Blood-based Next-generation Sequencing Research Articles

Tucatinib and trastuzumab for previously treated HER2−mutated metastatic breast cancer (SGNTUC−019): A phase 2 basket study.

1105 Background: Approximately 2-5% of breast cancers harbor HER2 mutations, often occurring in hormone receptor-positive (HR+) disease. There are currently no approved treatment options for patients (pts) with HER2-mutated metastatic breast cancer (HER2-mut MBC). Tucatinib (TUC) is a tyrosine kinase inhibitor highly selective for HER2 and is approved for previously treated HER2+ MBC with or without brain metastases in combination with trastuzumab (Tras) and capecitabine. Here, we report the efficacy and safety results of TUC combined with Tras in pts with previously treated HER2-mut MBC. Methods: SGNTUC-019 (NCT04579380) is an open-label phase 2 basket study evaluating efficacy, safety, and tolerability of TUC and Tras in pts with metastatic HER2-altered solid tumors. Pts in the HER2-mut MBC cohort must have HER2 mutations determined locally by tissue- or blood-based next-generation sequencing, not be HER2+ per local testing, been previously treated with ≥1 systemic therapy in the locally advanced, unresectable, or metastatic setting, and if HR+, have received a CDK4/6 inhibitor. Pts were treated in 21-day cycles with TUC (300 mg orally twice a day) and Tras (8 mg/kg IV followed by 6 mg/kg every 3 wks). Pts with HR+ disease also received fulvestrant (F; 500 mg IM once every 4 wks starting from cycle 1 day 1, and cycle 1 day 15). Disease status was determined based on RECIST v1.1 with assessments performed every 6 wks for 24 wks and every 12 wks thereafter. The primary endpoint is cORR per investigator assessment. Secondary endpoints include OS, DCR, DOR, PFS, and safety. Results: As of Nov 1, 2023, 31 pts were enrolled in the HER2-mut MBC cohort. The median duration of follow-up for OS was 15.0 months. Twenty-seven (87%) pts had HR+ disease and 18 (58%) had lobular histology. The pts received a median of 4 prior lines of systemic therapy in any setting. cORR was 41.9% (90% CI, 26.9-58.2) with 13 responses including 2 complete responses. Median DOR was 12.6 months (90% CI, 4.7, not estimable), DCR was 80.6% (n=25; 90% CI, 65.3-91.2), median PFS was 9.5 months (90% CI, 5.4-13.8), and median OS was 20.1 months (90% CI, 15.9 to not estimable). The most common treatment-emergent adverse events (TEAEs) reported were diarrhea (64.5%) and nausea (35.5%). The most common grade ≥3 TEAEs reported were diarrhea (13%), alanine aminotransferase increase (10%), and hypertension (10%). Two (6.5%) pts discontinued TUC due to TEAEs, but these pts continued Tras. No deaths were due to TEAEs. Additional biomarker analyses will be included in the presentation. Conclusions: The investigational combination of TUC and Tras, plus F in pts with HR+ disease, was well tolerated and had clinical activity in pts with previously treated HER2-mut MBC. The results support further evaluation of the combination of TUC and Tras as a potential treatment option for this pt population. Clinical trial information: NCT04579380 .

Abstract 2414: Feasibility and clinical utility of blood based NGS in head and neck carcinomas: A single center experience from precision medicine program

Abstract Background: While blood-based next-generation sequencing is increasingly integral to clinical practice across various malignancies, the routine assessment of circulating tumor DNA (ctDNA) in head and neck cancer remains underexplored, with limited supportive data. Methods: This study focused on head and neck cancer patients enrolled in the Gustave Roussy precision medicine program (STING, NCT04932525), undergoing liquid biopsy (LB) with the FoundationOne Liquid CDX panel. The Molecular Tumor Board discussed cases, calculating Tumor Fraction (TF) based on aneuploidy, categorizing it as high or low with a 10% cutoff. Results: The analysis encompassed 239 LBs from 214 patients with relapsed or metastatic head and neck cancers. Of these, 59 LBs were from 57 patients showing stability or positive response (SD/R), while 180 were from 167 patients at diagnosis or disease progression (BL/PD). Notably, 156 (73%) were male, with a median age of 61 years. Within the cohort, 65% of LBs were from patients with squamous cell carcinomas (SCC), 15% adenoid cystic carcinomas (ACC), and 20% other histologies mainly adenocarcinomas. The anatomical distribution included 59 LBs from salivary gland (SG) cancers, 49 oropharynx (OP), 48 oral cavity (OC), and others including larynx, hypopharynx, sinus and nasopharynx. Among LBs performed at BL/PD, 72% were informative, while only 36% were so at SD/R. The proportion of informative biopsies varied across anatomical sites. For SCC, TP53 mutations were most prevalent (71%), followed by TERT and PIK3CA variants, and FGF19 and FGF3 amplifications. ACCs showed NOTCH1 mutations (6/19, 32%) as the most common, followed by TP53 and various other variants. In the entire cohort, clonal hematopoiesis-related variants were identified, with 40% showing at least one of DNMT3A, CHEK2, or ASXL1. Patients with low TF at BL/PD exhibited significantly improved overall survival (21.6 vs. 7.6 months, HR 0.35, 95% CI 0.23 - 0.53, p < 0.0001), consistent across subgroups except for OP.Conclusion: This study demonstrates the feasibility of liquid biopsy in HNSCC and rare head and neck tumors, providing valuable therapeutic and prognostic insights. The findings underscore the potential of liquid biopsy as a valuable tool in clinical decision-making for head and neck cancer patients. Citation Format: Filippo Gustavo Dall'Olio, Damien Vasseur, Lea Loriguet, Francois Regis Ferrand, Antoine Moya-Plana, Yungan Tao, Mariana Iacob, Karim Benihoud, Odile CASIRAGHI, Catherine Brenner, Pierre Busson, Philippe Gorphe, Santiago Ponce, Pierre Blanchard, Etienne Rouleau, Yohann Loriot, Ludovic Lacroix, Antoine Italiano, Ingrid Breuskin, Caroline Even. Feasibility and clinical utility of blood based NGS in head and neck carcinomas: A single center experience from precision medicine program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2414.

