bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cell-free RNA-based next-generation sequencing (NGS) assay for the detection of actionable gene fusions in patients with non–small cell lung cancer (NSCLC).
Authors: Choudhury Yukti , Cher Chae Yin , Ho Jia Min , Chan Claire , Teh Mun Wei , Ngeow Kao Chin , Pek Michelle 
Published: June 2022

3040 Background: Gene fusions and alternate RNA splice forms represent clinically actionable driver and resistance-conferring alterations in NSCLC and other cancers. Where tissue samples are inadequate for molecular testing, liquid biopsies could address the gap in detection of clinically relevant gene fusions. Targeted cell-free (cf) DNA-based NGS methods are typically used for non-invasive blood-based testing of gene fusions, but have limited sensitivity if fusion breakpoints involve long intronic regions or repetitive sequences (e.g. NTRKs and NRG1). RNA-based approaches are not affected by introns, can identify expressed fusion genes and can discriminate splicing. We developed an NGS assay optimized for cfRNA analyte for the detection of actionable gene fusions and exon deletion/skipping events in liquid biopsies. Methods: A highly multiplexed molecular-barcoded primer panel was designed for cfRNA-based detection of actionable fusion genes in NSCLC ( ALK, BRAF, FGFR2, FGFR3, MET (including exon 14 skipping), NRG1, NTRK1/2/3, RET and ROS1) covering > 90% of reported driver and partner gene exons in COSMIC database. The panel also targets housekeeping genes as endogenous sample controls. We developed a custom bioinformatics pipeline to call fusions and exon skipping based on split and spanning reads. Results: In initial analytical validation using fragmented RNA from pre-characterized reference material (representing 32 unique fusions at known copy numbers), the assay could detect as low as 10 fusion copies with a sensitivity of 97.6% and a specificity of 100%. For clinical testing, cfRNA co-eluted with cfDNA in nucleic acid extracts from plasma was used. In plasma samples (n = 103) from advanced NSCLC, 76% (15/21) of fusions (5 ALK, 3 RET, 2 ROS1, 5 MET ex14 skipping, 1 FGFR3-TACC3) detected in a clinically validated cfDNA assay (LiquidHALLMARK) were also detected in corresponding cfRNA. In a subset of samples that were driver-negative untreated or tyrosine kinase-inhibitor treated, the cfRNA assay yielded 9 gene fusions or breakpoints (1 CD74-NRG1, 4 BRAF, 2 MET, 2 FGFR3-TACC3 fusions) that could not be detected by the cfDNA assay. This represents an increase of 8.7% (9/103) of actionable alterations (driver or resistance) identified using cfRNA. Together cfRNA and cfDNA resulted in 30 fusion events to be detected compared to 21 by the cfDNA assay alone, representing a 42.8% (9/21) increase in fusion-specific detection of the combined assay. Conclusions: This novel cfRNA assay can detect actionable gene fusions and exon skipping events in liquid biopsies with high sensitivity. Combining cfRNA with more routine cfDNA testing can increase the total actionable diagnostic information from non-invasive testing in NSCLC patients where tissue samples are lacking, especially for gene fusions not amenable to detection in cfDNA.
Cell-free RNA in liquid biopsy and biomarkers profiling of hematologic and solid tumors.
Authors: Albitar Maher , Zhang Hong , Charifa Ahmad , Ip Andrew , De Dios Ivan , Ma Wanlong , McCloskey James , Donato Michele , Siegel David Samuel DiCapua , Waintraub Stanley E. , Gutierrez Martin , Pecora Andrew L , Goy Andre 
Published: June 2022

3047 Background: Expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate fragmented RNA from peripheral blood plasma and explored its potential to be used in liquid biopsy. Methods: Peripheral blood cfRNA was extracted from patients with neoplasms in B-cell (#105), T-cell (#16), Myeloid (#73), and from solid tumors (#44), Normal individuals (#51), and reactive post-transplant (#137). RNA was sequenced using a 1459-gene panel. Expression profile was generated using Cufflinks. Results: cfRNA levels of various solid tumor biomarkers (CA-125, CA-15-3, CEA 8, Keratin19, Keratin6A...) were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers (CD19, CD22, CD79A, and CD79B...) and cfRNA myeloid markers (CD33, CD14, CD117, CD56...) were all higher in B-cell lymphoid neoplasms and myeloid neoplasms, respectively (P < 0.0001), as compared with control. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (median 3.40 and 2.23, respectively, P < 0.0002). Solid tumor cfRNA showed CTLA4:CD8B ratio significantly higher in tumors than in normal (median 0.74 vs 0.19, P = 0.0001), while there was no difference in cfRNA PD-L1:CD8B ratio (median 1.45 vs 1.77, P = 0.96). Similar distinct patterns are noted for various cytokine and chemokines. cfRNA was highly predictive of diagnosis (AUC > 0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms as compared with normal control. When a specific neoplastic disease was considered against all cases including control and other neoplasms, the AUC varied between 0.77 and 0.949. Conclusions: This data shows that liquid biopsy using targeted sequencing of cfRNA in patients with various types of cancer provides comprehensive and reliable information on the neoplastic disease as well as the host. [Table: see text]
Serum concentrations of oncometabolite, 2-hydroxyglutarate (2HG), as biomarkers for isocitrate dehydrogenase (IDH1/2) mutations in cholangiocarcinoma (ICCA).
