bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-tumor analyses of kinase fusions detected in circulating tumor DNA (ctDNA) and concordance with paired tissue.
Authors: Lee Jessica Kim , Lieber Daniel , Madison Russell , Chung Jon , Schrock Alexa Betzig , Creeden James , Venstrom Jeffrey , Alexander Brian Michael , Hazar-Rethinam Mehlika 
Published: May 2020

3517 Background: Oncogenic kinase gene fusions are targetable with approved and investigational therapies and can also emerge as acquired resistance (AR) to targeted therapy. To understand the clinical validity of liquid biopsy comprehensive genomic profiling (CGP) to detect kinase fusions, we compared patient-matched plasma and tissue-based CGP. Methods: Hybrid capture-based CGP was performed on 28,743 plasma and 325,131 tumor tissue samples in the course of clinical care. Complete exonic regions of 13 kinases involved in oncogenic fusions plus select introns in ALK, EGFR, FGFR2/3, PDGFRA, RET, and ROS1 were sequenced to capture fusions with well characterized breakpoints. ctDNA fraction was estimated by maximum somatic allele frequency (MSAF). Results: 86% of cases had detectable ctDNA in plasma (MSAF > 0). Kinase fusions were detected in 2.1% of ctDNA cases (478/23,294) and were most prevalent in patients (pts) with bladder cancer (4.5%), non-small cell lung cancer (NSCLC) (4.3%), and cholangiocarcinoma (3.9%). The most commonly rearranged kinases were ALK (60%, 162/271) and RET (19%, 51/271) in NSCLC, FGFR2 (85%, 11/13) in cholangiocarcinoma, and FGFR3 (88%, 7/8) in bladder cancer. ALK fusions were detected in 26% (54/207) of fusion+ non-NSCLC cases. Paired tissue and ctDNA samples where ≥1 sample harbored a kinase fusion were available for 147 pts; median time between sample collection was 150 days (interquartile range: 444 days). Positive percent agreement (PPA) to tissue and liquid biopsies was 76% and 80%. Median MSAF in concordant and discordant ctDNA samples was 2.3% and 0.41% (p = 0.04) and median time between specimen collection for concordant and discordant pairs was 110 and 344 days (p = 0.04). PPA to tissue and liquid was 86% and 88% for pairs collected < 60 days apart (n = 53), versus 70% and 74% for pairs collected > 60 days apart. 6 pts with paired samples all collected > 196 days apart (median 593 days) had initial tissue samples with EGFR driver mutations and had an acquired kinase fusion (4 ALK, 1 FGFR2, 1 FGFR3) in the 2nd ctDNA sample, likely representing AR. Conclusions: Kinase gene fusions identified by tissue-based CGP were detected by liquid biopsy CGP in 85% of temporally-matched plasma samples. Kinase fusion detection by liquid biopsy CGP is feasible and had high PPA to tissue-based CGP. Subsequent sampling by liquid biopsy identified acquired fusions in EGFR driver positive cases consistent with known mechanisms of resistance to EGFR inhibitors suggesting utility of liquid biopsy at progression to identify targetable mechanisms of AR.
Demonstrating the value of liquid biopsy for lung cancer in a public health care system.
Authors: Juergens Rosalyn A. , Ezeife Doreen Anuli , Laskin Janessa J. , Agulnik Jason Scott , Hao Desiree , Laurie Scott Andrew , Law Jennifer H. , Le Lisa W , Kiedrowski Lesli Ann , Shepherd Frances A. , Cohen Victor , Shokoohi Aria , Vandermeer Rachel , Li Janice Juanning , Hanson Inna , Fernandes Roxanne , Salvarrey Alexandra Maria , Lanman Richard B. , Leighl Natasha B. 