Abstract 5041: Next generation liquid biopsy reference material performance across NGS assays and platforms

Abstract Liquid biopsy testing has grown to support early disease diagnosis, therapy selection, and disease and treatment surveillance in cancer survivors. Recent advances in next generation sequencing (NGS) have enabled larger panel sizes, pan-cancer target sets, and wider ranges of genomic alterations. More inclusive analytical validation materials are needed to assess assay sensitivity, specificity, and limit of detection of all variant types to serve the expanded utility of liquid biopsy testing. Here we describe the development and multisite evaluation of expanded Seraseq® ctDNA Mutation Mix v4 reference materials. Genomic DNA from the GM24385 cell line was blended with 93 clinically relevant biosynthetic DNA variants including single nucleotide variants (SNVs), insertions and deletions (indels), structural variants (SVs), copy number variations (CNVs), and mono- and dinucleotide biomarkers for microsatellite instability (MSI). Variant allele frequency (VAF) was targeted to 0.5% and total copy number for CNVs was targeted to 2.5 and verified using the Bio-Rad QX-200 Droplet Digital PCR (ddPCR) System. The DNA mix was fragmented and purified to create ctDNA-like size profiles. Wild-type (WT) material was prepared for comparison and identification of background variants. Agilent Bioanalyzer High Sensitivity DNA and TapeStation Cell-free DNA ScreenTape analyses were used to assess fragment size. The ctDNA mixes were analyzed with the Illumina TruSight™ Oncology 500 (TSO 500) ctDNA assay, the Thermo Oncomine™ Precision assay, and additional assays. All biosynthetic SNVs, indels, SVs, and CNVs in the 0.5% ctDNA mix were detected near target values. The average fragment size was about 190 bp, similar to native ctDNA. The VAFs and CNVs observed in the TSO 500 data correlated well with those that were obtained by dPCR. Variants reported by all evaluation site assays showed good concordance of VAF values. The two sites that tested the materials with TSO 500 revealed consistency in both VAF and total copies with an average CV of 16.1% and 2.5%, respectively. The sequencing performance of the reference material was similar to patient samples and showed comparable levels of background noise. The performance of the Seraseq ctDNA v4 mutation mix across NGS assays, supported by robust digital PCR data, demonstrated that these materials will allow for assessment of complex and sensitive liquid biopsy tests. Comparing data measured at different sites highlights the variability in liquid biopsy assay performance and the importance of highly multiplexed and consistent reference materials. Remnant samples are typically not an option due to limited yields from a standard blood draw, thus contrived standards are especially needed. Expanded variant content and improvements in the methods used to produce the Seraseq ctDNA Mutation Mix v4 materials will enable advancements in the blood-based NGS clinical diagnostics space. Citation Format: Dana Ruminski Lowe, Sanchita Jamindar, Yves Konigshofer, Andrew Anfora, Krystyna Nahilk, Dianren Xia, Edward S. Davis, David Merriam, Catherine Huang, Russell Garlick, Bharathi Anekella. Next generation liquid biopsy reference material performance across NGS assays and platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5041.

Comprehensive Genomic Analysis of Patients With Non-Small-Cell Lung Cancer Using Blood-Based Circulating Tumor DNA Assay: Findings From the BFAST Database of a Single Center in Taiwan.

The Blood First Assay Screening Trial (BFAST) is a prospective study using next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) in treatment-naïve advanced/metastatic non-small-cell lung cancer (NSCLC). We compared liquid biopsy to tissue testing and analyzed genomic alterations in Taiwanese patients with NSCLC using the BFAST database. A total of 269 patients underwent FoundationOne Liquid Companion Diagnostic (F1LCDx) assay at the National Taiwan University Hospital, of whom 264 underwent tissue-based genetic testing also. We analyzed the actionable mutations and the concordance between tissue-based genetic testing, which was limited to EGFR, ALK, ROS1, and BRAF, in a real-life clinical setting and blood-based NGS in the clinical trial. Additionally, we analyzed the co-occurring genomic alterations from the blood-based ctDNA assay. A total of 76.2% patients showed actionable mutations. Standard tissue testing did not detect known driver alterations in about 22.7% of the patients (sensitivity, 70.24%). Liquid NGS detected additional mutations (RET, KRAS, MET, and ErbB2) in 14% of the patients, which went undetected by the standard-of-care testing. The complementary use of ctDNA NGS increased the detection rate by 42%. The F1LCDx assay had a sensitivity of 83.41%. Lower tumor and metastasis stages predicted nondetected blood-based NGS ctDNA results. Common co-occurring mutations in the blood-based NGS ctDNA assay were TP53, DNMT3A, TET2, PIK3CA, CTNNB1, and RB1. Among the patients with EGFR-mutated NSCLC, TET2 co-occurring alterations correlated with shorter progression-free survival of EGFR tyrosine kinase inhibitor treatment. NGS ctDNA analysis in comprehensive genetic testing improves actionable mutation identification, vital for treating Asian NSCLC cases with high actionable mutation rates. Lower stages correlated with undetected blood-based NGS ctDNA assay results.

Real-World Clinical Outcomes after Genomic Profiling of Circulating Tumor DNA in Patients with Previously Treated Advanced Non-Small Cell Lung Cancer.