Authors: Lee Cha Len , Mason Warren P. , O'Kane Grainne M. , Grant Robert C. , Knox Jennifer J. , Cruz Candice , Zhang Wenjiang , Zadeh Gelareh , Chen Eric Xueyu 
Published: June 2022

3049 Background: Mutations in IDH1/2 genes are common in low-grade glioma (GM) and occur in approximately 20% of intrahepatic cholangiocarcinoma (ICCA). Mutant IDHs leads to preferential accumulation of the R-relative (R2HG) to the S-enantiomer (S2HG) of 2HG. We investigated the utility of circulating R2HG, total R2HG+S2HG (tRS) and ratio of R2HG/S2HG (rRS) as biomarkers in GM and ICCA patients (pts). Methods: Blood and tumor tissues samples were obtained from pts with IDH1/2-mutant GM and ICCA. IDH mutation was confirmed by either immunohistochemistry (GM pts) or next generation sequencing (ICCA pts). Samples were analyzed for S2HG and R2HG using a validated HPLC tandem mass spectrometry method. Tissue and serum R2HG, tRS and rRS were compared with paired t-tests for GM pts. Serum S2HG, R2HG, tRS and rRS were compared with unpaired t-tests between GM and ICCA pts. A p<0.05 was considered statistically significant. Results: Blood and tumor samples were collected from 21 pts (GM = 11, ICCA=10). Tumor tissues were insufficient for analysis in 1 GM and 8 ICCA pts. Tissue S2HG, R2HG, tRS, and rRS were 0.72±0.68 ng/g, 48.92±58.92 ng/g, 66.87±80.35 ng/g and 55.77±36.23 for GM pts. There were no differences in R2HG and tRS between tissue and serum samples, while S2HG was significantly higher in serum samples ( p = 0.001) and rRS was significantly higher in tissue samples for GM pts ( p = 0.001). rRS were 144.8 and 244.9 respectively in 2 ICCA pts with sufficient tissues. There was no difference in serum S2HG between GM and ICCA pts. However, serum R2HG, tRS and rRS were significantly higher in ICCA pts. Conclusions: In IDH1/2 mutant GM and ICCA pts, R2HG was increased relative to S2HG in tumor tissues. In GM pts, the accumulation of R2HG in tumor tissues was not reflected in blood, likely due to the inability of 2HG to diffuse across the blood-brain barrier. Serum R2HG, tRS and rRS were significantly elevated in ICCA pts. These biomarkers have no clinical utilities in GM pts. However, they can potentially be used to identify IDH mutations in ICCA pts, especially given the inability to obtain tumor tissue in some ICCA pts. Clinical trial information: NCT03991832. [Table: see text]
DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues.
