      Age64.010.5
      Tobacco Status
      Current tobacco use2717%
      Former tobacco use7548%
      Never tobacco use3120%
      Unknown tobacco history2415%
      ECOG PS at Diagnosis
      02617%
      15434%
      23019%
      3-41610%
      Unknown3120%
      Histology
      Adenocarcinoma12278%
      Squamous cell carcinoma2516%
      Poorly differentiated carcinoma85%
      Large cell carcinoma21%
      Insurance Status
      Medicaid4931%
      Private Insurance4428%
      Medicare3623%
      None32%
      Unknown2516%

      Molecular Testing Trends Over Time

      For all patients (n = 157), the rates of tissue NGS, liquid NGS, and PD-L1 testing increased over time with a corresponding decrease in limited molecular testing (Figure 1A). For the subgroup of patients with squamous cell carcinoma (n = 25) the increase in liquid biopsy over time (0% to 7%) was far less pronounced than that seen in all NSCLC (0% to 41%), as seen in Figure 1. Of the 146 patients across both time periods who had molecular testing of any kind, 135 (92%) had molecular testing within 6 months of initial lung cancer diagnosis. Twenty of these 146 patients (14%) had serial NGS (either liquid, tissue, or both) conducted during the course of their disease. Among patients with non-squamous histology (n = 132), 37 actionable biomarkers were detected via limited molecular testing (28%) with 15 additional actionable biomarkers detected via NGS (11%). Among patients with squamous histology, 3 actionable biomarkers were detected on limited molecular testing (12%) including one ALK and two EGFR mutations; on NGS a single EGFR mutation was detected (4%). Table 2
      Figure 1
      Figure 1Among all patients with NSCLC, the percentage receiving tissue NGS (p = 1.08 × 10−5), liquid NGS (p = 1.4 × 10−9), and PD-L1 testing (p = 0.004) increased over time. Patients with SCC received limited molecular testing in the pre-guideline period less often than all patients with NSCLC (p = 0.003). There was notably less implementation of liquid NGS among patients with SCC over time compared to patients with non-squamous histology (p = 0.04).
      Table 2Molecular Testing Performed Over Time by Histologic Subtype
      Molecular Testing PerformedTime Period: Pre- vs Post-GuidelineAll NSCLC (n = 157, 69 pre- and 88 post-guideline)Squamous (n = 25, 10 pre- and 15 post-guideline)Non-Squamous (n = 132, 59 pre- and 73 post-guideline)
      No Molecular Testing

      N (% of total for histologic subtype within time period)
      Pre6 (9%)4 (40%)2 (3%)
      Post5 (6%)2 (13%)3 (4%)
      Limited Molecular TestingPre57 (83%)5 (50%)52 (88%)
      Post33 (38%)6 (40%)27 (37%)
      Comprehensive Molecular

      Testing
      Pre6 (9%)1 (10%)5 (8%)
      Post50 (57%)7 (46%)43 (59%)
      Tissue NGSPre6 (9%)1 (10%)5 (8%)
      Post35 (40%)6 (40%)29 (40%)
      Liquid NGSPre0 (0%)0 (0%)0 (0%)
      Post36 (41%)1 (7%)35 (48%)
      PD-L1Pre34 (49%)5 (50%)29 (49%)
      Post63 (72%)12 (80%51 (70%)

      Testing Over Time by Race

      Data were also analyzed by self-identified race within the time cohorts. For all patients, 6 of 69 (9%) underwent comprehensive molecular testing (either tissue or liquid NGS) in the pre-guideline period and 50 of 88 (57%) had NGS in the post-guideline period. For self-identified black patients, 3 of 34 (9%) had NGS in the pre-guideline period and 22 of 34 (65%) had NGS in the post-guideline period. For white patients, 3 of 24 (12.5%) patients in the pre-guideline period and 13 of 28 (46%) in the post-guideline period underwent NGS. Among Asian patients, 0 of 3 patients had NGS in the pre-guideline period and 7 of 13 (54%) had NGS in the post-guideline period. For patients of other races, 0 of 8 had NGS in the pre-guideline period and 8 of 13 (62%) underwent NGS in the post-guideline period. A Chi-Square test of independence was performed on the post-guideline group with the null hypothesis that no association exists between race and completion of NGS with an alpha value set at 0.05. The p-value from this analysis was 0.52, and the null hypothesis was therefore not rejected. These results are summarized in Figure 2.
      Figure 2
      Figure 2Among all NSCLC histologies, the proportion of patients receiving tissue or liquid NGS markedly increased over time (p = 4.16 × 10−10). No racial disparities in completion of NGS were noted when comparing self-identified racial groups (p = 0.52).