Comprehensive genomic profiling for advanced non-small cell lung cancer (NSCLC) can identify patients for molecularly targeted therapies that improve clinical outcomes. We analyzed data from 3084 patients (median age 65 years, 72.9% with adenocarcinoma) with advanced NSCLC registered in a real-world healthcare claims database (GuardantINFORMTM, Guardant Health) who underwent next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) testing (Guardant360®, Guardant Health) after first-line therapy (28.0% with agents targeted against genomic alterations). ctDNA was detected in 2771 samples (89.9%), of which 41.9% harbored actionable alterations, most commonly EGFR (epidermal growth factor receptor) mutations (29.7%). Actionable alterations were detected in 26.7% of patients (534/2001) previously treated with non-targeted agents. Emerging potentially targetable mutations were found in 40.1% (309/770) of patients previously treated with targeted therapies. Among patients with qualifying alterations detected by ctDNA testing, the time to treatment discontinuation (median 8.8 vs. 4.2 months; hazard ratio 1.97, p < 0.001) and overall survival (median 36.1 vs. 16.6 months; hazard ratio 2.08, p < 0.001) were longer for those who received matched second-line therapy versus unmatched second-line therapy. In real-world practice, results of a blood-based NGS assay prior to second-line treatment inform therapeutic decisions that can improve clinical outcomes for patients with advanced NSCLC.

Efficacy/safety of entrectinib in patients (pts) with ROS1-positive (ROS1+) advanced/metastatic NSCLC from the Blood First Assay Screening Trial (BFAST).

LBA9023 Background: Tissue-based biomarker testing remains challenging as tumor biopsies are often inadequate for comprehensive biomarker testing and repeat biopsies can be risky in pts with advanced/metastatic NSCLC. These challenges could be overcome by using blood-based testing to identify the most appropriate targeted therapy. BFAST (NCT03178552) is a global open-label, multicohort trial evaluating the efficacy and safety of selected therapies in pts with advanced/metastatic NSCLC harboring actionable genetic alterations, as identified by next-generation sequencing (NGS) in cell-free DNA (liquid biopsies). We present data from the ROS1+ cohort: this is the first evaluation of entrectinib efficacy in pts identified by prospective blood-based NGS. Methods: In this single-arm analysis, adults (≥18 years) with treatment-naïve measurable stage IIIB/IV NSCLC, identified as ROS1+ by the FoundationOne®Liquid CDx CTA blood-based NGS test, received oral entrectinib 600 mg/day until disease progression (PD), unacceptable toxicity, consent withdrawal or death. Pts with asymptomatic brain metastases at screening were eligible. Tumor scans were performed at baseline and every 8 weeks thereafter for all disease involvement areas (brain imaging not mandated in pts without baseline CNS disease). Primary endpoint: investigator (INV)-assessed objective response rate (ORR; RECIST 1.1). Secondary endpoints: INV-assessed duration of response (DoR) and progression-free survival (PFS); independent review facility (IRF)-assessed ORR, DoR, PFS; overall survival (OS); time to CNS PD; safety. Results: 55 pts with ROS1+ NSCLC identified by blood-based NGS were enrolled and treated with entrectinib. Median age was 56 yrs; 58% of pts were female and 75% had no history of tobacco use. Non-squamous adenocarcinoma was the most common histology (n = 48/55; 87%); 4 pts (7.3%) had baseline CNS disease. Median follow-up: 18.3 months. At data cut-off (26 Nov 2021, n = 54 pts with measurable disease), confirmed ORR was 81.5% (n = 44/54; 95% CI 68.6–90.8) by INV (2 complete responses [CR], 42 partial responses [PR]) and IRF (3 CR, 41 PR). Median DoR was 13.0 months (95% CI 6.3–18.4) by INV and 16.7 months (95% CI 5.6–24.0) by IRF. Median PFS was 12.9 months (95% CI 8.7–18.5) by INV, and 14.8 months (95% CI 7.2–24.0) by IRF. OS data were immature with 20 events (36.4%) recorded. Median time to CNS PD was not reached (INV: 9 events; IRF: 6 events). Most treatment-related adverse events were non-serious with no treatment-related deaths. Conclusion: These data support the clinical value of blood-based NGS as another method to inform clinical decision-making in ROS1+ NSCLC. Pts with ROS1+ NSCLC (by blood-based NGS) treated with entrectinib showed deep and durable responses, consistent with results from entrectinib trials that used tissue-based testing. No new safety signals were observed. Clinical trial information: NCT03178552.

Concordance Between Tissue ALK Detection by Immunohistochemistry and Plasma ALK Detection by Next-Generation Sequencing in the Randomized Phase 3 ALEX Study in Patients With Treatment-Naive Advanced ALK-Positive NSCLC

IntroductionThe Blood First Assay Screening Trial revealed the clinical applicability of blood-based next-generation sequencing to identify patients with ALK-positive NSCLC for alectinib treatment. To understand the relationship between tissue-based versus blood-based testing, we retrospectively investigated concordance between VENTANA ALK (D5F3) CDx immunohistochemistry and the FoundationACT (FACT; Foundation Medicine, Inc.) plasma assay, and compared clinical efficacy between phase 3 ALEX study subpopulations. MethodsPatients with advanced ALK-positive (by immunohistochemistry) NSCLC were randomized 1:1 to alectinib 600 mg or crizotinib 250 mg, twice daily. Assessable baseline plasma samples were analyzed for ALK positivity by FACT; positive percent agreement with immunohistochemistry was evaluated. Progression-free survival (PFS), duration of response, and objective response rate were compared between intention-to-treat (ITT) and biomarker-evaluable populations, and plasma ALK-positive and plasma ALK-negative subpopulations. ResultsIn the ITT population (303 patients; alectinib, 152; crizotinib, 151), all patients had ALK-positive tumors by immunohistochemistry. In the biomarker-evaluable population (149 patients; alectinib, 76; crizotinib, 73), 105 had plasma ALK-positive and 44 had plasma ALK-negative tumors. Positive percent agreement between immunohistochemistry and FACT was 70.5% (105 of 149; 95% confidence interval: 62.5–77.7). Baseline characteristics were generally balanced, with some exceptions, notably tumor burden. Median PFS in plasma ALK-positive and ALK-negative patients was 22.4 months and not estimable with alectinib and 7.3 months and 12.9 months with crizotinib, respectively; median duration of response was 25.9 months and not estimable with alectinib and 5.6 months and 11.5 months with crizotinib, respectively. ConclusionsReasonable concordance between FACT and immunohistochemistry was observed; both methods are valuable in identifying ALK-positive patients, separately or concurrently. Alectinib was found to have superior PFS in the plasma ALK-positive population, as in the ITT population.