Authors: Gu Hongcang , Zhang Shirong , He Shutao , Zhu Xin , Wang Yunfei , Xie Qionghuan , Wang Wenxian , Ma Shenglin , Shi Jiantao 
Published: June 2022

3079 Background: Metastatic cancers with uncertain primary sites account for a significant portion of new cases. Among them, 3-9% are eventually assigned to cancer of unknown primary (CUP) site after a comprehensive diagnostic workup. Accurate identification of the primary site is the starting point for cancer diagnosis worldwide, and it is critical to guide the subsequent treatments of metastatic cancers. Here we presented a new DNA methylation sequencing-based method to predict the tissues of origin for metastatic cancers, including CUP. Methods: Cancer diagnosis relies substantially on histological and immunohistochemical analyses of formalin-fixed paraffin-embedded (FFPE) tissues. To take advantage of sample accessibility, we developed an optimized and streamlined method that was particularly used to generate reduced represent bisulfite sequencing (RRBS) libraries for genome-wide DNA methylation profiling with degraded DNA fragments. After confirming that data quality generated using the new FFPE-RRBS method was comparable with regular RRBS, we created an RRBS database using 541 fresh frozen samples across ten most common cancer types and 58 tumor-adjacent normal tissues. By incorporating four distinct methylation summary scores and seven machine learning approaches, 28 models were trained and compared for multi-class classification using our database. Lastly, we selected the best classifier to predict the tissues of origin utilizing 249 FFPE samples across ten metastatic cancer types and 12 FFPE samples from CUP patients. Meanwhile, the classifier was also cross-validated using a DNA methylation microarray data set of 4702 patients diagnosed with corresponding primary cancers in the TCGA project. Results: FFPE-RRBS allowed to construct decent libraries with heavily degraded genomic DNA within 20 hours. Comparable DNA methylation metrics were obtained for the RRBS libraries of paired primary cancer tissues (fresh frozen vs. FFPE) and the libraries of paired FFPE samples derived from primary and metastatic tissues. Among the 28 methylation-based classifiers, the mean methylation-based LinearSVC model performed the best, achieving an overall accuracy of 81% with an AUC of 0.95 in determining the primary sites of 10 metastatic cancers. In a cross-validation assay using the TCGA data set of 4702 cancer patients, the overall prediction accuracy and AUC were 92% and 0.99, respectively. Lastly, our model successfully identified the tissues of origin in 10 of 12 CUP patients in a prospective study. Conclusions: The FFPE-RRBS is a novel method for efficient profiling of heavily degraded FFPE samples and the mean methylation-based LinearSVC model can predict the tissues of origin for metastatic cancers and CUP with high accuracy.
Mechanisms of acquired resistance to TRK inhibitors.
Authors: Harada Guilherme , Choudhury Noura J. , Schram Alison M. , Rosen Ezra , Murciano-Goroff Yonina R. , Falcon Christina J. , Wilhelm Clare , Kaplanis Lauren A. , Liu Dazhi , Chang Jason C. , Yang Soo-Ryum , Dhawan Aradhika , Evans Patrick , Savin Casey , Grimaldi Grace , Shah Ronak H. , Cocco Emiliano , Drilon Alexander E. 
Published: June 2022

3104 Background: First-generation TRK tyrosine kinase inhibitors (TKIs) are approved in a tumor-agnostic fashion in more than 40 countries for patients with NTRK fusion-positive adult and pediatric cancers. While resistance to these agents has previously been described, the exact frequency with which major mechanisms of resistance emerges is not clearly understood. Methods: Patients with an NTRK-fusion-positive tumor who received a first-generation TRK TKI were eligible. We retrospectively identified those patients that had post-progression tumor tissue analyzed by next-generation sequencing (NGS). The pattern of serial resistance to a second-generation TKI was analyzed when available. Results: Eighteen patients were identified. The median age was 46 years (range 2-67). Nine unique fusions were detected in ten different tumor types. NTRK1, NTRK2, and NTRK3 fusions were found in eight (44%), one (6%), and nine (50%) patients, respectively. Thirteen patients (72%) were treated with larotrectinib and five patients (28%) received entrectinib. NGS (MSK-IMPACT n = 17, Foundation One n = 1) carried out on post-progression tissue revealed the following profile of acquired resistance: on-target resistance (83%, n = 15/18), off-target resistance (11%, n = 2/18), and no identifiable mechanism (6%, n = 1/18). Among patients with on-target resistance, the most common mutation involved the solvent front (87%, n = 13/15: n = 7 NTRK3 G623R, n = 4 NTRK1 G595R, n = 1 NTRK2 G639L, n = 1 NTRK3 G623E) followed by the gatekeeper region (13%, n = 2/15: n = 1 NTRK1 F589L, n = 1 NTRK3 F617I). Two patients developed off-target alterations. One acquired BRAF V600E mutation and the other MET amplification. Interestingly, solvent front mutation loss was observed in two patients who transitioned to and progressed on a second-generation TRK TKI. One patient with a baseline NTRK1 G595R mutation developed polyclonal resistance with acquisition of KRAS G12A and NTRK1 G667A alterations as well as NTRK1 G595R loss. The other patient with NTRK3 G623R developed an NTRK3 F617I gatekeeper mutation with NTRK3 G623R loss. Conclusions: In NTRK fusion-positive cancers, on-target resistance preferentially involving the solvent front is more frequent than off-target resistance to first-generation TKI therapy. Furthermore, the sequential use of second-generation therapy appears to alter the evolutionary kinetics of mutation retention and acquisition.