      Examining Reasons for Lack of NGS

      The category of NGS was further examined by tissue-based and liquid-based testing. Of the 116 patients of all histologies who did not receive tissue-based NGS, reasons for lack of testing were abstracted from individual charts and categorized, with four main categories emerging: lack of physician ordering (n = 75, 65%), driver mutation detected on limited molecular testing (23, 20%), insufficient tissue on biopsy (13, 11%), and patient death while awaiting biopsy (5, 4%). Some of these patients who did not receive tissue NGS ultimately underwent liquid NGS, and this propensity for liquid testing varied by reason for lack of tissue testing. For example, patients who did not get tissue NGS due to insufficient tissue on initial biopsy were more likely to undergo liquid NGS (10, 77%) than patients who did not receive tissue NGS due to a lack of physician ordering (3, 4%). The number of patients not receiving tissue NGS including those ultimately receiving liquid NGS is displayed below in Figure 3.
      Figure 3
      Figure 3Patients who did not receive tissue NGS were categorized by reason for lack of tissue testing. The most common reason for not performing tissue NGS was lack of physician ordering. Few patients who did not have tissue NGS ordered went on to receive liquid NGS. Patients with insufficient tissue on biopsy were significantly more likely to undergo liquid NGS than those who did not receive tissue NGS for other reasons.

      Discussion

      Achieving Equitable Access to NGS

      A review of molecular testing practices at our safety net hospital yielded several key findings. A central interest of our work, particularly given our diverse patient population, resided in identifying any racial disparities in molecular testing practices of our patients with stage IV NSCLC. This information was of particular interest due to documented underrepresentation of patients from minority communities in lung cancer trials and the known decreased likelihood of black patients receiving chemotherapy or immunotherapy when indicated as compared to white patients
      • Verma V
      • Haque W
      • Cushman TR
      • et al.
      Racial and Insurance-related Disparities in Delivery of Immunotherapy-type Compounds in the United States.
      ,
      • Hardy D
      • Liu CC
      • Xia R
      • et al.
      Racial disparities and treatment trends in a large cohort of elderly black and white patients with nonsmall cell lung cancer.
      . In addition, black patients have poorer 5-year survival rates for lung cancer (18%) compared to white patients (21%)
      • Harrison S
      • Judd J
      • Chin S
      • Ragin C.
      Disparities in Lung Cancer Treatment [published online ahead of print, 2022 Jan 26].
      . With regard to racial inequities in molecular testing of advanced NSCLC specifically, few studies exist. One group utilizing the Surveillance, Epidemiology, and End Results (SEER) database found no significant difference in the rate of EGFR testing between black and white patients. However, this was confounded by the differing geography of the patients, which is known to be a key determinant of access to and completion of molecular testing
      • Pennell NA
      • Arcila ME
      • Gandara DR
      • West H.
      Biomarker Testing for Patients With Advanced Non-Small Cell Lung Cancer: Real-World Issues and Tough Choices.
      . A separate study utilizing data from SEER-Medicare found black patients were less likely to receive molecular testing than white patients, though the exclusion of patients under age 65 limits the generalizability of this finding
      • Stein JN
      • Rivera MP
      • Weiner A
      • et al.
      Sociodemographic disparities in the management of advanced lung cancer: a narrative review.
      .
      At the 2021 ASCO meeting, Bruno et al. presented data obtained from the Flatiron Health database suggesting that white patients were approximately 10% more likely to receive NGS than black patients (50.1% vs 39.8%)
      • Bruno DS
      • Hess LM
      • Li X
      • Su EW
      • Zhu YE
      • Patel M.
      Racial disparities in biomarker testing and clinical trial enrollment in non-small cell lung cancer (NSCLC).
      . While this presents a compelling portrait of inequity, the compilation of patients from many different institutions with their own distinct testing practices may sully the full picture; it is possible that discrepancies in testing practices are most pronounced between institutions themselves and this results in the observed disparity. This concern is supported by an August 2021 study in JCO Oncology Practice, in which 639 medical oncologists who treat advanced NSCLC in their practice were surveyed nationally to identify barriers to care. Among the respondents surveyed, 33.3% cited no protocol for biomarker testing in their cancer program
      • Salgia R
      • Boehmer LM
      • Celestin C
      • Yu H
      • Spigel DR.
      Improving Care for Patients With Stage III or IV NSCLC: Learnings for Multidisciplinary Teams From the ACCC National Quality Survey.
      . Before the national coverage determination (NCD) on NGS was levied by the Centers for Medicare & Medicaid Services, it was contested that economic factors may be majorly contributing to the observed racial disparity in NGS completion. After the determination was rendered, one study examining pre- and post-decision patterns found that the NCD did not narrow previously observed disparities between racial groups in NGS completion
      • Sheinson DM
      • Wong WB
      • Meyer CS
      • et al.
      Trends in Use of Next-Generation Sequencing in Patients With Solid Tumors by Race and Ethnicity After Implementation of the Medicare National Coverage Determination.
      . These findings again raise the point that other forces, such as inter-institutional variability, may be driving observed differences.
      This constellation of findings poses a natural next question for investigation: do these racial disparities also exist within single institutions? While addressing this precise question is challenging, we feel shedding light on real-world testing practices at a single racially diverse institution helps to further characterize the reasons for the disparity observed in Bruno et al. Importantly, we observed no statistically significant difference between self-identified racial groups in the proportion of patients receiving NGS or PD-L1 testing at our institution, nor did we note a lag in the use of NGS over time for any racial group. Our institution's statistically significant increase in molecular testing over the past 7 years for both black and white patients mirrors that noted in both U.S. and international populations
      • Li W
      • Lyu Y
      • Wang S
      • et al.
      Trends in Molecular Testing of Lung Cancer in Mainland People's Republic of China Over the Decade 2010 to 2019.
      . To further characterize the complex interplay of factors driving the racial disparities we observe in large population databases, it will be imperative to seek data and perspectives from other racially diverse individual institutions.