Blood-Based Next-Generation Sequencing in Adrenocortical Carcinoma.

BackgroundAdrenocortical carcinoma (ACC) is a rare and heterogeneous malignancy with poor prognosis. We aimed to evaluate the feasibility of next-generation sequencing (NGS) testing of circulating cell-free tumor DNA (ctDNA) in patients with ACC, to characterize the genomic landscape of alterations, and to identify potential clinically actionable mutations.MethodsRetrospective analysis of genomic data from 120 patients with ACC who had ctDNA testing between 12/2016 and 10/2021 using Guardant360 (Guardant Health, CA) was performed. ctDNA NGS analysis interrogated single nucleotide variants, fusions, indels, and copy number amplifications of up to 83 genes. The frequency of genomic alterations, landscape of co-occurring mutations, and pathogenic/likely pathogenic alterations with potential targeted therapies was identified. The prevalence of alterations identified in ctDNA was compared to those detected in tissue using a publicly available database (cBioPortal).ResultsThe median age of this cohort was 53 years (range 21-81), and 56% of patients were female. Ninety-six patients (80%) had ≥1 somatic alteration detected. TP53 (52%), EGFR (23%), CTNNB1 (18%), MET (18%), and ATM (14%) were found to be the most frequently altered genes in ACC samples. Pathogenic and/or likely pathogenic mutations in therapeutically relevant genes were observed in 56 patients (47%) and included EGFR, BRAF, MET, CDKN2A, CDK4/6, and ATM. The most frequent co-occurring mutations were EGFR + MET (9%), MET + CDK4 (7%), EGFR + CDK4 (7%), and BRAF + MET (7%). The frequencies of mutations detected in ctDNA were similar to those detected in tissue.ConclusionsUtilizing blood-based NGS to characterize genomic alterations in advanced ACC is feasible in over 80% of patients. Almost half of the patients had actionable mutations with approved therapies in other cancers. This approach might inform the development of personalized treatment options or identify clinical trials available for this aggressive malignancy.

P24.04 Concordance of Tissue and Cell-Free DNA-Based Next-Generation Sequencing in Patients With Lung Adenocarcinoma

Panel-based next-generation sequencing (NGS) to detect targetable somatic genetic events is guideline-recommended initial diagnostic testing in lung adenocarcinoma. Tissue biopsy has a number of limitations, including expense and biopsy-related adverse events. “Liquid biopsy” uses blood-based NGS on cell-free DNA (cfDNA). Prior investigations have demonstrated high rates of concordance at initial diagnosis. However, concordance at time of progression remains unknown.

Blood First Assay Screening Trial (BFAST) in Treatment-Naive Advanced or Metastatic NSCLC: Initial Results of the Phase 2 ALK-Positive Cohort

IntroductionThe Blood First Assay Screening Trial is an ongoing open-label, multicohort study, prospectively evaluating the relationship between blood-based next-generation sequencing (NGS) detection of actionable genetic alterations and activity of targeted therapies or immunotherapy in treatment-naive advanced or metastatic NSCLC. We present data from the ALK-positive cohort. MethodsPatients aged more than or equal to 18 years with stage IIIB or IV NSCLC and ALK rearrangements detected by blood-based NGS using hybrid capture technology (FoundationACT) received alectinib 600 mg twice daily. Asymptomatic or treated central nervous system (CNS) metastases were permitted. Primary end point was investigator-assessed objective response rate (ORR; Response Evaluation Criteria in Solid Tumors version 1.1). Secondary end points were independent review facility-assessed ORR, duration of response, progression-free survival (PFS), overall survival, and safety. Exploratory end points were investigator-assessed ORR in patients with baseline CNS metastases and relationship between circulating biomarkers and response. ResultsIn total, 2219 patients were screened and blood-based NGS yielded results in 98.6% of the cases. Of these, 119 patients (5.4%) had ALK-positive disease; 87 were enrolled and received alectinib. Median follow-up was 12.6 months (range: 2.6–18.7). Confirmed ORR was 87.4% (95% confidence interval [CI]: 78.5–93.5) by investigator and 92.0% (95% CI: 84.1–96.7) by independent review facility. Investigator-confirmed 12-month duration of response was 75.9% (95% CI: 63.6–88.2). In 35 patients (40%) with baseline CNS disease, investigator-assessed ORR was 91.4% (95% CI: 76.9–98.2). Median PFS was not reached; 12-month investigator-assessed PFS was 78.4% (95% CI: 69.1–87.7). Safety data were consistent with the known tolerability profile of alectinib. ConclusionsThese results reveal the clinical application of blood-based NGS as a method to inform clinical decision-making in ALK-positive NSCLC.