Phase I dose-escalation study of IBI351 (GFH925) monotherapy in patients with advanced solid tumors.
Authors: Zhou Qing , Yang Nong , Zhao Jun , Dong Xiaorong , Wang Huijuan , Yuan Ying , Yu Yan , Zhang Meijiang , Zhang Sujie , Huang Mengna , Shen Yuping , Wu Yi-Long 
Published: June 2022

3110 Background: IBI351(GFH925) is an irreversibly covalent inhibitor of KRASG12C. In this first-in-human dose-escalation study, we report the preliminary safety and anti-tumor activity of IBI351 (GFH925) in patients (pts) with advanced solid tumors harboring the KRAS p.G12C mutation. Methods: Pts with locally advanced, recurrent or metastatic solid tumors with KRASG12C mutation for whom standard therapy had failed were enrolled. Phase I dose escalation had an accelerated titration design for dose level 250mg QD and a BOIN design with 450/700/900mg QD. The primary end points were safety and tolerabilityThe secondary end points were pharmacokinetics (PK) and anti-tumor activity of IBI351(GFH925) monotherapy per RECIST v1.1. Results: As of Feb 07 2022, 15 pts (13 men, 2 women; median age: 62 yrs, range: 48–74 yrs) were enrolled, among whom 12 had non-small cell lung cancer (NSCLC), and 3 had colorectal cancer (CRC). 4 pts had ≥3 prior lines of treatment (tx). Median tx duration was 66.5 ds (range: 21–98 ds). No dose-limiting toxicity (DLT) or any ≥grade 3 treatment-related adverse events were observed in any dose cohorts. A total of 12 patients (80.0%) had treatment-related adverse events (grade 1, n = 6; grade 2, n = 6). By investigator-assessment, tumor response was evaluated in 9 pts (4 with ≥2 assessments); 6 pts had not reached their first assessment. 2 pts had PR (1 NSCLC at wks 12, 450mg, tx ongoing; 1 CRC at wks 6, 700mg, tx ongoing), 4 pts (NSCLC) had SD, and 3 pts had PD (1 NSCLC at wks 12, 2 CRC at wks 6). As data cut-off date, 11 pts were continuing to receive IBI351 (GFH925). Conclusions: IBI351(GFH925) was well-tolerated without unanticipated adverse events across all doses explored in pts with advanced solid tumors harboring the KRAS p.G12C mutation. The data also demonstrated the preliminary efficacy signal of IBI351 (GFH925) in previously treated advanced NSCLC and CRC. Clinical trial information: NCT05005234.
Perioperative chemotherapy with mFOLFOX6 or CAPOX for patients with locally advanced colon cancer (OPTICAL): A multicenter, randomized, phase 3 trial.
