Maximum Somatic Allele Frequency Research Articles

Abstract 3664: Evaluation of on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in patients (pts) with metastatic non-small cell lung cancer (NSCLC): An exploratory analysis of KEYNOTE-598

Abstract Background: ctDNA-based pWES is a promising tool to examine tumor genomics using a non-invasive liquid biopsy to serially monitor changes during tumor evolution and treatment. Here, we evaluate on-treatment tumor molecular dynamics using ctDNA-based pWGS and pWES in pts with metastatic NSCLC that responded to pembrolizumab (pembro) monotherapy and later experienced PD in KEYNOTE-598 (NCT03302234). Methods: In KEYNOTE-598, pts had metastatic NSCLC (PD-L1 tumor proportion score ≥50%) and received first-line pembro ± ipilimumab for ≤35 cycles. Cell-free DNA (cfDNA) was isolated and sequenced from plasma samples at baseline (BL), during on-treatment response (cycle 5 [C5]), and at PD (discontinuation [D]) from pts with objective response to pembro monotherapy and subsequent PD. ctDNA burden (tumor fraction [TF]) was estimated using low-pass pWGS by quantifying tumor content in cfDNA as a function of aneuploidy. All samples with TF >1.5% underwent high-depth pWES. ctDNA burden was estimated from pWES data using maximum somatic allele frequency (MSAF). Correlation between TF and MSAF was evaluated using the Spearman coefficient (r). Variant allele frequency (VAF) and normalized VAF (nVAF) were used to determine variant clonality. Results: In total, 23 pts with initial response to pembro and subsequent PD had plasma samples available from BL, C5, and D. Samples from 22 pts had TF >1.5% by pWGS and underwent pWES. MSAF by pWES was correlated with TF by pWGS at BL (r = 0.68), C5 (0.80), and D (0.59). ctDNA TFs at BL and D (mean = 8.1% and 4.9%, respectively) were higher than C5 (2.0%). In a pooled variant-level analysis (nVAF >0.25) of samples from pts with high TF (≥2.5%) at both BL and D (n = 10), 786 (46%) of variants were present at BL and D, 391 (23%) were present at BL only, and 540 (32%) were present at D only. Variants shared between BL and D had higher clonality (mean nVAF = 0.46) than BL-only (0.38) or D-only variants (0.4). In general, shared variants had similar nVAFs at BL and D but in some pts nVAFs increased at D, suggesting evolution of tumor subclones during treatment. TP53 was mutated in 9 of 10 pts with high TF and was shared at BL and D in 6 pts (mean nVAF = 0.49), present at BL only in 1 pt (0.11) and at D only in 2 pts (0.43). KRAS G12V and Q61H hotspot mutations were observed in 2 pts at D-only and may be related to immune editing. Conclusions: Comprehensive pWES is feasible with sufficient ctDNA burden (TF ≥2.5%). ctDNA dynamics demonstrated molecular profiles characteristic of recurrence with high TF at BL and D and were consistent with radiographic determination of response/progression. Tumor variants at BL and D generally had a common clonal trunk with clones disappearing or appearing de novo. Citation Format: Minita Shah, EJ Dettman, Andrew Albright, Cai Chen, Julie Kobie, Vinay Varadan, Ayman Samkari, Carol Peña, Razvan Cristescu, Z Alexander Cao. Evaluation of on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in patients (pts) with metastatic non-small cell lung cancer (NSCLC): An exploratory analysis of KEYNOTE-598 [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 3664.

Abstract 962: Monitoring on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in advanced esophageal cancer: An exploratory analysis of KEYNOTE-590

Abstract Background: We evaluated on-treatment tumor molecular dynamics using ctDNA-based pWGS and pWES in patients (pts) with locally advanced or metastatic esophageal cancer that responded to pembro + chemo or chemo alone and later experienced PD in KEYNOTE-590 (NCT03189719). Methods: Pts with locally advanced, unresectable, or metastatic esophageal or Siewert type 1 gastroesophageal junction cancer were randomized 1:1 to first-line pembro 200 mg or placebo + chemo (5-fluorouracil + cisplatin) Q3W for ≤35 cycles. Cell-free DNA (cfDNA) was isolated and sequenced from plasma samples collected at baseline (BL), during on-treatment response (cycle 5 [C5]), and at PD (discontinuation [D]) from pts with response and subsequent PD. ctDNA burden (tumor fraction [TF]) was estimated using low-pass pWGS by quantifying tumor aneuploidy in cfDNA. All samples with TF >1.5% underwent high-depth pWES. ctDNA burden from pWES was estimated as maximum somatic allele frequency (MSAF). Associations of TF with MSAF were assessed using Spearman correlation coefficient r. For each subject, Jaccard index (JI) was calculated to evaluate the overlap of variants between BL and D. Variant allele frequency (VAF) and normalized VAF (nVAF) were used to determine variant clonality. Results: 108 pts (pembro + chemo, 59; chemo, 49) with initial response and subsequent PD had plasma samples available from BL, C5, and D. Samples from 94 pts had TF >1.5% by pWGS and underwent pWES. MSAF correlated with TF at BL (r = 0.84), C5 (0.56), and D (0.86). ctDNA TF was lower at C5 than at BL and D, with a mean of 4.4% (C5) vs 20.9% (BL) and 14.0% (D) with pembro + chemo and 4.0% (C5) vs 15.8% (BL) and 15.5% (D) with chemo. In variant-level analyses of pWES data from samples with high TF (≥2.5%) at BL and D (n = 65), 39.2% and 44.2% of variants were shared between BL and D with pembro + chemo and chemo, respectively. Higher overlap was observed for variants between BL and D for the chemo arm (JI: median, 0.54; range, 0.04-0.91) vs pembro + chemo (0.37; 0.01-0.92). Shared variants between BL and D had higher clonality compared with variants at BL-only or D-only with pembro + chemo (BL and D mean nVAF = 0.50 vs BL-only = 0.39, and D-only = 0.38) and chemo (0.49 vs 0.38 and 0.38). In pooled variant analyses, TP53 was the most commonly observed mutation and was rarely lost or acquired at D. Conclusions: Comprehensive pWES was feasible with sufficient ctDNA burden (TF ≥2.5%). ctDNA burden dynamics followed high disease burden at BL and D, consistent with radiographic determination of response/PD. Tumor variants at BL and D generally had a common clonal trunk and a higher overlap of variants was observed at D in the chemo arm. These results provide preliminary molecular evidence of immune editing in pts receiving immunotherapy that warrants further study. Citation Format: Minita Shah, E.J. Dettman, Andrew Albright, Cai Chen, Julie Kobie, Sukrut Shah, Carol Peña, Razvan Cristescu, Z Alexander Cao. Monitoring on-treatment tumor molecular dynamics using plasma whole genome sequencing (pWGS) and whole exome sequencing (pWES) of circulating tumor DNA (ctDNA) in advanced esophageal cancer: An exploratory analysis of KEYNOTE-590 [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 962.