Published: May 2020

3546 Background: Given the challenges of molecular profiling in patients with advanced lung cancer, this prospective study examines clinical outcomes and utility of liquid biopsy in treatment naive stage IV lung adenocarcinoma patients (Cohort 1) and in the setting of resistance to targeted therapy (Cohort 2; not reported here). Methods: This study is being conducted at 6 Canadian centres (NCT03576937) using Guardant 360 (G360), a validated cell-free DNA next-generation sequencing assay that identifies variants in 74 cancer-associated genes, including fusions and copy number gain. Cohort 1 (N = 150) includes patients with treatment-naïve advanced non-squamous lung carcinoma, ≤10 pack-year smoking history, and measurable disease. Patients received standard of care tumour tissue (TT) molecular profiling ( EGFR, ALK +/- ROS1) and liquid biopsy (LB). The primary endpoint was response rate to first-line therapy (RECIST 1.1); secondary endpoints include incremental targetable alterations identified through G360 ( EGFR, ALK, BRAF, ERBB2, KRAS (G12C), NTRK, MET (amplification, exon 14 skipping), RET, ROS1), turn-around time (TAT) and successful molecular profiling rates. Results: To date, 84 eligible patients with clinical data have been accrued to Cohort 1. Median age is 64 (range 23-91), 64% are female, 85% never smokers, 96% have adenocarcinoma. Actionable targets have been identified in 55% of patients using G360 ( EGFR/ALK in 37%), 39% using standard TT profiling. Eight EGFR/ALK aberrations were identified in TT but not LB, while 6 were identified in LB but not TT. TT profiling for EGFR/ALK was unsuccessful in 8% of patients (insufficient tissue, failed biopsy). Fourteen patients (17%) had no ctDNA alterations detected by G360 (low disease burden vs. non-shedding). Of 75 patients receiving first-line treatment, 57% received targeted therapy, 28% chemotherapy combinations, 11% checkpoint inhibitors and 4% were observed. Treatment decisions were informed by G360 alone in 37% and by G360+TT results in 27% (by physician report). Among 46 evaluable patients, ORR was 54% (25/46). Using G360, ORR was 75% (15/20) in those with actionable alterations and 38.5% (10/26) in those without. Using TT, ORR was 67% (14/21) in those with actionable alterations and 44% (11/25) in those without. Mean TAT was 7.9 days (SD+/-1.7) for LB vs 19.9 days (SD+/- 9.8) for TT. Conclusions: Liquid biopsy using G360 identifies actionable targets beyond tissue profiling alone in newly diagnosed lung cancer patients, has faster TAT and yields similar outcomes with targeted and non-targeted therapy. Clinical trial information: NCT03576937 .
The prevalence of KRASG12C mutations utilizing circulating tumor DNA (ctDNA) in 80,911 patients with cancer.
Authors: Thein Kyaw , Banks Kimberly , Saam Jennifer , Raymond Victoria M. , Roszik Jason , Meric-Bernstam Funda , Janku Filip , Hong David S. 
Published: May 2020

3547 Background: Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most commonly mutated proto-oncogene identified in cancer and still remains an arduous therapeutic challenge. Recently, KRASG12C mutation has become special interest since it has now been considered potentially druggable after the introduction of covalent small-molecule KRASG12C inhibitors. Advances in next-generation sequencing (NGS) and embracing utilization of ctDNA have uncovered more genetic alterations in many cancers. We present a comprehensive analysis on the prevalence of KRASG12C mutations identified by ctDNA. Methods: We conducted a 5-year (July 2014 to June 2019) retrospective review of ctDNA NGS analysis in the Guardant360 CLIA database inclusive of treatment-naïve and previously treated patients with metastatic solid tumors. Data were retrieved from the 80,911 unique patients with ctDNA detected. Clonality and co-occurrence of cancer type were analyzed. Clonality was defined as variant allele fraction(AF) / maximum somatic AF in the sample. Results: 80,911 patients, which included more than 100 tumor histologies, were identified. 