Authors: Hu Huabin , Huang Meijin , Li Yunfeng , Wang Ziqiang , Wang Xiaozhong , Liu Ping , Zhang Ruyi , Zhang Hao , Huang Zhongcheng , Pei Haiping , Zeng Yongming , Lai Jiajun , Chen Wenbin , Chen Jiansi , Ding Zhijie , Wei Hongbo , Xu Qingwen , Chen Jigui , Wang Jianping , Deng Yanhong ,   Chinese Southwest Oncology Group (CSWOG)
Published: June 2022

3500 Background: Adjuvant chemotherapy is the recommended standard treatment for resected stage III and high-risk stage II colon cancer, but disease recurrence remain common. Perioperative chemotherapy has proved effective in several tumors, but not in colon cancer. We aimed to assess whether perioperative chemotherapy could improve outcomes in patients with locally advanced colon cancer. Methods: In this multicenter, randomized, phase 3 trial, participants were recruited from 28 hospitals in China. Eligible patients were aged 18-75 years, had a colon adenocarcinoma, with radiologically staged locally advanced (T3 with ≥5 mm invasion beyond the muscularis propria or T4 assessed by CT). Patients were randomly assigned (1:1) to either the experimental group or standard of care group, stratified by center, cT stage, and cN stage. The experimental group received 3 months of neoadjuvant chemotherapy with mFOLFOX6 or CAPOX, then surgery, then 3 months of adjuvant chemotherapy. The standard of care group received immediate surgery, and optional adjuvant chemotherapy (per physician’s discretion according to pathological stage ). The primary endpoint was disease-free survival assessed in the intention-to-treat population at 3 years. Results: Between January 6, 2016, and April 3, 2021, 752 patients were enrolled and randomly assigned to a treatment, of whom 744 were eligible (371 in the experimental group; 373 in the standard of care group). At a median follow-up of 32.5 months (IQR 19.2-45.7), 3-year disease-free survival rates were 78.7% (95%CI 73.8-83.5) in the experimental group and 76.6% (95%CI 71.8-81.4) in the standard of care group (stratified HR 0.83, 95%CI 0.60-1.15; p = 0.138). A pathological complete response was achieved in 26 (7%) of 371 patients in the experimental group. 69 (19%) patients in the experimental group had low pathological disease stage (pT0-2N0) compared with 16 (4%) of 373 in the standard of care group (p < 0.0001). 3-year overall survival rates were 94.9% (95%CI 92.1-97.7) in the experimental group and 88.6% (95%CI 84.6-92.5) in the standard of care group (stratified HR 0.47, 95%CI 0.25-0.87; p = 0.012). The post hoc subgroup analyses revealed perioperative chemotherapy induced an increase in disease-free survival in female patients (HR 0.54, 95%CI 0.31-0.83; p = 0.025). Conclusions: In patients with locally advanced colon cancer, perioperative chemotherapy with mFOLFOX6/CAPOX increased chance of pathological downstaging, but did not improve disease-free survival compared with standard of care. Clinical trial information: NCT02572141. [Table: see text]
Real-world outcomes of biosimilar bevacizumab-awwb versus reference bevacizumab in patients with metastatic colorectal cancer.
Authors: Pham Catherine , Niu Fang , Delate Thomas , Buchschacher Gary L , Li Yan , Ekinci Ekim , Le Kim , Hui Rita L. 
Published: June 2022

3552 Background: Bevacizumab-awwb was the first biosimilar approved by the U.S. Food and Drug Administration (FDA) for treatment of cancer and became available for use in July 2019. Clinical comparative efficacy and safety of bevacizumab-awwb to bevacizumab was established in a single study of adult patients with advanced non-squamous non-small cell lung cancer. Approval based on extrapolation was granted by the FDA for all other indications, including metastatic colorectal cancer (mCRC). The objective of this study was to evaluate the real-world effectiveness and safety outcomes of patients with mCRC initiated on bevacizumab-awwb versus bevacizumab in an integrated healthcare delivery system. Methods: This was an observational cohort study of patients with mCRC in Kaiser Permanente California, Colorado, and Mid-Atlantic States who were initiated on bevacizumab-awwb between July 2019 and March 2020 or reference bevacizumab between July 2015 and June 2018. Patients with history of bevacizumab use in the 6 months prior to the index treatment date were excluded. Patients were followed until 12 months after treatment initiation, end of plan membership, or death, whichever occurred first. The primary outcome of overall survival (OS) was analyzed using a non-inferiority test with lower margin of 10% and Cox proportional-hazards modeling. Secondary outcomes included count of doses received, treatment duration, all-cause hospitalizations, and incidence of serious adverse events. Results: A total of 1,445 patients initiated on either bevacizumab-awwb (n=239) or bevacizumab (n=1,206) were included in the analysis. The mean overall age was 60 ± 13 years and 54% of patients were male. The OS rate was 72.8% and 73.1% for patients receiving bevacizumab-awwb and bevacizumab, respectively ( p<0.01 for non-inferiority). The adjusted hazard ratio for mortality was 1.01 (0.77-1.33, p=0.93). There were no statistically significant differences in secondary outcomes between the 2 study groups (Table). Conclusions: Bevacizumab-awwb is a safe and effective option when compared to the reference bevacizumab in the treatment of mCRC. Future studies should evaluate outcomes after longer follow-up time and in different cancer types. [Table: see text]