Liquid biopsy-based circulating tumour (ct)DNA analysis of a spectrum of myeloid and lymphoid malignancies yields clinically actionable results.

Liquid biopsy (LBx)-based next-generation sequencing (NGS) of circulating tumour DNA (ctDNA) can facilitate molecular profiling of haematopoietic neoplasms (HNs), particularly when tissue-based NGS is infeasible. We studied HN LBx samples tested with FoundationOne Liquid CDx, FoundationOne Liquid, or FoundationACT between July 2016 and March 2022. We identified 271 samples: 89 non-Hodgkin lymphoma (NHL), 43 plasma-cell neoplasm (PCN), 41 histiocytoses, 27 myelodysplastic syndrome (MDS), 25 diffuse large B-cell lymphoma (DLBCL), 22 myeloproliferative neoplasm (MPN), 14 Hodgkin lymphoma (HL), and 10 acute myeloid leukaemia (AML). Among 73.4% with detectable pathogenic alterations, median maximum somatic allele frequency (MSAF) was 16.6%, with AML (36.2%), MDS (19.7%), and MPN (44.5%) having higher MSAFs than DLBCL (3.9%), NHL (8.4%), HL (1.5%), PCN (2.8%), and histiocytoses (1.8%) (P = 0.001). LBx detected characteristic alterations across HNs, including in TP53, KRAS, MYD88, and BTK in NHLs; TP53, KRAS, NRAS, and BRAF in PCNs; IGH in DLBCL; TP53, ATM, and PDCD1LG2 in HL; BRAF and MAP2K1 in histiocytoses; TP53, SF3B1, DNMT3A, TET2, and ASXL1 in MDS; JAK2 in MPNs; and FLT3, IDH2, and NPM1 in AML. Among 24 samples, the positive percent agreement by LBx was 75.7% for variants present in paired buffy coat, marrow, or tissues. Also, 75.0% of pairs exhibited alterations only present on LBx. These were predominantly subclonal (clonal fraction of 3.8%), reflecting the analytical sensitivity of LBx. These data demonstrate that LBx can detect relevant genomic alterations across HNs, including at low clonal fractions, suggesting a potential clinical utility for identifying residual or emerging therapy-resistant clones that may be undetectable in site-specific tissue biopsies.

Predictive biomarkers of response and survival following immunotherapy with a PD-L1 inhibitor benmelstobart (TQB2450) and antiangiogenic therapy with a VEGFR inhibitor anlotinib for pretreated advanced triple negative breast cancer

In our phase Ib trial (ClinialTrials.gov Identifier: NCT03855358), benmelstobart (TQB2450), a novel humanized IgG1 antibody against PD-L1, plus antiangiogenic multikinase inhibitor, anlotinib, demonstrated promising antitumor activities in pretreated triple negative breast cancer (TNBC) patients. We conducted explorative analyses of genomic biomarkers to explore the associations with treatment response and survival outcomes. Targeted next generation sequencing (NGS) was undertaken toward circulating tumor DNA (ctDNA) collected from peripheral blood samples prior to the start of treatment and after disease progression. A total of 31 patients received targeted NGS and functional driver mutations in 29 patients were analyzed. The most frequent mutations were TP53 (72%), MLL3 (28%), and PIK3CA (17%). At a blood-based tumor mutational burden (bTMB) cutoff of 6.7 mutations per megabase, patients with low bTMB showed better response to anlotinib plus TQB2450 (50% vs. 7%, P = 0.015) and gained greater PFS benefits (7.3 vs. 4.1 months, P = 0.012) than those with high bTMB. At a maximum somatic allele frequency (MSAF) cutoff of 10%, a low MSAF indicated a better objective response (43% vs. 20%) as well as a significantly longer median PFS (7.9 vs. 2.7 months, P < 0.001). Patients with both low MSAF and low bTMB showed a notably better objective response to anlotinib plus TQB2450 (70% vs. 11%, P < 0.001) and a significantly longer median PFS (11.0 vs. 2.9 months, P < 0.001) than patients with other scenarios. Our findings support future studes and validation of MSAF and the combined bTMB-MSAF classification as predictive biomarkers of immune checkpoint inhibitor-based regimens in advanced TNBC patients.

Evaluation of tissue- and plasma-derived tumor mutational burden (TMB) and genomic alterations of interest in CheckMate 848, a study of nivolumab combined with ipilimumab and nivolumab alone in patients with advanced or metastatic solid tumors with high TMB

BackgroundAn accumulation of somatic mutations in tumors leads to increased neoantigen levels and antitumor immune response. Tumor mutational burden (TMB) reflects the rate of somatic mutations in the tumor genome,...

Serial ctDNA monitoring to predict response in mCRC patients treated with anlotinib in combination with oxaliplatin and capecitabine (CAPEOX) as the first-line therapy.

e15581 Background: Circulating tumour DNA (ctDNA) sequencing offers a non-invasive approach to monitor therapeutic efficacy in colorectal cancer. However, the mutational landscape of ctDNA during treatment and its impact on clinical outcomes remain unknown. This study aimed to investigate the value of ctDNA in predicting treatment response and PFS in mCRC patients treated with anlotinib plus CAPEOX as first-line therapy. Methods: We conducted a multicenter, single-arm, phase II, exploratory study of patients with RAS/BRAF wild-type unresectable metastatic colorectal cancer (mCRC) who underwent Anlotinib in combination with CAPEOX as the first-line therapy (NCT04080843). Plasma samples from 26 patients were collected at three timepoints: 1 week before treatment (baseline), close to the time of optimal remission (C1) and the time of the last blood collection or the time of disease progression (C2). The maximum somatic allele frequency (MSAF) was calculated for each case and used to provide an estimate of the ctDNA fraction in the blood. Results: 77 plasma samples from the 26 enrolled mCRC patients were sequenced by NGS based on a panel comprising 202 genes. 90 variations were detected in baseline plasma, with a positive rate of 96.2% (25/26). Adenomatous polyposis coli ( APC), was the most mutated gene (84.6%, 22/26). Other mutated genes were TP53 (80.8%, 21/26), FBXW7 (19.2%, 5/26), KRAS (11.5%, 3/26), PIK3CA (11.5%, 3/26) and ROS1 (11.5%, 3/26). The median MSAF of baseline ctDNA was significantly higher in patients who had only liver metastases. Compared with baseline, the ctDNA MSAF level at C1 timepoint was decreased among the whole 26 patients (p &lt; 0.001). By comparing ctDNA positive group (ctDNA MSAF &gt; 0) and ctDNA negative group (ctDNA MSAF = 0) at C1 timepoint, CR cases were mainly in ctDNA negative group, while PD cases accounted for a high proportion in the ctDNA positive group. The median progression-free survival (mPFS) of the whole patients was 11.27 months (95%CI 7.33m to 14.52m). The mPFS was 14.52 months (95% CI 14.4 to NR) of patients with ctDNA negative at C1, which was longer than 9.17 months (95% CI 7.16 to 14.06) of patients with ctDNA positive at C1 (p = 0.012). For 25 patients who had plasma samples of three timepoints, we divided the patients into Non-PD group and PD group according to the clinical outcome at C2 timepoint. Compared with C1 timepoint, the ctDNA MSAF level at C2 timepoint was increased in both Non-PD group and PD group. However, the increment of ctDNA MSAF level in PD group was higher than that in non-PD group (p = 0.000069 vs p = 0.024). Conclusions: This ctDNA profiling study revealed the utility of ctDNA in predicting clinical outcomes in mCRC patients under first-line treatment. Serial ctDNA monitoring might become useful in an active surveillance strategy for the management of mCRC. Clinical trial information: NCT04080843 .