2,985 patients (3.7%) with > 40 tumor types had KRASG12C mutations identified in ctDNA. KRASG12C prevalence by cancer type were as follows: sarcomatoid lung carcinoma (13.5%), lung cancer NOS (9%), large cell lung carcinoma (9%), lung adenocarcinoma (7.4%), NSCLC (6.9%), carcinoma of unknown primary (CUP) (4.1%), lung carcinoid (4%), CRC (3.5%), squamous cell lung carcinoma (2%), small cell lung carcinoma (1.5%), pancreatic ductal adenocarcinoma (PDAC) (1.2%), cholangiocarcinoma (1.2%), bladder cancer (0.6%), ovarian cancer (0.6%) and breast cancer (0.3%). 53 additional patients with KRASG12C were identified across 24 other tumor types. The KRASG12C mutation was found to be clonal (clonality > 0.9%) in the majority of patients with lung adenocarcinoma, NSCLC, CUP, squamous cell lung carcinoma, and PDAC, compared to patients with CRC and breast cancer who had bimodal distribution of clonal and sub clonal mutations. Conclusions: To our knowledge, this is the largest analysis on the prevalence of KRASG12C mutations identified by ctDNA. Our study demonstrated the feasibility of utilizing ctDNA to identify KRASG12C mutations across solid tumors with the highest prevalence in lung cancer as previously reported in tissue. The clonality information available from ctDNA-based genotyping may provide insights into the clinical efficacy of targeting KRASG12C in different tumor types.
Phase I study of mesothelin-targeted immunotoxin LMB-100 given as a long infusion with or without nab-paclitaxel.
Authors: Pegna Guillaume Joe , Ahmad Mehwish Iqra , Yu Yunkai , Yuno Akira , Lee Min-Jung , Peer Cody J. , Steinberg Seth M. , Cao Liang , Trepel Jane B , Figg William Douglas , Hassan Raffit , Pastan Ira , Alewine Christine Campo 
Published: May 2020

3553 Background: LMB-100 recombinant immunotoxin consists of a mesothelin-binding Fab for targeting a modified Pseudomonas exotoxin A payload. Previous Phase 1 clinical testing of a 30-minute LMB-100 “short” infusion format identified a serum half-life of ~1 hour. Pre-clinical data suggested that extending infusion time could improve anti-tumor efficacy by increasing tumor cell duration of exposure to LMB-100. The primary objective of this study was to determine the safety and tolerability of administering LMB-100 in a long infusion format over 24-48 hours alone or with nab-paclitaxel chemotherapy in patients with mesothelin-expressing solid tumors. Methods: Patients (n = 15) with pancreatic adenocarcinoma and other mesothelin-expressing solid tumors (n = 3; mesothelioma, colon, and ampullary cancers) treated on 3 dose levels received long infusion of LMB-100 (65 or 100 mcg/kg/day) for 24 hour on Days 1 and 4 (n = 6) or 48 hour on Day 1 (n = 9) with or without a loading dose (40 mcg/kg over 30 minutes) for up to 2 cycles. In the second arm, patients (n = 5) with pancreatic adenocarcinoma were treated with LMB-100 over 24 hours on Day 1 concurrently with nab-paclitaxel (125 mg/m2) for up to 3 cycles. Results: DLT of proteinuria (grade 3) in one patient and acute kidney injury (grade 1) in one patient were observed amongst patients receiving 100 mcg/kg/day over 48 hours and 24 hours, respectively. No objective responses were seen but all patients receiving nab-paclitaxel had > 50% decrease in CA 19-9. Patients at all single agent dose levels (8 of 10 evaluable) developed high titer anti-drug antibodies (ADAs) against LMB-100. Those with ADAs (8 of 8) had undetectable cycle 2 peak plasma LMB-100 concentration. Development of high titer ADAs occurred more frequently with long infusion than seen previously with “short” infusion LMB-100. Most long infusion patients (19 of 20) developed increased serum IL-6 within 24 hours of LMB-100 infusion. However, the systemic inflammatory response to LMB-100 (as measured by increased serum CRP) which occurs in most “short” infusion patients was not observed. Conclusions: Long infusion format LMB-100 is generally well tolerated but immunogenicity limits treatment to 1 effective cycle. No anti-tumor efficacy of the single agent was observed. Clinical trial information: NCT02810418 .