      Barriers to Completing Tissue NGS

      We additionally learned that only 35% of patients at our institution diagnosed with stage IV NSCLC since January 2015 received any tissue NGS testing. In 2018, The IASLC, AMP, and CAP issued updated molecular testing guidelines which broadened molecular testing recommendations to encompass the biomarkers ERBB2, MET, KRAS, and RET, which are tested on NGS comprehensive panels
      • Lindeman NI
      • Cagle PT
      • Aisner DL
      • et al.
      Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology.
      . Utilization of NGS at our institution increased in the subsequent years: 40% of our patients with NSCLC of any histologic subtype diagnosed between April 2018 and January 2022 have received tissue NGS, and 57% have received either tissue or liquid NGS. Despite this increase, we note that there is clearly progress yet to be made both for our institution and the greater oncology community. To reflect on how we might advance this percentage, we examine findings from other institutions.
      Paz-Ares et al. recently conducted an investigation of 3,050 patients in the Flatiron Health database with non-squamous advanced NSCLC between January 2018 and June 2019 and found that 46% of patients received NGS
      • Paz-Ares L
      • Gondos A
      • Saldana D
      • et al.
      Genomic testing among patients with newly diagnosed advanced non-small cell lung cancer in the United States: A contemporary clinical practice patterns study.
      . A 2022 study from Robert et al. similarly found that less than half of patients in their community cancer network received testing for all 5 biomarkers performed on limited panels (EGFR, ALK, ROS1, BRAF, PD-L1)
      • Robert NJ
      • Espirito JL
      • Chen L
      • et al.
      Biomarker testing and tissue journey among patients with metastatic non-small cell lung cancer receiving first-line therapy in The US Oncology Network Biomarker testing in metastatic NSCLC with first-line therapy.
      . A 2020 IASLC survey sought to identify health care professionals’ perceptions of molecular testing barriers in an international population
      • Smeltzer MP
      • Wynes MW
      • Lantuejoul S
      • et al.
      The International Association for the Study of Lung Cancer Global Survey on Molecular Testing in Lung Cancer.
      . The most cited barrier in this survey was cost. However, this barrier is less significant to our patient population given our institution's 77% public payer mix of insurance, as both Medicare and Medicaid cover the cost of NGS for stage IV NSCLC

      Center for Health and Information Analysis of Massachusetts. Boston Medical Center 2017 Hospital Profile. https://www.chiamass.gov/assets/docs/r/hospital-profiles/2017/bmc.pdf. 2017. Accessed January 29 2022.