A retrospective analysis examining the use of tissue-based and blood-based NGS in patients (pts) with advanced non-small cell lung cancer (NSCLC).

e21195 Background: Next generation sequencing (NGS) of tumor has become an integral part of cancer diagnostics and therapeutics today. While tissue-based (TB) NGS is still considered gold-standard, cell-free DNA NGS obtained from peripheral blood (blood-based or BB) offers many advantages because of its quicker turnaround time, minimally-invasive nature and ability to address tumor heterogeneity and track development of resistance mutations over time. It however does have its disadvantages, predominant of which is its lower sensitivity. Integration of BB and TB NGS can both optimize turnaround time and increase detection of targetable mutations. Methods: We conducted a single institution, IRB approved, retrospective study evaluating NGS testing patterns in patients with advanced NSCLC treated at our institution between 1/1/16 and 3/31/20. Our primary endpoint was to evaluate the number of patients who had BB NGS performed at any point during their clinical course in addition to TB NGS testing. Our secondary endpoint was to evaluate the number of patients for who BB NGS led to change in treatment plan. Exploratory points included the concordance rate between BB and TB NGS performed within 1 month of each other and the details of discordance if any. Results: There was a total of 437 eligible advanced NSCLC patients who were treated at our institution between January 2016 and March 2020. Out of these, 104 (23.8%) had BB NGS performed at some point in their disease course. The median number of BB NGS testing done for these patients was 2 and ranged from 1 to 4. 32/104 (30.8%) of patients had change in management because of BB NGS results. TB and BB NGS were performed within one month of each other in 52 patients. 11 of these (21.2%) had detection of identical actionable mutations (AM) on both BB and TB NGS assays. 5 of the patients (9.6%) had AM detected on TB NGS alone and 6 of the patients (11.5%) had AM detected on BB NGS alone. 30/52 patients (57.7%) had no AM identified on both BB and TB NGS. Conclusions: BB NGS has added tremendous value to diagnosis and treatment of NSCLC. It is increasingly used in practice, in tandem with TB NGS. Nearly a fourth of our patients had BB NGS performed at some point in their clinical course. Nearly 20% of simultaneously performed BB and TB NGS were discordant and an AM was identified in only one of the biopsies. Although further research is needed, our study supports simultaneous BB and TB testing at diagnosis and progression thereby maximizing therapeutic potential.

Clinicogenomic real-world data analysis of patients (pts) with KRAS G12C-mutant advanced non-small cell lung cancer (aNSCLC) from the natural history cohort of the Blood First Assay Screening Trial (BFAST).

9023 Background: BFAST (NCT03178552) is a global, multicohort trial of targeted therapies or cancer immunotherapy (CIT) in treatment (tx)-naive aNSCLC. Pts are screened for the study using comprehensive blood-based next-generation sequencing (NGS). In the BFAST natural history cohort, data were collected for pts who received tx or care outside the study’s interventional cohorts. Here, we analyzed the subset of pts whose tumors have KRAS G12C mutations (mut). Methods: Pts eligible for blood-based NGS screening had unresectable aNSCLC, ECOG PS 0-2 and no prior systemic tx for aNSCLC. Pts without tissue samples were eligible. Key genomic and molecular features, including bTMB, PD-L1 and ctDNA concentration; cancer tx; tx response and survival data were collected and analyzed in an exploratory analysis. Results: In the full BFAST screening population through December 2020 (N = 5917), 23% of pts had tumors with any KRAS mut; 9% were KRAS G12C. Pts were enrolled in the natural history cohort from October 2018 to October 2020 (n = 1017); 63 pts had tumors with KRAS G12C mut. Median age was 68 y, 59% were male, 86% had ECOG PS 0-1 and 84% had non-squamous histology. Co-mut in TP53 (60%) and STK11 and/or KEAP1 (25%) were detected; 8% of pts had bTMB ≥16. High PD-L1 expression per local testing was reported in 32% of pts; 38% were not tested. Among pts with 1L tx (n = 50), 50%, 28% and 20% received chemo, CIT or CIT + chemo, respectively, with real-world response rates (CR/PR per physician assessment) of 20%, 29% and 30%, respectively. Of the 13 pts (21%) without documented 1L tx, 7 died ≤3 mo from enrollment. Median OS was 14 mo overall, with differences found between key genomic subsets (Table). Conclusions: BFAST is the first study to identify KRAS G12C mut using blood-based NGS and describe the natural history, clinical characteristics and genomic landscape of this pt subset. Up to 21% of pts may not receive 1L tx. Pts with TP53 co-mut appear to have favorable outcomes, while those with STK11 and/or KEAP1 co-mut appear to have inferior outcomes vs pts without these mut. The lack of PD-L1 testing in many pts indicates a lack of tissue for comprehensive tissue testing, highlighting a potential benefit of blood-based detection of biomarkers, including KRAS G12C. Clinical trial information: NCT03178552. [Table: see text]

Molecular Profiling and Targeted Therapy in Cholangiocarcinoma: An Observational, Retrospective Multicenter Study.

Cholangiocarcinoma (CCA) is an aggressive biliary tract malignancy and overall prognosis remains poor, with a median survival of less than 24months. Sequencing studies have revealed a high prevalence of genomic alterations in CCA, with multiple potential therapeutic targets. Next-generation sequencing (NGS) can identify actionable mutations such as FGFR, IDH, BRAF, ERBB2, ROS1, or microsatellite instability (MSI-H), among others. We conducted a retrospective multicenter study in Spain in 2019. Thirty consecutive patients from 15 centers were included. All patients were diagnosed with advanced CCA and underwent NGS (FoundationOne®) in 2019. Twenty-four patients underwent tissue-based NGS (FoundationOne® CDx), and 6 patients underwent blood-based NGS (FoundationOne®Liquid) with sequencing panels of 324 and 70 genes, respectively RESULTS: We identified 12 patients (40%) with an actionable genetic alteration in tissue: 2 FGFR2 fusions, 6 IDH1 mutations, 1 ERBB2 mutation, 1 ROS1 fusion, 1 PIK3CA mutation, and 1 MSI-H. Comprehensive genomic profiling (CGP) in cholangiocarcinoma can identify, in a high proportion of patients, clinically relevant genomic alterations that can lead to targeted therapies, expanding treatment options.