Abstract 4528: Evaluation of plasma circulating tumor DNA (ctDNA)-based whole genome sequencing (pWGS) and whole exome sequencing (pWES) and concordance with tumor tissue whole exome sequencing (tWES): a pilot study in patients with recurrent or metastatic head and neck squamous cell carcinoma or metastatic urothelial carcinoma

Abstract Background: The genetic heterogeneity and clonal evolution of tumors is hypothesized to influence disease response and acquisition of resistance during treatment. However, comprehensive analysis of the changing tumor molecular landscape to support evaluation of such a hypothesis is often difficult to quantify due to the lack of accessibility to longitudinal biopsy samples in a large number of patients (pts). Longitudinal analyses using pWGS or pWES may allow the delineation of the genetic evolution of tumors and its impact on treatment outcomes. We conducted a pilot study to evaluate the feasibility of obtaining pWGS and pWES data from ctDNA in pretreatment samples from pts enrolled in 2 phase 3 trials that evaluated second-line pembrolizumab versus chemotherapy/standard-of-care therapy: KEYNOTE-040 (recurrent or metastatic head and neck squamous cell carcinoma; NCT02252042) and KEYNOTE-045 (metastatic urothelial carcinoma, NCT02256436). Concordance between pWES and tWES was also evaluated. Methods: Cell-free DNA was isolated from 1-3 mL of plasma; pWGS (via low-pass WGS) and pWES were performed on samples from pts with available tWES data generated as part of planned tissue biomarker analyses for the respective studies. Tumor burden in ctDNA was estimated from pWES data using single nucleotide variant (SNV)-based maximum somatic allele frequency (MSAF) and from pWGS data using a copy number variation-based measure of mutational burden in the tumor fraction. Concordance between the pWES and tWES mutational spectrum was determined using the Jaccard index. Concordance of key driver somatic events (FGFR3, TP53, and HPV status) was evaluated. Results: Plasma samples from 47 pts (KEYNOTE-040, n = 24; KEYNOTE-045, n = 23) were analyzed. Tumor burden estimates from pWGS (median coverage, 5.84; range, 4.28-8.18) and pWES (median coverage, 1806; range, 1038-2413) data were highly correlated (Spearman ρ = 0.94). A range of 0 to 956 nonsynonymous SNVs (median, 50) per pt was identified in ctDNA. When the ctDNA tumor burden was high (MSAF ≥5%, observed in two-thirds of pts), a relatively high concordance was observed for individual alterations in TP53, FGFR3, and HPV status (overall agreement: 0.87, 0.97, and 0.96, respectively); between tissue- and plasma-based tumor mutational burden (R = 0.49); and in overall mutational landscape overlap (Jaccard index: median, 0.30; range, 0.002-0.53). Conclusions: These data show that pWES exhibits reasonably high concordance with tWES when the tumor burden in ctDNA is relatively high and may be informative regarding tumor genomic characteristics. Extensive longitudinal studies are still needed to understand tumor genetic evolution using plasma ctDNA. Citation Format: Razvan Cristescu, Andrew Albright, Steven Townson, Cai Chen, Blanca Homet Moreno, Nati Lerman, Z. Alexander Cao, Carol Peña. Evaluation of plasma circulating tumor DNA (ctDNA)-based whole genome sequencing (pWGS) and whole exome sequencing (pWES) and concordance with tumor tissue whole exome sequencing (tWES): a pilot study in patients with recurrent or metastatic head and neck squamous cell carcinoma or metastatic urothelial carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4528.

Maximum Somatic Allele Frequency-Adjusted Blood-Based Tumor Mutational Burden Predicts the Efficacy of Immune Checkpoint Inhibitors in Advanced Non-Small Cell Lung Cancer.

Recent studies exhibited the unstable prediction ability of blood-based tumor mutational burden (bTMB) when predicting the response of immune checkpoint inhibitors (ICIs) therapy in patients with non-small cell lung cancer (NSCLC). Circulating tumor DNA (ctDNA) abundance, usually represented by maximum somatic allele frequency (MSAF), was one possible confounding factor influencing bTMB ability in ICIs response prediction. MSAF-adjusted bTMB (Ma-bTMB) was established and validated in patients with advanced NSCLC among Geneplus Cancer Genome Database (GCGD, n = 1679), Zhuo (n = 35), Wang (n = 45), POPLAR (NCT01903993, n = 211) and OAK (NCT02008227, n = 642) cohorts. MSAF demonstrated a modest positive correlation with bTMB and a negative one with survival benefit. Improved survival outcomes of ICIs therapy have been observed among patients with high-Ma-bTMB compared to those with low-Ma-bTMB in Zhuo and Wang cohorts. In addition, compared to low-Ma-bTMB, high-Ma-bTMB was associated with more positive clinical benefits from ICIs therapy than chemotherapy both in POPLAR and OAK cohorts. Further exploration suggested that Ma-bTMB could precisely identify more potential ICIs beneficiaries compared to bTMB and LAF-bTMB, complementary to PD-L1 expression. We developed Ma-bTMB, a convenient, readily available, non-invasive predictive biomarker effectively differentiates beneficiaries of ICIs therapy in advanced NSCLC, warranting future clinical trials.