      ,

      Center for Medicare and Medicaid Services: CMS finalizes coverage of next generation sequencing tests, ensuring enhanced access for cancer patients. https://www.cms.gov/newsroom/press-releases/cms-finalizes-coverage-next-generation-sequencing-tests-ensuring-enhanced-access-cancer-patients

      . Still, in the oncology community at large this remains a concern. In 2016, one Brazilian group found that patients who underwent testing for four of the NCCN-recommended biomarkers in adenocarcinoma via NGS incurred an extra $3479 per actionable biomarker alteration detected as compared to traditional FISH and RT-PCR testing
      • Schluckebier L
      • Caetano R
      • Garay OU
      • et al.
      Cost-effectiveness analysis comparing companion diagnostic tests for EGFR, ALK, and ROS1 versus next-generation sequencing (NGS) in advanced adenocarcinoma lung cancer patients.
      . Another group in 2019 discerned the cost differential between single marker genetic testing and multigene panel sequencing to be about $148,000 per life-year gained
      • Steuten L
      • Goulart B
      • Meropol NJ
      • Pritchard D
      • Ramsey SD.
      Cost Effectiveness of Multigene Panel Sequencing for Patients With Advanced Non-Small-Cell Lung Cancer.
      . However, increasing market competition over the past 5 years along with the development of cheaper instruments and reagents continues to temper this cost barrier

      Global Next Generation Sequencing Markets 2021-2028: Rise in Competition Amongst Prominent Market Entities- ResearchAndMarkets.com. www.businesswire.com. Published October 4, 2021. Accessed June 24, 2022. https://www.businesswire.com/news/home/20211004005472/en/Global-Next-Generation-Sequencing-Markets-2021-2028-Rise-in-Competition-Amongst-Prominent-Market-Entities—ResearchAndMarkets.com.