Clinically aggressive malignancies associated with STK11 germline mutations (STK11GCa): A comprehensive genomic profiling (CGP) study.
Authors: Sokol Ethan , Danziger Natalie , Pavlick Dean , Elvin Julia Andrea , Vergilio Jo-Anne , Killian Jonathan Keith , Lin Douglas I. , Ramkissoon Shakti H. , Severson Eric Allan , Hemmerich Amanda , Duncan Daniel , Edgerly Claire I. , Huang Richard , Chung Jon , Reddy Venkataprasanth P. , McGregor Kimberly , Venstrom Jeffrey , Schrock Alexa Betzig , Alexander Brian Michael , Ross Jeffrey S. 
Published: May 2020

3558 Background: Germline mutations in the STK11 ( LKB1) mTOR pathway gene are associated with Peutz-Jehger’s Syndrome and a variety of malignancies of variable clinical aggressiveness. Recent evidence also links STK11 inactivation with failure to benefit from anti-cancer immune checkpoint inhibitor (IO) therapy in NSCLC. Methods: Using hybrid capture based CGP on extracted tumor DNA and a published “somatic-germline-zygosity” SGZ data analysis algorithm on 212,470 samples of clinically advanced malignancies, we identified 103 (0.05%) STK11GCa inactivating base substitutions or indels. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on 114 loci. PD-L1 expression was determined by IHC (Dako 22C3). Results: 57 (55%) STK11GCa cases were NSCLC, 7 (7%) STK11GCa cases each were CRC, breast, pancreatic and unknown primary carcinomas, and 3 (3%) were gynecologic cancers. Amongst all samples included in this analysis, STK11 germline alterations were found in 0.15% NSCLC, 0.03% CRC, 0.03% breast, 0.08% pancreas, 0.06% unknown primary carcinoma and 0.03% of gynecologic cancers. Additional malignancies harboring STK11GCa included melanoma, gastroesophageal, HNSCC, bladder, HCC, lymphoma and mesothelioma. In STK11GCa, the median patient age at sequencing was 61 years (range 2 to > 89 years); gender distribution was 52% female and 48% male. STK11GCa cases had a median of 6.5 genomic alterations (GA)/tumor and KEAP1, another IO resistance gene, was co-altered in 10%. Currently untargetable GA were detected in TP53 (50%), KRAS (38% with 9% in potentially targetable G12C), CDKN2A (32%), CDKN2B (22%), SMARCA4 (19%), MYC (11%), and APC (10%). Potentially targetable GA, which have also been linked in some studies to IO efficacy, included GA in BRAF (10%), EGFR (9%) and PBRM1 (4%). No targetable gene rearrangements or fusions were identified. No MSI High cases were identified. The median TMB was 5 mut/Mb with 23 % >10 mut/Mb and 4% >20 mut/Mb. 15% of 20 evaluated STK11GCA cases were PD-L1 high (>50% tumor cell staining). Conclusions: STK11GCa include a wide variety of primary tumors with a paucity of co-occurring targetable GA. Although these tumors have significant PD-L1 staining and a subset harbor other markers of potential IO efficacy, the inactivated STK11 in these tumors may contribute to IO resistance and lack of responsiveness to immunotherapies.
A prospective study of prognostic role of plasma circulating tumor DNA (ctDNA) in patients (pts) with early-stage malignancies.