Liquid Biopsy-Based Next-Generation Sequencing Is an Alternative to Tissue Molecular Profiling of Lymphoid, Plasma-Cell, and Myeloid Neoplasms

Background: Liquid biopsy (LB)-based next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) fragments can facilitate the molecular profiling of hematopoietic neoplasms (HNs), particularly in patients for whom conventional NGS is infeasible due to insufficient tumor in the blood, bone marrow, or tissue, or when tissue biopsy cannot be performed. Because HNs shed ctDNA into the plasma at levels comparable to those shed by solid tumors, LB assays initially designed for solid tumors can be adapted for use in hematology. We evaluated a LB-based ctDNA approach in patients with HNs. Methods: Retrospective study of LB samples from patients reported to have HNs tested using hybrid-capture NGS using the FoundationOne Liquid CDx (targeting 324 genes), FoundationOne Liquid (70 genes), or FoundationACT (62 genes) assays between 7/2016 and 3/2022. Paired buffy coat, bone marrow aspirate, or tissue samples undergoing conventional NGS with the FoundationOne Heme (406 genes), FoundationOne CDx (324 genes), or FoundationOne (322 genes) assays were sought where available, and genomic alterations baited across both the LB- and tissue-based assays were assessed for concordance. Results: Among 67,500 unique patient samples submitted for LB-based NGS, 271 were from HNs, including 89 non-Hodgkin lymphoma (NHL), 43 plasma-cell neoplasm (PCN), 41 histiocytosis, 27 myelodysplastic syndrome (MDS), 25 diffuse large B-cell lymphoma (DLBCL), 22 myeloproliferative neoplasm (MPN), 14 Hodgkin lymphoma (HL), and 10 acute myeloid leukemia (AML) cases. The median (interquartile range [IQR]) patient age was 68.0 (55.5-78.0) years, and 121 (44.6%) patients were female. Samples were sequenced to a median exon coverage of 8,564× and pathogenic alterations were detected in 73.4% (199/271) of cases. The median maximum somatic allele frequency (MSAF) among all cases was 7.3% (IQR, 1.1-42.7%), with higher median MSAFs in MPN (45.8%), AML (30.9%), and MDS (19.7%) than in NHL (8.4%), DLBCL (7.1%), histiocytosis (3.1%), HL (2.1%), and PCN (2.0%) cases (P = 0.02, Kruskal-Wallis test), not unexpected given that myeloid neoplasms naturally circulate (Figure 1). LB detected characteristic genomic alterations across HNs, including in TP53, KRAS, MYD88, and BTK in NHLs; TP53, KRAS, NRAS, and BRAF in PCNs; IGH in DLBCL; TP53, ATM, and PDCD1LG2 in HL; BRAF and MAP2K1 in histiocytoses; TP53, SF3B1, DNMT3A, TET2, and ASXL1 in MDS; JAK2 in MPNs; and FLT3, IDH2, and NPM1 in AML, among others (Figure 2). Paired buffy coat, bone marrow aspirate, or tissue specimens collected a median of 118 (IQR 36-346) days apart from the LB specimens sequenced to a median exon coverage of 810× were available for 42 patients. Of 95 variants in 20 HN-associated genes equally baited across the pairs, 31 (32.6%) were detected in both specimens. Of 42 variants detected on buffy coat, bone marrow aspirate, or tissue sequencing, 31 were also detected by LB (positive percent agreement = 73.8%). Eight pairs harbored variants detected in tissue only, all of which were explainable by either low ctDNA shed (e.g., a BRAF fusion was not detected in a LB sample with MSAF = 0.1%) or heterogeneity related to the disease course (e.g., a FLT3 tyrosine kinase domain variant identified by conventional tissue NGS was not detected on follow-up LB two years later, post-treatment). Conversely, 22 samples had ≥1 variant detected in the LB sample only, including in NF1 (n=4), KRAS (n=3), and BRAF (n=2), likely reflecting the enhanced sensitivity of LB for detecting low-level disease clones. Conclusions: LB detected relevant genomic alterations in the majority of patients with a variety of HNs. Given its analytical sensitivity, LB may also detect low-level residual or emerging therapy-resistant clones unable to be detected in a single tissue specimen and may play a role in the evaluation of the patient's disease course and in associated treatment decisions. This pilot study suggests the potential value of LB in the clinical management of patients; however, further prospective evidence would be required to quantify the utility of LB for patients with HNs. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Abstract 2139: Evaluation of tissue- and plasma-derived tumor mutational burden and genomic alterations of interest from the CheckMate 848 clinical trial

Abstract Tumor mutational burden (TMB) derived from tissue biopsies (tTMB) has been associated with clinical efficacy in patients treated with immune checkpoint inhibitors; the clinical utility of TMB derived from blood samples (bTMB) has also been demonstrated but is less widely studied. Little is known about the concordance between tissue- and blood-derived genomic assessments and the factors that contribute to their discordance, underlying the need for further investigation of sequence alteration profiles for successful adoption of noninvasive tumor profiling. We explored the genomic landscape, including concordance between tTMB and bTMB, in samples from patients who were screened for enrollment into CheckMate 848, a prospective, phase 2 study of nivolumab plus ipilimumab and nivolumab monotherapy in patients with advanced or metastatic solid tumors with high TMB (NCT03668119). Of 1954 screened patients, 212 were randomized, with a cap of 15% per tumor type. Tissue- (FoundationOne® CDx—based Clinical Trial Assay) and blood-based (Foundation Medicine bTMB Clinical Trial Assay) genomic data were utilized for analysis of genomic variants, tTMB, and bTMB. In total, 1438 unique tissue and 1720 unique plasma samples were analyzed during trial screening (June 2021 database lock). Of over 100 screened disease ontologies (taken from the tissue diagnosis), pancreatic (9.7%), breast (8.8%), and ovarian (6.1%) cancers, as well as cholangiocarcinoma (5.2%), were the most common. A total of 1141 tissue and 1573 plasma samples passed established quality control criteria, resulting in ascertainment levels of 79.3% for tTMB and 91.5% for bTMB. A correlation between tTMB and bTMB scores was identified across 1017 tissue and plasma sample pairs (Spearman’s r, 0.48; P &amp;lt; 0.0001). Median (range) tTMB and bTMB were 3.8 (0—452.6) and 3.5 (0—1027.5) mutations per megabase (mut/Mb), respectively. High microsatellite instability (MSI) was detected in 25 (2.5%) MSI-evaluable tissue samples; in these patients, median tTMB was 25.2 mut/Mb. At the prespecified cutoff of 10 mut/Mb, 15.8% and 20.7% of samples had high tTMB and bTMB, respectively; the positive (PPA), negative, and overall percentage agreements between assays were 60%, 88%, and 84%, respectively. TMB correlation (Spearman’s r, 0.54; P &amp;lt; 0.0001) and PPA (66%) were improved among 806 (79.3%) sample pairs with plasma maximum somatic allele frequency ≥ 1%. In CheckMate 848, data from paired biopsies revealed the complementary nature of TMB assessments from tissue and blood, suggesting that both approaches may have the potential to identify high mutational burden in samples obtained from patients with advanced solid tumors. Further interrogation of the biological and analytical factors affecting tumor- and blood-derived genomic profiling is warranted to support their implementation in clinical settings. Citation Format: Jie He, Natallia Kalinava, Parul Doshi, Jie Ma, Dean C. Pavlick, Lee A. Albacker, Hanna Tukachinsky, Gina Fusaro, Geoffrey R. Oxnard, George Green, David Fabrizio, Jonathan Baden. Evaluation of tissue- and plasma-derived tumor mutational burden and genomic alterations of interest from the CheckMate 848 clinical trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2139.