      .
      Other common reasons for not receiving NGS tissue testing include inconsistent sample quantity and quality of biopsy
      • Smeltzer MP
      • Wynes MW
      • Lantuejoul S
      • et al.
      The International Association for the Study of Lung Cancer Global Survey on Molecular Testing in Lung Cancer.
      , which was also a common reason for NGS tissue biopsy failure in our patient population. In the aforementioned survey of medical oncologists by Salgia et al., respondents cited the most challenging barrier to comprehensive tissue testing as an insufficient quantity of material for biomarker testing (25.1% of respondents)
      • Salgia R
      • Boehmer LM
      • Celestin C
      • Yu H
      • Spigel DR.
      Improving Care for Patients With Stage III or IV NSCLC: Learnings for Multidisciplinary Teams From the ACCC National Quality Survey.
      . We suspect that we may increase NGS completion at our own institution by making NGS reflexive for all non-squamous NSCLC biopsy specimens, removing the onus on the physician to place the order for each specimen. There is often hesitation around this approach due to the sparsity of available tissue for testing, frequently motivating the testing of only the highest-yield biomarkers via other modalities. However, one group found that switching to reflexive NGS from its previous approach of IHC followed by NGS for confirmatory testing if positive led to a reduced amount of tissue required for testing
      • Zacharias M
      • Absenger G
      • Kashofer K
      • et al.
      Reflex testing in non-small cell lung carcinoma using DNA- and RNA-based next-generation sequencing-a single-center experience.
      .
      While cost and biopsy yield are certainly formidable barriers, our review of our own institutional practices did reveal that a lack of oncologist ordering was the most common reason for tissue NGS not being completed. This finding hints at a growing specter in the oncology community: genomic sequencing technology and best practices are moving at an increasingly frenetic pace. While these advances have certainly been advantageous to patient care, they necessitate a rapacious appetite for continuing education in the oncologist community. In one early review of 15 New Jersey community oncology practices from 2013-2015, 52% of patients who met criteria for EGFR and ALK testing received chemotherapy without any documented reason for the lack of biomarker testing
      • Gutierrez ME
      • Choi K
      • Lanman RB
      • et al.
      Genomic Profiling of Advanced Non-Small Cell Lung Cancer in Community Settings: Gaps and Opportunities.
      . The haziness that can accompany new guidelines is also felt from the patient's chair. In one 2014 survey of patients with advanced cancer, just 48% of patients reported having sufficient knowledge to make an informed decision regarding biomarker testing
      • Blanchette PS
      • Spreafico A
      • Miller FA
      • et al.
      Genomic testing in cancer: patient knowledge, attitudes, and expectations.
      . Even for those with a plethora of experience, consensus guidelines can still pose challenges for physicians. A group of oncologists with a median of 100 genomic sequencing tests ordered per physician per year still cited significant limitations in interpreting these results for patients. As one oncologist described, “You have to keep up with the literature and understand what these sequences could potentially mean, and that takes a certain amount of education on our part”
      • Gray SW
      • Park ER
      • Najita J
      • et al.
      Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.
      . A 2019 review of NGS in the clinical oncology workflow also identifies barriers such as integrating molecular testing results into the EHR results platform and varying clinician trust in NGS
      • Conway JR
      • Warner JL
      • Rubinstein WS
      • Miller RS.
      Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action.
      . One 2021 narrative review of oncologist attitudes toward NGS cited a desire for continuing medical education as a top concern of the group
      • Shirdarreh M
      • Aziza O
      • Pezo RC
      • Jerzak KJ
      • Warner E.
      Patients' and Oncologists' Knowledge and Expectations Regarding Tumor Multigene Next-Generation Sequencing: A Narrative Review.
      . It is clear that for our institution and others, a successful strategy for expanding NGS in advanced NSCLC patients mandates an approach which includes ongoing, time-sensitive physician education.
      These studies examining barriers to NGS are predicated on the idea that moving away from limited testing, and toward initial testing with NGS, is advantageous to patients. A 2017 retrospective analysis of 1,436 patients revealed that NGS testing demonstrated higher rates of successful completion than single-gene testing when 4 or more biomarkers were tested
      • Yu T
      • Tradonsky A
      • Layton A.
      Practical implications of single-gene versus NGS testing in advanced NSCLC.
      . Furthermore, a review of the sensitivity of NGS compared to standard molecular testing ranged from 86% to 100% for clinically actionable mutations
      • Zheng Y
      • Vioix H
      • Liu FX
      • Singh B
      • Sharma S
      • Sharda D.
      Diagnostic and economic value of biomarker testing for targetable mutations in non-small-cell lung cancer: a literature review.
      . In a 2020 cost-effective analysis, Tan et al. found that upfront NGS testing would result in an additional 1% of patients with actionable alterations being identified without significant increase in time to test results or in cost
      • Tan A
      • Lai G
      • San Tan G
      • et al.
      Utility of incorporating next-generation sequencing (NGS) in an Asian non-small cell lung cancer (NSCLC) population: incremental yield of actionable alterations and cost–effectiveness analysis.
      . Building on these findings, Pennell et al. modeled a comparison of broad NGS testing compared to single gene testing for EGFR/ALK mutations and identified life-years gained at a reduced cost per life-year gained compared to single gene testing
      • Pennell NA
      • Zhou J
      • Hobbs B.
      A model comparing the value of broad next-gen sequencing (NGS)-based testing to single gene testing (SGT) in patients with nonsquamous non-small cell lung cancer (NSCLC) in the United States.
      . In our own investigation, we found 16 additional actionable biomarkers (10%) via NGS which were not detected on more limited molecular testing. Our findings, in conjunction with the existing body of literature, speak to the benefit of initial molecular testing with NGS.