Abstract B20: Prolonged time to clearance of circulating-tumor DNA from patients with limited-stage small-cell lung cancer is associated with inferior progression-free and overall survival

Abstract Introduction: Despite recent incremental advances, patients with small-cell lung cancer (SCLC) continue to have a poor prognosis, with a median overall survival (OS) of 12-20 months in limited-stage disease (LS-SCLC) and approximately 12 months in extensive-stage disease (ES-SCLC). In an attempt to improve the detection and monitoring of SCLC, assays of circulating tumor DNA (ctDNA) via blood-based next-generation sequencing (NGS) have been validated. In this study, we used a blood-based 14 gene SCLC ctDNA NGS panel to evaluate the prognostic significance of the diagnostic maximum ctDNA variant allele frequency (VAF), diagnostic mean ctDNA VAF, and time to ctDNA clearance while on first-line therapy. Design: In our previous work, we developed a ctDNA assay to sequence 14 genes (TP53, RB1, BRAF, KIT, NOTCH1-4, PIK3CA, PTEN, FGFR1, MYC, MYCL1, and MYCN) that are commonly mutated in SCLC. A total of 104 plasma samples were analyzed from a cohort of 14 patients with LS-SCLC who completed definitive chemoradiation (n=13) or surgical resection (n=1) and had an end-of-treatment blood collection within nine weeks (mean 10.5 days, range 0-63 days) of completion of definitive initial therapy. We used a Cox Proportional Hazards model to estimate the hazard ratio (HR) for progression-free survival (PFS) or death based on the diagnostic maximum ctDNA VAF, diagnostic mean ctDNA VAF, and time to ctDNA clearance on first-line therapy. Results: In our 14-patient cohort, we did not observe any association between progression or death and maximum diagnostic ctDNA VAF (PFS HR: 1.01, CI 0.97-1.05; OS HR: 1, CI 0.95-1.04) or mean diagnostic ctDNA VAF (PFS HR: 1.01, CI 0.94-1.08; OS HR: 0.99, CI 0.91-1.07). Of the specific mutations representing the maximum diagnostic ctDNA VAF, TP53 represented 14.2% (n=2), while the remaining included RB1 associated mutations (n=5), PIK3CA (n=1), MYCL1 amplification (n=1), or no ctDNA at diagnosis (n=5). Among patients with clearance of ctDNA during first-line therapy (n=9), delayed time to ctDNA clearance was associated with inferior PFS (HR 1.1, CI 1.01-1.19) and OS (HR 1.07, CI 1.01-1.15), with median time to clearance of 63 days (range 29-92 days). Notably, 3 patients cleared ctDNA on their first on-treatment draw at approximately 30 days (29, days, 29 days, and 32 days). These patients have had no evidence of relapse and all remain alive since the start of first-line treatment (1467, 965, and 383 days of follow-up). Of the patients who had disease recurrence, the median time to clearance on first-line therapy was 65 days and median time to progression was 249 days, with all but 1 patient succumbing to their disease (median OS 437 days). Conclusion: In patients with LS-SCLC, prolonged time to ctDNA clearance during first-line therapy is associated with inferior PFS and OS. Larger patient cohorts are needed to validate this finding. Citation Format: Christopher Cann, Prasad Kopparapu, Yingjun Yan, Anel Muterspaugh, Heidi Chen, Zhiguo Zhao, Sally York, Leora Horn, Kristen Ancell, Kenneth Wyman, Caterina Bertucci, Tristan Shaffer, Lauren Hodson, Kavita Garg, Seyed Ali Hosseini, Lee Lim, Christine M. Lovly, Wade Iams. Prolonged time to clearance of circulating-tumor DNA from patients with limited-stage small-cell lung cancer is associated with inferior progression-free and overall survival [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B20.

Blood-based next-generation sequencing analysis of neuroendocrine neoplasms.

Background: Neuroendocrine neoplasms (NENs) are a heterogeneous group of neoplasms that span from well-differentiated neuroendocrine tumors (NETs) to highly aggressive neoplasms classified as neuroendocrine carcinomas (NECs). The genomic landscape of NENs has not been well studied. The aim of this study is to confirm the feasibility of next generation sequencing (NGS) testing circulating tumor DNA (ctDNA) in patients with NENs and characterize common alterations in the genomic landscape. Results: Of the 320 NEN patients, 182 (57%) were male with a median age of 63 years (range: 8-93) years. Tumor type included pancreatic NET (N = 165, 52%), gastrointestinal NEC (N = 52, 16%), large cell lung NEC (N = 21, 7%), nasopharyngeal NEC (N = 16, 5%) and NEC/NET not otherwise specified (N = 64, 20%). ctDNA NGS testing was performed on 338 plasma samples; 14 patients had testing performed twice and 2 patients had testing performed three times. Genomic alterations were defined in 280 (87.5%) samples with a total of 1,012 alterations identified after excluding variants of uncertain significance (VUSs) and synonymous mutations. Of the 280 samples with alterations, TP53 associated genes were most commonly altered (N = 145, 52%), followed by KRAS (N = 61, 22%), EGFR (N = 33, 12%), PIK3CA (N = 30, 11%), BRAF (N = 28, 10%), MYC (N = 28, 10%), CCNE1 (N = 28, 10%), CDK6 (N = 22, 8%), RB1 (N = 19, 7%), NF1 (N = 19, 7%), MET (N = 19, 7%), FGFR1 (N = 19, 7%), APC (N = 19, 7%), ERBB2 (N = 16, 6%) and PTEN (N = 14, 5%). Conclusions: Evaluation of ctDNA was feasible among individuals with NEN. Liquid biopsies are non-invasive methods that can provide personalized options for targeted therapies in NEN patients. Patients and Methods: Molecular alterations in 338 plasma samples from 320 patients with NEN were evaluated using clinical-grade NGS of ctDNA (Guardant360®) across multiple institutions. The test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes.