Maximum somatic allele frequency-adjusted blood-based tumor mutational burden balances the effect of intratumor heterogeneity on response to immune checkpoint Inhibitors in non-small cell lung cancer patients.

e21137 Background: ctDNA abundance can influence the accuracy of blood-based tumor mutational burden (bTMB), driving a paradox of bTMB in predicting response and survival benefit of patients with non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitors (ICIs) therapy. However, the optimal algorithm of ctDNA adjusted bTMB remains largely unestablished. We aimed to develop a novel approach to optimize the calculation of bTMB by integrating maximum somatic allele frequency (MSAF) to better differentiate the ICI-beneficial NSCLC patients, as well as explore the correlated mechanism. Methods: A 1021-gene panel-based targeted capture sequencing was utilized to evaluate the correlation between MSAF and bTMB based on blood samples in 1679 Chinese NSCLC patients (GCGD database, N = 1679). The establishment of MSAF-adjusted bTMB (Ma-bTMB) was derived from three independent NSCLC cohorts treated with programmed death ligand 1 (PD-L1) or the programmed death 1 (PD-1) inhibitors, including POPLAR cohort (N = 231) as training set, and OAK (N = 642) and Wang (N = 81) cohorts as validation sets separately. PyClone was employed to estimate clonal and subclonal populations. Results: MSAF demonstrated a modest positive correlation between bTMB and MSAF (Spearman’s R = 0.41, P &lt; 0.001, GCGD cohort) and was negatively correlated with survival benefit (Spearman’s rank sum test, overall survival (OS): R = −0.39, P &lt; 0.001; progression-free survival (PFS): R = −0.41, P &lt; 0.001, Wang cohort). Patients with high Ma-bTMB (Ma-bTMB-H) demonstrated improved survival outcomes of anti-PD(L)-1 therapy compared to chemotherapy in POPLAR (PFS, hazard ratio (HR) = 0.63, interaction P = 0.030; OS, HR = 0.44, interaction P = 0.020), which was validated in OAK cohorts (PFS, HR = 0.72, interaction P = 0.040; OS, HR = 0.50, interaction P = 0.010). In addition, Ma-bTMB-H was associated with a better clinical benefit compared to low Ma-bTMB (Ma-bTMB-L) in Wang cohort (PFS, HR = 0.55, P = 0.012; OS, HR = 0.46, P = 0.036). Furthermore, there was a positive correlation between intratumor heterogeneity (ITH) and MSAF (R = 0.37, P &lt; 0.001) in GCGD database, and the effect of ITH on Ma-bTMB (subclones, P = 0.57; subclonal mutations, P = 0.8) was substantially reduced compared to traditional bTMB (subclones, P &lt; 0.001; subclonal mutations, P &lt; 0.001) in Wang cohort. Conclusions: We developed and validated Ma-bTMB, a convenient, readily available, non-invasive predictive biomarker, which reduced the confounding effect of ITH and could effectively differentiate beneficiaries of anti-PD(L)1 therapy, warranting investigation in future clinical trials. Clinical trial information: NCC2018-092.

Genomic landscape and peripheral blood biomarkers of advanced triple-negative breast cancer treated with immune checkpoint blockade: An exploratory analysis of the TQB2450-Ib-07 trial.

1080 Background: Immune checkpoint inhibitor (ICI) has emerged as a novel therapeutic option for advanced triple-negative breast cancer (aTNBC). However, no robust biomarker indicative of clinical outcomes has been identified. Herein, we portraited the genomic landscape and explored the biomarkers for patients with aTNBC receiving ICI-based therapy. Methods: This is a prospective, multicenter, phase 1b clinical trial (NCT03855358) to assess the efficacy and safety profiles of TQB2450, a humanized monoclonal PD-L1 antibody, plus anlotinib in pretreated TNBC. Eligible patients undergo liquid biopsy at baseline and the timepoint of disease progression. NGS-based assay was performed based on circulating tumor DNA (ctDNA) in the bloodstream. Meanwhile, results of laboratory blood tests were dynamically collected and blood markers, including neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), and platelet to lymphocyte ratio (PLR), were successively evaluated. The primary endpoints were progression-free survival (PFS) and clinical efficacy assigned via guidelines for response criteria for use in trials testing immunotherapies (iRECIST). Results: Between May 29, 2019, and December 31, 2020, 34 patients with aTNBC were enrolled. Gene alternations primarily comprised mutation, amplification, or deletion of TP53, MLL3, DNMT3A, PI3KCA, EP300, PTEN, LRP1B, MDM2, and NCOR1. The median maximum somatic allele frequency (MSAF) was 9.97% significantly indicative of PFS, which was 3.58 months for the MSAF-high group and 13.34 months for the MSAF-low group (P = 3e-04), respectively. Else, a strong association was also signified between MSAF and tumor shrinkage (CR/PR vs. SD/PD, P = 0.012). For blood tumor mutation burden (bTMB), the median was 6.72 muts/Mb, which the bTMB-low group was suggestive of a better PFS (11.09 months vs. 5.52 months, P = 0.007), yet no obvious association existing in terms of clinical response. Dynamic analysis revealed that a decline in MSAF was significantly associated with a better PFS (7.10 months vs. 2.74 months, P = 0.018), while no correlations were detected between bTMB and PFS. Based on NLR week 2/0 of 0.95, PFS was significantly worse in the NLR-low group (11.0 months vs. 3.5 months, P = 0.006) and likely distinguished the clinical response (CR/PR vs. SD vs. PD, P = 0.049; non-PD vs. PD, P = 0.022). Moreover, NLR week 2/0 could notably foretell the clinical response for patients with aTNBC with the AUC of 0.82 (0.61-1.00). No comparable utilities were identified regarding LMR and PLR. Conclusions: For aTNBC treated with ICI, MSAF tended to be a robust indicator for both PFS and clinical response. NLR week 2/0 presented a favorable profile indicative of PFS as well as a strong predictor for clinical responsiveness of patients with aTNBC receiving immune checkpoint blockade. Clinical trial information: NCT03855358.