      The Role of ct-DNA

      The IASLC issued a consensus statement in 2021 recommending ct-DNA for genotyping of newly diagnosed lung cancer patients and as first-line for retesting after acquired resistance to tyrosine kinase inhibitor therapy
      • Rolfo C
      • Mack P
      • Scagliotti GV
      • et al.
      Liquid Biopsy for Advanced NSCLC: A Consensus Statement From the International Association for the Study of Lung Cancer.
      . Despite this recommendation, only 77% of our patients with insufficient tissue on biopsy for NGS went on to receive liquid ct-DNA-based NGS. There is also emerging data that ct-DNA levels may hold clinical utility in longitudinal disease activity monitoring, which indicates that we may see an expanding role for ct-DNA in clinical practice in the future, making an understanding of the barriers to ct-DNA testing even more critical
      • Lan V
      • Zhang J
      • Wu C
      • et al.
      Genotype-Specific Differences in Circulating Tumor DNA Levels in Advanced NSCLC.
      . One of the most frequently cited benefits of ct-DNA remains its quicker turnaround time to results compared to tissue NGS. In 2018, the IASLC, AMP, and CAP put forth a benchmark time-to-results for NGS of 10 business days
      • Kalemkerian GP
      • Narula N
      • Kennedy EB
      • et al.
      Molecular Testing Guideline for the Selection of Patients With Lung Cancer for Treatment With Targeted Tyrosine Kinase Inhibitors: American Society of Clinical Oncology Endorsement of the College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology Clinical Practice Guideline Update.
      . One academic medical center performed a retrospective review of all advanced NSCLC specimens collected at their institution in 2015 to assess real-world performance against this benchmark. Their group found that 81.5% of lung cancer tissue specimens sent for molecular testing met the suggested timeline, suggesting the feasibility of meeting the benchmark
      • DiStasio M
      • Chen Y
      • Rangachari D
      • Costa DB
      • Heher YK
      • VanderLaan PA.
      Molecular Testing Turnaround Time for Non-Small Cell Lung Cancer in Routine Clinical Practice Confirms Feasibility of CAP/IASLC/AMP Guideline Recommendations: A Single-center Analysis.
      . Other groups still experience a marked lag in turnaround time to tissue NGS results compared to liquid NGS results; the mean turnaround time for liquid biopsy was 7 days compared to 22 days for tissue biopsy in a cohort of metastatic colorectal cancer patients at one institution
      • Procaccio L
      • Bergamo F
      • Daniel F
      • et al.
      A Real-World Application of Liquid Biopsy in Metastatic Colorectal Cancer: The Poseidon Study.
      . The implications of this difference can be substantial. One survey of oncologists noted that in their collective clinical experience, many stage IV NSCLC patients were started on empiric platinum-based chemotherapy if patients were noted to be psychologically distressed or with a high symptom burden while awaiting tissue biopsy scheduling or tissue NGS results
      • Gregg JP
      • Li T
      • Yoneda KY.
      Molecular testing strategies in non-small cell lung cancer: optimizing the diagnostic journey.
      . While liquid NGS is not considered a substitute for tissue NGS at this time, practicality necessitates the consideration of employing liquid biopsy first in these patients who may otherwise choose to subject themselves to chemotherapy while awaiting tissue biopsy. Like tissue biopsy, the broader adoption of liquid biopsy will continue to require additional investment in patient and physician education. Many U.S. clinicians continue to cite a lack of awareness as a barrier to NGS
      • Smeltzer MP
      • Wynes MW
      • Lantuejoul S
      • et al.
      The International Association for the Study of Lung Cancer Global Survey on Molecular Testing in Lung Cancer.
      .

      The Conundrum of NGS in NSCLC with Squamous Histology

      Current NCCN guidelines recommend biomarker testing for EGFR, ALK, KRAS, ROS1, BRAF, NTRK 1/2/3, METex14 skipping, RET, and HER2 in patients diagnosed with adenocarcinoma, large cell carcinoma, or NSCLC not otherwise specified (NOS)

      National Comprehensive Cancer Network (NCCN). NCCN Clinical Practice Guidelines in Oncology. Non-Small Cell Lung Cancer. Version 1.2022. Accessed January 2, 2022.