Authors: Fedyanin Mikhail , Boyarskikh Uljana , Polyanskaya Elizaveta , Aliev Vechaslav , Mamedli Zaman , Kechin Andrey , Oscorbin Igor , Shamovskaya Darya , Popova Anna , Polyakov Alexandr , Kudashkin Nikolay , Arzumanyan Alla L. , Trigolosov Arkadiy , Nikulin Maxim P. , Nered Sergey N. , Stilidi Ivan , Moroz Ekaterina , Chekini Antonio , Filipenko Maxim , Tjulandin Sergei 
Published: May 2020

3559 Background: Recently, conflicting evidence has emerged showing the association of ctDNA level and cancer progression. The aim of our study was the development of a method for detecting ctDNA in plasma and the investigation of the prognostic value of ctDNA retention after surgery in the prospective way. Methods: This prospective, single-center, sample collection study; pts with early-stage malignancies of the different origin were included. Tumor somatic mutations were determined by target sequencing of DNA from FFPE tumor blocks. Sequencing was performed using the custom NGS panel covering regions of frequent somatic mutations in 50 genes. Tumor-specific mutations were monitored in plasma samples taken before and after surgery. The median time between surgery and plasma collection was 7 days (5-15). Mutations of plasma ctDNA were determined by ddPCR. The plasma sample was considered "positive" if the content of ctDNA was more than 0.5 copies of mutant DNA in ml plasma. We needed 265 pts for improving 1-year disease free survival (DFS) from 60% to 80% with α=0.01, β=0.1, 10% loss of f.-up and duration of the study for 2 years. Results: The study comprised 271 pts with various cancers including colorectal – 91 (33,6%), pancreatic – 37 (13,7%), breast – 66 (24,4%), lung – 35 (12,9%) and gastric cancer – 42 (15,5%). Pts with stage I was 50 (18,5%), stage II – 118 (43,5%) and stage III – 103 (38%). The median time of the f.-up was 9 mos. (1-37). No significant association was found between the level of ctDNA before surgery and DFS either in the general group or in groups stratified by tumor sites (HR 2.4, 95%CI 0.8-7.1, р=0.12 and HR 1.5, 95%CI 0.4-6.3, р=0.5, correspondingly). ctDNA was detected in the plasma after surgery in 57 (10%) pts: 9 (9.9%) cases of colorectal, 10 (27%) - pancreatic, 9 (13.6%) - breast, 19 (54.3%) - lung, and 10 (23.8%) - gastric cancer. Progression of the disease was detected in 28/57 (49%) pts with ctDNA(+) and 17/214 (8%) - in ctDNA(-) pts (p<0.001). One-year DFS in ctDNA(+) and ctDNA(-) pts were 57% and 87%, respectively (HR 6.1, 95%CI 3.3-11.2, p<0,001). ctDNA positivity after surgery was an independent negative prognostic factor according to Cox regression model fitted to T, N, and adjuvant chemotherapy (HR 5.7, 95%CI 3.1-10.8, p <0.001). Conclusions: These results demonstrate the prognostic significance of ctDNA persisting after surgery in pts with the early stage of the different malignancies. Further clinical validation of this approach is required in trails with modifications of the adjuvant treatment, according to the content of ctDNA.
Platform comparison of HTG EdgeSeq and RNA-Seq for gene expression profiling of tumor tissue specimens.