Liquid biopsy (LB)-based comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) for the evaluation of patients with myeloid neoplasms.

e19064 Background: LB-based CGP of ctDNA can facilitate the diagnosis, molecular profiling, and monitoring of patients with myeloid neoplasia, particularly when standard CGP is not feasible due to a lack of circulating disease or insufficient tumor in the marrow or tissue. Methods: Retrospective study of LB samples from patients reported to have histiocytic neoplasms (HNs), myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), or acute myeloid leukemia (AML) tested using hybrid-capture next-generation sequencing using the FoundationOne Liquid CDx (targeting 324 genes), FoundationOne Liquid (70 genes), or FoundationACT (62 genes) assays during routine clinical care between 5/2016 and 9/2021. Results: Among 48,459 unique patient samples submitted for CGP, 83 were from myeloid neoplasia: 34 HN, 23 MDS, 15 MPN, and 11 AML. The median cell-free DNA yield was 74.9 ng (interquartile range [IQR]: 52.0-167.4), well above the minimum needed for analysis. Reportable pathogenic alterations were detected in 62.7% (52/83) of cases. The median maximum somatic allele frequency (MSAF) was 17.0% (IQR: 1.7-49.0%), with AML (45.7%), MDS (25.9%), and MPN (43.8%) having higher median MSAFs than HNs (3.2%), not unexpected given that the former naturally circulate. In all, 147 pathogenic short variants and 6 pathogenic rearrangements were detected (median variant allele frequency [VAF]: 2.1%, IQR: 0.3-20.5%, range: 0.11-99.8%). Sixty-one had VAFs &lt; 1.0%, indicating excellent sensitivity. HNs exhibited activating RAS-RAF-MEK pathway alterations in BRAF (31.3% of cases in which pathogenic alterations were identified), NF1 (12.5%), MAP2K1 (6.3%), and NRAS (6.3%), detected at VAFs as low as 0.21%, 0.13%, 0.11%, and 4.0%, respectively. AML cases exhibited pathogenic alterations in TP53 (57.1%), FLT3 (28.6%), IDH2 (28.6%), NPM1 (28.6%), KRAS (14.3%), and NRAS (14.3%), among others. Subclonal heterogeneity was identified, including an AML case with KRAS G12A and G13R and NRAS G12A mutations detected at VAFs of 0.24%, 0.19%, and 0.2%, respectively. Altered genes in patients undergoing workup for MDS or MPN included TP53 (41.4%), JAK2 (37.9%), DNMT3A (13.8%), CHEK2 (10.3%), PTPN11 (10.3%), SF3B1 (10.3%), TET2 (10.3%), ASXL1 (6.9%), MPL (3.5%), and U2AF1 (3.5%), among others. Last, among 48,243 patients with a LB for a solid tumor diagnosis, 3,487 JAK2 V617F, 366 CALR C-terminal truncation, and 343 MPL W515X mutations were detected, potentially indicating a concurrent or occult MPN. Conclusions: LB identified clinically relevant genomic alterations in myeloid neoplasia, offering a powerful tool that may be used pre- or post-treatment when CGP of the buffy coat, marrow, or tissue is infeasible. Given its low limit of detection, LB can also identify low-level emerging or persistent subclones, which may facilitate monitoring and minimal residual disease testing.

Utility of liquid biopsy (LB)-based comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) in lymphomas and plasma cell neoplasms.

e19543 Background: LB-based CGP of ctDNA can facilitate the molecular evaluation of lymphoid and plasma cell neoplasms (PCNs), especially when traditional CGP is infeasible due to insufficient tumor in the blood or tissue or when tissue biopsy itself cannot be performed. Methods: Retrospective study of LB samples from patients reported to have lymphomas or PCNs tested using hybrid-capture next-generation sequencing using the FoundationOne Liquid CDx (targeting 324 genes), FoundationOne Liquid (70 genes), or FoundationACT (62 genes) assays during routine clinical care between 5/2016 and 9/2021. Results: Among 48,459 unique patient samples submitted for CGP, 133 were from lymphomas or PCNs: 69 non-Hodgkin lymphoma (NHL), 32 PCN, 16 diffuse large B-cell lymphoma (DLBCL), and 16 classic Hodgkin lymphoma (cHL) cases. The median cell-free DNA yield was 72.7 ng (interquartile range [IQR]: 46.0-157.0), well above the minimum quantity needed for analysis. Reportable pathogenic genomic alterations were detected in 67.7% (90/133) of cases. The median maximum somatic allele frequency (MSAF) was 3.8% (IQR: 1.1-19.6%), with no statistically significant differences noted between DLBCL (8.2%), NHL (5.6%), cHL (1.7%), and PCNs (1.4%) ( P= 0.13, Kruskal-Wallis test). In all, 322 pathogenic short variants and 3 pathogenic rearrangements were detected (median variant allele frequency [VAF]: 0.6%, IQR: 0.3-2.6%, range: 0.09-81.8%). One hundred ninety-seven had VAFs &lt; 1.0%, indicating excellent sensitivity. NHLs exhibited pathogenic alterations in TP53 (53.2% of cases in which pathogenic alterations were identified), KMT2D (14.9%), NF1 (10.6%), MYD88 (8.5%), BCL2 (6.4%), BRAF (6.4%), EZH2 (6.4%), NRAS (6.4%), BTK (4.3%, all of which were C481X ibrutinib resistance mutations in cases of chronic lymphocytic leukemia detected at VAFs ranging from 0.18-5.5%), KRAS (4.3%), RB1 (4.3%), and TNFAIP3 (4.3%), among others. PCNs exhibited pathogenic alterations in TP53 (54.6%), KRAS (18.2%), NF1 (13.6%), PTPN11 (13.6%), BRAF (9.1%), NRAS (9.1%), MAP2K1 (4.6%), and RB1 (4.6%), among others. DLBCLs exhibited pathogenic alterations in TP53 (63.6%), MYD88 (27.3%), CCND2/3 (9.1%), EZH2 (9.1%), and KMT2D (9.1%), among others. CD274 (PD-L1) and PDCD1LG2 (PD-L2) amplification and IGH- PAX5 and IGH- MYC fusions were also detected in individual cases of DLBCL. cHLs exhibited pathogenic alterations in TP53 (40.0%), ATM (20.0%), BCOR (10.0%), KRAS (10.0%), MYD88 (10.0%), and PDCD1LG2 (PD-L2) (10.0%), among others. Conclusions: LB identified clinically actionable genomic alterations in lymphomas and PCNs and may be used when traditional CGP of tumor biopsy specimens cannot be performed. Given its low limit of detection, LB may also allow for minimally invasive dynamic monitoring of response to therapy.