      . A topic of debate in the field of biomarker testing in NSCLC remains the testing of patients with squamous histology. Present NCCN guidelines recommend consideration of testing for these same biomarkers in patients with squamous histology, but this is an area of controversy. Sands et al. performed NGS tissue testing of 172 patients with NSCLC with squamous histology and found that 38% of these patients had at least one potentially targetable genomic alteration as defined by inclusion criteria in the Lung Master Protocol (Lung-MAP) clinical trial
      • Sands JM
      • Nguyen T
      • Shivdasani P
      • et al.
      Next-generation sequencing informs diagnosis and identifies unexpected therapeutic targets in lung squamous cell carcinomas.
      . Similarly, Lam et al. performed liquid NGS on a cohort of 492 patients with NSCLC with squamous histology and found 10.5% of patients possessed an actionable alteration of one of the NCCN biomarkers currently recommended for patients with non-squamous histology
      • Lam VK
      • Tran HT
      • Banks KC
      • et al.
      Targeted Tissue and Cell-Free Tumor DNA Sequencing of Advanced Lung Squamous-Cell Carcinoma Reveals Clinically Significant Prevalence of Actionable Alterations.
      . At present, patients with SCC at our institution are receiving liquid NGS at significantly lower rates than our patients with non-squamous histology (p = 0.04). Though our cohort was limited in size, we found that 4 of our 19 patients with squamous histology who underwent molecular testing (21%) had a clinically relevant genomic alteration, similar to the findings of Sands et al. and Lam et al.. The detection of actionable biomarkers in SCC has known clinical benefit. Previous studies have shown patients with SCC with EGFR mutations are responsive to TKI therapy
      • Mosele F
      • Remon J
      • Mateo J
      • et al.
      Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group.
      , though with reduced progression-free survival (PFS) compared to their counterparts with EGFR-mutated adenocarcinoma
      • Fang W
      • Zhang J
      • Liang W
      • et al.
      Efficacy of epidermal growth factor receptor-tyrosine kinase inhibitors for Chinese patients with squamous cell carcinoma of lung harboring EGFR mutation.
      . Jin at al. looked at outcomes for a cohort of 28 EGFR- mutant SCC patients and found certain co-occurring mutations may predict the responsiveness of EGFR-mutated SCC to TKIs
      • Jin R
      • Peng L
      • Shou J
      • et al.
      EGFR-Mutated Squamous Cell Lung Cancer and Its Association With Outcomes.
      . Our results echo the findings of similar studies, adding to a body of literature which suggests that patients with squamous histology may benefit from increased implementation of the NCCN recommendation to consider NGS, particularly as cost and turnaround time barriers continue to erode.

      Conclusion

      After examining our own institutional molecular testing practices, we now look toward the future of NGS in the broader oncology community with several points in mind. Given that we did not identify any racial disparities in molecular testing practices in advanced NSCLC at our institution across time, this raises the possibility that known racial disparities in molecular testing practices may arise from differences between, rather than within, individual institutions. Thus, there is a need for additional studies examining racial disparities at individual institutions to elucidate the true cause of observed racial differences in testing practices on a population level. Additionally, although limited molecular testing and PD-L1 are performed at many institutions, it remains unfortunately common for patients with advanced NSCLC not to have comprehensive molecular testing ordered. One mechanism we propose for reducing the burden on oncologists to proactively order molecular testing is an expansion of reflexive, or automated, molecular testing for advanced NSCLC regardless of histologic subtype. As discussed in the above case, even patients with squamous cell carcinoma may derive benefit from molecular testing, though additional studies with larger cohorts remain necessary. Currently, such testing is not reflexive for these patients at our institution and others. Our findings also suggest the need for ongoing education within the oncology community regarding molecular testing best practices, particularly given recommendations have been evolving rapidly over the past decade. Within the realm of NGS, increased education regarding the utility of ct-DNA is essential.
      Below is a listing of individual author contributions to this work:
      Laura Burns: Investigation, Data curation, Formal analysis, Writing – original draft
      Chinmay Jani: Data curation, writing – review & editing
      Amr Radwan: Data curation, writing- review & editing
      Omar Al Omari: Data curation, writing – review & editing
      Mohini Patel: Data curation, writing – review & editing
      Geoffrey R. Oxnard: Writing – review & editing
      Umit Tapan: Conceptualization, supervision, writing – review & editing

      Funding Disclosure

      This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

      Conflict of Interest Statement

      Dr. Oxnard is employed by Foundation Medicine and holds equity in Roche. Dr. Tapan is receiving an educational grant from Pfizer, Inc, is serving as an advisory board member for Sanofi/Genzyme/Regeneron and as an outside consultant to Glaxo Smith Klein, and has served as a speaker at an Astra Zeneca-sponsored symposium.

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