Authors: Ran Di , Moharil Janhavi , Lu James , Gustafson Heather , Culm-Merdek Kerry , Strand-Tibbitts Kristen , Benjamin Laura , Navratil Marian 
Published: May 2020

3566 Background: Clinical biomarker studies are often hindered by the availability of tissue specimens of sufficient quality and quantity. While RNA-Seq is often considered the gold standard for measuring mRNA expression levels in cancer tissue, it typically requires multiple formalin-fixed paraffin-embedded (FFPE) tissue sections to extract a sufficient amount of quality RNA for subsequent gene expression profiling analysis. The HTG EdgeSeq technology is a gene expression profiling platform that combines quantitative nuclease protection assay technology with next-generation sequencing detection. Unlike RNA-Seq, the HTG EdgeSeq technology does not require RNA extraction, and can use small amounts of tissue material, typically several mm2, to generate reproducible gene expression profiles. Methods: This study compares the performance of RNA-Seq and HTG's profiling panel, the HTG EdgeSeq Precision Immuno-Oncology Panel (PIP), which is designed to measure expression levels of 1,392 genes focused on tumor/immune interaction. Approximately 1,200 samples from three tumor indications (gastric cancer, colorectal cancer and ovarian cancer) were tested using both technologies. Results: Up to four FFPE slides were used for RNA extraction to support RNA-Seq testing; out of the 1,202 samples processed, 1,099 generated extracted RNA of sufficient quality and quantity (as measured by RNA concentration, RIN score and %DV200) to proceed to sequencing, which resulted in a pass rate of 91.4% for RNA-Seq. The HTG EdgeSeq PIP panel resulted in a pass rate of 97.3% (samples passing QC metrics) when the same 1,200 samples were tested, and required only a single FFPE section owing to the small sample requirement. The t-SNE (a non-linear dimensionality reduction method) analysis of the common 1,358 genes revealed similar clustering of the three cancer indications between the two methods. Correlations across individual genes by sample resulted in the mean Spearman correlation coefficient of 0.73 (95% confidence interval of 0.61 - 0.80). Additionally, gene-wise comparisons across all samples were also evaluated. Conclusions: These data demonstrate that HTG EdgeSeq gene expression panels can be used as a competitive alternative to RNA-Seq, generating equivalent gene expression results, while offering the added benefits of a small sample size requirement, lack of RNA extraction bias, and fully automated data analysis pipeline.
Genomic analysis of driver-negative lung adenocarcinoma (LA) in lifetime never smokers.
Authors: Fares Aline Fusco , Martins-Filho Sebastiao N. , Li Quan , Seto Andrew , Stewart Erin L. , Zhang Tong , Lau Sally CM , Ravi Deepti , Weiss Jessica , Patel Devalben , Pham Nhu-An , Sacher Adrian G. , Bradbury Penelope Ann , Stockley Tracy , Leighl Natasha B. , Shepherd Frances A. , Tsao Ming Sound , Liu Geoffrey 
Published: May 2020

3571 Background: Genomic events giving rise to driver negative LA in never smokers remain elusive. Here we report results of whole exome sequencing (WES) and targeted RNA sequencing in NS who had no mutation drivers found on routine clinical testing by targeted next generation sequencing (NGS). Methods: The cohort of never smokers with EGFR/ALK negative LA by clinical biomarker testing at Princess Margaret Cancer Centre, were first subjected to various clinical NGS profiling platforms (table). Where tissue was available, those negative for potential drivers in the clinical NGS then underwent WES (mean coverage > 200x) and Oncomine comprehensive v.3 RNA sequencing. We analyzed mutational signatures (MS) of the driver negative cohort based on the COSMIC catalog and assessed the median tumor mutation burden (mTMB mut/Mb -Megabase) in cases without a smoking MS, to avoid confounders. Results: Of 159 never smokers profiled with clinical NGS, potential drivers were found in 86 (54%): 75 (87%) with mutations in known LA driver genes and 11 (13%) with fusions. Among the remaining never smokers that tested negative by clinical NGS, 35 (48%) had available tissue for further testing. The Oncomine panel identified 9 cases (25%) with fusions or MET exon14 mutation (n = 7). Within the driver negative group, 24 (92%) underwent WES. Three tumors had WES base substitution patterns that were consistent with a smoking-related MS (MS4). Twenty-one patients exhibited signatures found common across all cancer types (MS 5), associated with DNA mismatch repair (MS 6, MS 20) or APOBEC over-activation (MS 2, MS13). In the driver-negative group, we identified 7 pts with somatic mutations in the KMT2 family (4 KMT2C, 4 KMT2A, 1 KMT2D), known for putative tumor suppressors and histone methyltransferases. mTMB on the driver negative group was 1.92, while one outlier with APOBEC MS and KMT2C/A mutations had a TMB of 16.8. Conclusions: Never smokers with driver negative LA are a heterogeneous group, with different MS and a wide TMB range. Mutations on KMT2 family are frequently found in driver negative LA in never smokers and warrant further investigations. [Table: see text]