Total Number of Alterations in Liquid Biopsies Is an Independent Predictor of Survival in Patients With Advanced Cancers.

PURPOSEStudies have demonstrated an association between quantity of circulating tumor DNA (ctDNA) and poorer survival. We investigated the relationship between percent ctDNA (%ctDNA), total number of ctDNA alterations, and overall survival (OS) in liquid biopsies.MATERIALS AND METHODSOverall, 418 patients with blood-based next-generation sequencing (54 to 73 genes) were analyzed. Eligible patients included those who had advanced/metastatic solid tumor malignancies and never received immunotherapy treatment, which may alter the survival curve in patients with high mutational burden.RESULTSPatients with a high (≥ 5%) %ctDNA had significantly shorter OS versus those with intermediate (≥ 0.4% to < 5%) or low (< 0.4%) values (median OS, 7.0 v 14.1 v not reached [NR] months, respectively; P < .0001). Patients with a high (≥ 5) total number of alterations had significantly shorter OS versus those with intermediate (≥ 1.46 to < 5), low (< 1.46), or no alterations (median OS, 4.6 v 11.7 v 21.3 v NR months, respectively; P < .0001). The total number of alterations correlated with %ctDNA (r = 0.85; 95% CI, 0.81 to 0.87; P < .0001). However, only an intermediate to high total number of alterations (≥ 1.46) was an independent predictor of worse OS (hazard ratio, 1.96; 95% CI, 1.30 to 2.96; P = .0014; multivariate analysis).CONCLUSIONWe demonstrate that the total number of alterations and %ctDNA have prognostic value and correlate with one another, but only the total number of alterations was independently associated with survival outcomes. Our findings suggest that the total number of alterations in plasma may be an indicator of more aggressive tumor biology and therefore poorer survival.

Blood-Based Next-Generation Sequencing Analysis of Appendiceal Cancers.

Appendiceal cancers (ACs) are rare. The genomic landscape of ACs has not been well studied. The aim of this study was to confirm the feasibility of next-generation sequencing (NGS) using circulating tumor DNA (ctDNA) in ACs and characterize common genomic alterations. Molecular alterations in 372 plasma samples from 303 patients with AC using clinical-grade NGS of ctDNA (Guardant360) across multiple institutions were evaluated. Test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes. A total of 303 patients with AC were evaluated, of which 169 (56%) were female. Median age was 56.8 (25-83) years. ctDNA NGS testing was performed on 372 plasma samples; 48 patients had testing performed twice, 9 patients had testing performed three times, and 1 patient had testing performed four times. Genomic alterations were defined in 207 (n = 207/372, 55.6%) samples, and 288 alterations were identified excluding variants of uncertain significance and synonymous mutations. Alterations were identified in at least one sample from 184 patients; TP53-associated genes (n = 71, 38.6%), KRAS (n = 33, 17.9%), APC (n = 14, 7.6%), EGFR (n = 12, 6.5%), BRAF (n = 11, 5.9%), NF1 (n = 10, 5.4%), MYC (n = 9, 4.9%), GNAS (n = 8, 4.3%), MET (n = 6, 3.3%), PIK3CA (n = 5, 2.7%), and ATM (n = 5, 2.7%). Other low-frequency but clinically relevant genomic alterations were as follows: AR (n = 4, 2.2%), TERT (n = 4, 2.2%), ERBB2 (n = 4, 2.2%), SMAD4 (n = 3, 1.6%), CDK4 (n = 2, 1.1%), NRAS (n = 2, 1.1%), FGFR1 (n = 2, 1.1%), FGFR2 (n = 2, 1.1%), PTEN (n = 2, 1.1%), RB1 (n = 2, 1.1%), and CDK6, CDKN2A, BRCA1, BRCA2, JAK2, IDH2, MAPK, NTRK1, CDH1, ARID1A, and PDGFRA (n = 1, 0.5%). Evaluation of ctDNA is feasible among patients with AC. The frequency of genomic alterations is similar to that previously reported in tissue NGS. Liquid biopsies are not invasive and can provide personalized options for targeted therapies in patients with AC. The complexity of appendiceal cancer and its unique genomic characteristics suggest that customized combination therapy may be required for many patients. Theoretically, as more oncogenic pathways are discovered and more targeted therapies are approved, customized treatment based on the patient's unique molecular profile will lead to personalized care and improve patient outcomes. Liquid biopsies are noninvasive, cost-effective, and promising methods that provide patients with access to personalized treatment.

LBA81_PR - Phase II/III blood first assay screening trial (BFAST) in patients (pts) with treatment-naïve NSCLC: Initial results from the ALK+ cohort

LBA81_PR - Phase II/III blood first assay screening trial (BFAST) in patients (pts) with treatment-naïve NSCLC: Initial results from the ALK+ cohort

Blood-based next-generation sequencing analysis of neuroendocrine tumors.