Blood-based tumor mutational burden as a biomarker for atezolizumab in non-small cell lung cancer: the phase 2 B-F1RST trial

Tumor mutational burden (TMB) in circulating tumor DNA (ctDNA) has shown promise in predicting benefit from PD-L1/PD-1 inhibitors in retrospective studies. Aiming to assess blood TMB (bTMB) prospectively, we conducted B-F1RST (NCT02848651), an open-label, phase 2 trial that evaluated bTMB as a predictive biomarker for first-line atezolizumab monotherapy in locally advanced or metastatic stage IIIB–IVB non-small cell lung cancer (n = 152). The co-primary endpoints were investigator-assessed objective response rate (ORR) per RECIST version 1.1 and investigator-assessed progression-free survival (PFS) between high and low bTMB subgroups at the pre-defined bTMB ≥ 16 (14.5 mutations per megabase) cutoff. Secondary endpoints included investigator-assessed PFS, overall survival (OS) and duration of response at various bTMB cutoffs, as well as safety. Investigator-assessed PFS in the bTMB ≥ 16 versus bTMB < 16 groups was not statistically significant. However, bTMB ≥ 16 was associated with higher ORR, and ORR improved as bTMB cutoffs increased. No new safety signals were seen. In exploratory analyses, patients with maximum somatic allele frequency (MSAF) < 1% had higher ORR than patients with MSAF ≥ 1%. However, further analysis showed that this effect was driven by better baseline prognostics rather than by MSAF itself. At 36.5-month follow-up, an exploratory analysis of OS found that bTMB ≥ 16 was associated with longer OS than bTMB < 16. Further study and assay optimization will be required to develop bTMB as a predictive, standalone biomarker of immunotherapy or for use in conjunction with other biomarkers.

Genomic Profiling of Blood-Derived Circulating Tumor DNA from Patients with Advanced Biliary Tract Cancer.

Background: Biliary tract cancer is a highly lethal malignancy with poor clinical outcome. Accumulating evidence indicates targeted therapeutics may provide new hope for improving treatment response in BTC, hence better understanding the genomic profile is particularly important. Since tumor tissue may not be available for some patients, a complementary method is urgently needed. Circulating tumor DNA (ctDNA) provides a noninvasive means for detecting genomic alterations, and has been regarded as a promising tool to guide clinical therapies. Methods: Next-generation sequencing of 150 cancer-related genes was used to detect gene alterations in blood-derived ctDNA from 154 Chinese patients with BTC. Genomic alterations were analyzed and compared with an internal tissue genomic database and TCGA database. Results: 94.8% patients had at least one change detected in their ctDNA. The median maximum somatic allele frequency was 6.47% (ranging 0.1–34.8%). TP53 and KRAS were the most often mutated genes. The frequencies of single nucleotide variation in commonly mutated genes in ctDNA were similar to those detected in tissue samples, TP53 (35.1 vs. 40.4%) and KRAS (20.1 vs. 22.6%). Pathway analysis revealed that mutated genes were mapped to several key pathways including PI3K-Akt, p53, ErbB and Ras signaling pathway. In addition, patients harboring LRP1B, TP53, and ErbB family mutations presented significantly higher tumor mutation burden. Conclusions: These findings demonstrated that ctDNA testing by NGS was feasible in revealing genomic changes and could be a viable alternative to tissue biopsy in patients with metastatic BTC.

Characteristics of T-Cell Receptor Repertoire and Correlation With EGFR Mutations in All Stages of Lung Cancer.

Lung cancer is the leading cause of cancer-related deaths worldwide, and its occurrence is related to the accumulation of gene mutations and immune escape of the tumor. Sequencing of the T-cell receptor (TCR) repertoire can reveal the immunosurveillance status of the tumor microenvironment, which is related to tumor escape and immunotherapy. This study aimed to determine the characteristics and clinical significance of the TCR repertoire in lung cancer. To comprehensively profile the TCR repertoire, results from high-throughput sequencing of samples from 93 Chinese patients with lung cancer were analyzed. We found that the TCR clonality of tissues was related to smoking, with higher clonality in patients who had quit smoking for less than 1 year. As expected, TCR clonality was correlated with stages: patients with stage IV disease showed higher clonality than others. The correlation between TCR repertoire and epidermal growth factor receptor (EGFR) status was also investigated. Patients with EGFR non-L858R mutations showed higher clonality and a lower Shannon index than other groups, including patients with EGFR L858R mutation and wild-type EGFR. Furthermore, we analyzed the TCR similarity metrics—that is, the TCR shared between postoperative peripheral blood and tissue of patients with non-distant metastasis of lung cancer. A similar trend was found, in which patients with EGFR L858R mutations had lower overlap index (OLI) and Morisita index (MOI) scores. Moreover, the OLI showed a positive correlation with several clinical characteristics, including the tumor mutational burden of tissues and the maximum somatic allele frequency of blood; OLI showed a negative correlation with the ratio of CD4+CD28+ in CD4+ cells and the ratio of CD8+CD28+ in CD8+ cells. In conclusion, TCR clonality and TCR similarity metrics correlated with clinical characteristics of patients with lung cancer. Differences in TCR clonality, Shannon index, and OLI across EGFR subtypes provide information to improve understanding about varied responses to immunotherapy in patients with different EGFR mutations.

Abstract 707: Combinatorial assessment of ctDNA release and mutational burden predicts clinical outcome from anti-PD-(L)1 therapies in non-small-cell lung cancer

Abstract Background: Blood-based detection of circulating tumor DNA (ctDNA) is a non-invasive and clinical accessible source of biomarkers that enables selection of non-small-cell lung cancer (NSCLC) patients for treatment with anti-PD-(L)1 therapies. However, new approaches are necessary to improve enrichment of responders. Patients and Methods: Pretreatment plasma ctDNA from 97 advanced-stage NSCLC patients who underwent anti-PD-(L)1 therapy from December 2015 to August 2017, with matched tissue samples from 66 patients, were profiled using a targeted next-generation sequencing (NGS) panel (Geneseeq) encompassing 422 cancer-relevant genes. External validation was performed using two large randomized trials, POPLAR and OAK. Results: In the 72 patients with adequate ctDNA release (maximum somatic allele frequency, MSAF ≥2%), high blood tumor mutational burden (bTMB) was associated with significantly prolonged median PFS (110 vs 60 days, HR=0.54 [95%CI, 0.31-0.92]; log-rank p = 0.02) and a trend towards improved DCB (34.8% vs 22.5%, p=0.39). While a high concordance was observed between bTMB and tTMB (Spearman's ρ= 0.71), the greatest progression-free survival (PFS) improvement was achieved with concomitantly high bTMB and tTMB (mPFS, 156 vs 59 days, HR=0.47 [95%CI, 0.24-0.91], log-rank p=0.02). Remarkably, the subset of patients with low ctDNA release (MSAF&amp;lt;2%), and consequently non-evaluable bTMB, derived similar PFS benefit as those with high bTMB. The additive predictive value of MSAF and bTMB was externally validated by results from the two large randomized trials. Conclusions: Our findings validated panel-assessed bTMB as a promising biomarker that demonstrated added value over tissue testing alone for benefit with anti-PD-(L)-1 therapies. Our findings also provided the first clinical evidence suggesting that matched tissue and blood testing might be necessary to refine the predictive value of TMB. Moreover, we identified low ctDNA MSAF as an important and robust predictor of improved immunotherapy outcome. Citation Format: Wenfeng Fang, Yuxiang Ma, Jiani C. Yin, Huaqiang Zhou, Fufeng Wang, Hua Bao, Ao Wang, Xue Wu, Shaodong Hong, Yunpeng Yang, Yan Huang, Hongyun Zhao, Yang W. Shao, Li Zhang. Combinatorial assessment of ctDNA release and mutational burden predicts clinical outcome from anti-PD-(L)1 therapies in non-small-cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 707.