4110 Background: Neuroendocrine tumors (NET) comprise around 2% of all malignant tumors of the gastrointestinal system. The genomic landscape of NET has not been well studied. The aim of this study was to confirm the feasibility of next generation sequencing (NGS) using ctDNA in NET and characterize common alterations in the genomic profile. Methods: Molecular alterations in 114 plasma samples from 114 patients with NET using clinical-grade NGS of ctDNA (Guardant360Ò) across multiple institutions were evaluated. The test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes. Results: A total of 114 NET patients were evaluated, of which 64 (56.1%) were female. Mean age was 59.7 years with a range between 23-89 years. ctDNA NGS testing was performed on 114 plasma samples; 1 patient had testing performed twice. Genomic alterations were defined in 94 (n = 94/114, 82.5%) samples with a total of 289 alterations identified after excluding variants of uncertain significance (VUSs) and synonymous mutations. Alterations were identified in at least one sample from 83 patients; TP53 associated genes were most commonly altered (n = 83/289, 28.7%), followed by KRAS (n = 22, 7.6%), PI3CA (n = 15, 5.2%), CCNE1 (n = 15, 5.2%), BRAF (n = 13, 4.5%), MYC (n = 12, 4.1%), ERBB2 (n = 11, 3.8%), APC (n = 10, 3.5%), EGFR (n = 10, 3.5%), MET (n = 10, 3.5%), PTEN (n = 9, 3.1%), RB1 (n = 9, 3.1%), CDK6 (n = 7, 2.4%), AR (n = 5, 1.7%), ARID1A (n = 5, 1.7%), FGFR1 (n = 5, 1.7%), and PDGFRA (n = 5, 1.7%). Other genomic alterations of low frequency, but clinical relevance included: CDK4 (n = 4, 1.3%), NF1 (n = 4, 1.3%), RAF1 (n = 4, 1.3%), GNAS (n = 3, 1.0%), KIT (n = 3, 1.3%), BRCA2 (n = 2, 0.7%), CCND2 (n = 2, 0.7%), CTNNB1 (n = 2, 0.7%), JAK2 (n = 2, 0.7%), NRAS (n = 2, 0.7%), SMAD4 (n = 2, 0.7%), and TERT (n = 2, 0.7%). Alterations in AKT1, ALK, ATM, BRCA1, CCND1, CDKN2A, FGFR2, MTOR, RHOA, SMO and STK11 were all reported once (n = 1, 0.3%). Conclusions: Evaluation of ctDNA is feasible among individuals with NET. Liquid biopsies are not invasive and can provide personalized options for targeted therapies in NET patients.

Abstract 5706: A blood-based next-generation sequencing assay to determine tumor mutational burden (bTMB) is associated with benefit to an anti-PD-L1 inhibitor, atezolizumab

Abstract Background: Tumor mutational burden (TMB) has emerged as a new biomarker for response to checkpoint inhibitor immunotherapy. Recently, we described a novel assay to calculate TMB from the circulating tumor DNA (ctDNA) in the blood (bTMB) and demonstrated validation to support its application in a prospective phase III trial in 1L NSCLC comparing the anti-PD-L1 agent, atezolizumab, against standard of care chemotherapy. Herein, we demonstrate clinical utility of the bTMB assay across a retrospective study of 794 NSCLC patients from two randomized clinical trials evaluating progression free survival (PFS) and overall survival (OS) between atezolizumab and chemotherapy. Furthermore, we compare TMB between tissue and blood, and evaluate variant-level concordance between the bTMB assay and the CLIA-validated ctDNA assay, FoundationACT (FACT). Methods: Cell free DNA (cfDNA) from plasma was isolated from retrospective clinical samples. The bTMB assay delivered a count of somatic base substitutions in the ctDNA down to 0.5% allele frequency across 394 genes from as little as 1% tumor content, yielding a bTMB score. Tissue TMB was evaluated from formalin-fixed, paraffin embedded specimens using the FoundationOne assay. Results: Patients with bTMB ≥14 mut/Mb were considered high, and demonstrated significant enrichment for both PFS and OS in the phase II POPLAR study evaluating atezolizumab vs. chemotherapy (PFS HR = 0.57, OS HR = 0.56, n=211). Survival results were validated in the larger phase III study, OAK (PFS HR = 0.65, OS HR = 0.64, n=583). Significant enrichment in PFS was observed between bTMB-high and non-high patients receiving atezolizumab, however this effect was not observed for patients receiving chemotherapy. Amongst 259 patients with blood and tissue TMB, overall and positive percent agreement (PPA) in the TMB categorical result were 81.5% and 63.6%, respectively. When bTMB was restricted to the 62 gene FACT assay, the PPA dropped to 17.0%, suggesting a sufficiently sized panel is required to sensitively identify patients with high TMB. When samples were TMB-high in blood, the median percent overlap of TMB variants between blood and tissue was 70%. Blood samples tested in both the bTMB and FACT assays revealed that 93% of variants were detected in both assays across overlapping regions, with ≥99% of variants detected in both platforms with variant allele frequency ≥1.0%. Conclusions: The bTMB assay is analytically validated for high accuracy and precision, and demonstrates a high degree of variant level concordance with the FACT assay. High bTMB is significantly associated with improved survival to atezolizumab vs. chemotherapy in 2L NSCLC, and the survival benefit is specific to atezolizumab and not prognostic. Finally, TMB between blood and tissue is correlated and largely explained by overlapping variants present in both sample types. Citation Format: David Fabrizio, Daniel Lieber, Christine Malboeuf, Jacob Silterra, Emily White, Michael Coyne, Tina Brennan, Jie Ma, Mark Kennedy, Erica Schleifman, Sarah Paul, Yan Li, David Shames, Craig Cummings, Eric Peters, Marcin Kowanetz, Doron Lipson, Geoff Otto. A blood-based next-generation sequencing assay to determine tumor mutational burden (bTMB) is associated with benefit to an anti-PD-L1 inhibitor, atezolizumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5706.