Abstract 3632: Genomic profiling in circulating tumor DNA from Chinese advanced gastric adenocarcinomas patients

Abstract Background and Objective: Circulating tumor DNA (ctDNA) is considered to be an ideal sample for advanced unresectable cancer patients to perform gene sequencing to guide clinical therapy, which might help to avoid tumor heterogeneous, especially in gastric adenocarcinomas (GACs). However, the ctDNA genomic profiling of Chinese advanced GACs is still missing. Methods: Blood samples were obtained from 122 advanced GACs patients. Target sequencing were performed on ctDNA using a validated commercial 150-gene-panel NCC-GP150, which includes 100 microsatellite loci. Blood tumor mutation burden (bTMB) and blood microsatellite instability (bMSI) were calculated according to the NGS results. Statistical analysis was performed by the Mann-Whitney U test and Fisher exact test using GraphPad Prism. Results: In 122 patients, 47 (38.5%) were female and 75 (61.5%) were male, with the median age of 61 (range 24 to 84). A total of 660 somatic variations were identified in 118 genes as indicated by a maximum somatic allele frequency (MSAF) of &amp;gt;0.3%. One hundred and two (83.6%) patients carried at least one somatic variation and 84 (68.9%) patients had at least on pathogenic or likely pathogenic variations. The median pathogenic or likely pathogenic variations was 2.5 per patient in our cohort. The most frequent altered genes were TP53 (36.9%), LRP1B (18%), MYC (14.8%), RBM10 (13.9%), ERBB2 (13.9%), KRAS (12.3%), AR (11.5%) and FAT1 (10.7%). From the perspective of signaling pathway, the variations occurred frequently in RTK-Ras-MAPK pathway (53.3%), cell cycle pathway (52.5%), DNA damage repair (DDR) pathway (22.1%), Wnt pathway (18.9%), PI3K/AKT pathway (16.4%), and TGF-β pathway (2.5%). The median bTMB was 3 (mean 5.27, range 0 to 52); and 8 (7.8%) patients had high bMSI. The bMSI-H patients had significantly higher bTMB than bMSS patients (22 vs 3, p&amp;lt;0.0001) and patients harboring DDR pathway gene variations had significantly higher bTMB than wildtype subgroups (6 vs 3, p=0.0004). Conclusions: Our study revealed a comprehensive genomic profiling of advanced Chinese GACs patients. And the relationship between the genomic profiling and target-therapy as well as immunotherapy will be studied in an enlarged group of GACs patients. Citation Format: ZHE ZHANG, Hui Chen, Yifan Zhou, Bei Zhang, Yuezong Bai, Lieping Guo. Genomic profiling in circulating tumor DNA from Chinese advanced gastric adenocarcinomas patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3632.

Abstract 181: Pan-cancer clinical genomic profiling in circulating tumor DNA from 7345 Chinese advanced cancer patients

Abstract Purpose: Circulating tumor DNA (ctDNA) sequencing was implemented widely in advanced cancer patients for guiding matched therapy, which could avoid invasive specimen collection and tumor heterogeneous. However, clinical ctDNA genomic profiling of Chinese advanced pan-cancer patients is still unknown. Methods: 7624 blood samples were obtained from 7345 Chinese patients with advanced solid tumor, including 3506 lung cancer, 860 liver cancer, 674 colorectum cancer, 343 stomach cancer, 329 biliary tract cancer, 324 breast cancer, and 1588 other 17 tumor types. Genomic alterations (GAs), including SNV/Indels, CNVs, and rearrangements were identified via ctDNA sequencing with a 150 cancer-related gene panel. Potentially actionable GAs was annotated according to OncoKB database. Results: There are 85.2% (6497/7624) samples harbors maximum somatic allele frequency (MSAF) &amp;gt;0.3% and average 5.5 GAs per samples. 21253 known or likely deleterious alterations were identified in 137 genes, and average 3.3 known or likely deleterious GAs per samples. Additionally, 38.4% (2930/7624) samples had at least one potentially actionable GA (PAGA). The most frequently and potentially actionable altered genes were EGFR (13.2%), KRAS (8.6%), PIK3CA (5.1%), ERBB2 (4.0%), FGFR1 (3.6%) and BRAF (3.3%). Importantly, PAGAs in RTK-RAS-MAPK pathway was the most common with 33.7% samples (19.2% SNV/Indels only, 9.8% CNVs only, 1.4% rearrangements only, 3.4% either two or more types of alterations), followed by 5.9% PI3K/AKT/mTOR pathway, 2.1% TP53/cell cycle pathway, 0.8% Epigenetic pathway, 0.1% Hedgehog pathway, and 0.1% DDR pathway. The samples of at least one PAGA in aforementioned pathways were 53.1% in breast cancer, 49.6% in colorectum cancer, 44.0% in bladder/urinary tract cancer, 43.5% in lung cancer, 39.4% in stomach cancer, respectively. In all, 287 cases with PAGAs in RTK-RAS-MAPK pathway (ROS1, ALK, MET) could benefit from crizotinib; 49 cases with PAGAs in RTK-RAS-MAPK pathway (BRAF) could benefit from vemurafenib; 447 cases with PAGAs in PI3K/AKT/mTOR pathway (PIK3CA, PTEN, AKT1, mTOR) could benefit from everolimus; and 6 cases with PAGAs in DDR pathway (ATM) could benefit from olaparib. Conclusions: The study revealed a comprehensive ctDNA genomic profiling of Chinese patients with advanced solid tumors. And further larger cohorts validation for ctDNA sequencing as a diagnostic tool in target-therapy is needed. Citation Format: Wenhua Li, Hui Chen, Yifan Zhou, Danpeng Sun, Bei Zhang, Yuezong Bai, Qingqing Ding. Pan-cancer clinical genomic profiling in circulating tumor DNA from 7345 Chinese advanced cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 181.