bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing pre-analytical sample QC failure rates for cancer molecular genetic assays with SLIMamp technology.
Authors: Fink Lynn , Waring Paul Michael , Jaradi Binny , Stone Nathan , Anderson Lisa , Leo Paul , Marshall Mhairi , Ellis Jonathan , O'byrne Kenneth 
Published: June 2022

e15034 Background: Identification of somatic variants in cancer by high-throughput sequencing has become common clinical practice largely because many of these variants may be predictive biomarkers for targeted therapies. However, there can be high sample QC failure rates for some assays (sometimes up to 40%), preventing the return of results that may affect patient treatment decisions. Pillar Biosciences has incorporated their patented SLIMamp technology into commercially available cancer NGS testing kits with the claim that these kits can successfully interrogate challenging formalin-fixed paraffin-embedded tissue (FFPET) samples with low tumor purity, poor DNA quality, and/or low input DNA, resulting in a high sample QC pass rate. The aim of this study was to substantiate that claim using Pillar’s amplicon-based oncoReveal Solid Tumor Panel. Methods: We acquired 48 tumor samples that had failed one or more pre-analytical QC sample parameters for whole exome sequencing (WES) from ATGC’s ISO15189 accredited diagnostic genomics laboratory. XING Genomic Services performed an exploratory data analysis using our pre-analytical QC assays to characterise the samples and then sequenced the samples in our ISO15189 accredited laboratory using the validated oncoReveal Solid Tumor Panel. Results: We were able to achieve high sequencing coverage (>3000X) for all 48 samples and explored the determinants of sample “success”. We were able to generate clinical reports for 45 samples (94%), of which 38 (79%) contained clinically actionable or significant variants that would not have otherwise been identified. Ten samples had a higher number of total variant calls with over-representation of C>T transitions representing stochastically-amplified, formalin-induced artefacts in samples with very low input template DNA. Of these, 7 cases had reportable variants and 3 were deemed unreportable. We demonstrated that DNA integrity is the major determinant of success even in samples with low input DNA or low tumor purity and were able to further refine pre-analytical and post-analytical QC metrics to better identify samples with poor quality DNA that can be sequenced reliably. Conclusions: In this study, we showed that the Pillar Biosciences oncoReveal Solid Tumor Panel, which uses SLIMam technology, was able to generate reliable, interpretable results for 94% of samples that failed pre-analytical QC for WES, substantiating Pillar’s claim.
Clinical utility of a molecular tumor board (MTB) in a community oncology practice.
Authors: Amatruda Thomas , Malisetti Nithya , Hirst Jeff , Vadnais Malia , Katipamula-Malisetti Rajini 
Published: June 2022

e15038 Background: We convened a molecular tumor board in an oncology specialty practice of 60 oncologists. Monthly meetings were held remotely, with participation of molecular oncology experts from Caris Life Sciences. Cases were selected for MTB by CLS or clinicians, largely from patients whose genomic testing results did not suggest level 1 guideline therapy options. Methods: We reviewed the clinical value of the genomic test results. To measure the impact of the MTB on patient care, we reviewed a sample of cases with a database instrument. Results: Over calendar year 2021, 491 genomic tests were reported by CLS. These tests involved whole exome and whole transcriptome analysis of microdissected tumor samples. 151 tests showed no association with approved therapy on initial report. In addition to the reported analysis of mutations and fusions, supplemental data concerning emerging biomarkers such as deletions, homologous repair deficiency, and gene expression was provided by CLS for MTB discussion. Between May 2020 and February 2021, 47 cases were presented, representing 19 different diagnoses. 17 cases were reviewed in detail. In 88% of cases (15/17) a recommendation was made by the group. These included suggestions for standard therapy, on sequencing of therapies, on genetic counseling and testing for inherited mutations, and on clinical trial opportunities for emerging biomarker guided therapeutics. In 35% of cases (6/17), the tumor board presentation had an impact on care. In 17% of cases (6/17), we suggested germline genetic testing for patient or family. In 23% of cases (4/17), patient treatment was changed based on discussion. In 9 cases, recommendations were not acted on, because patients deteriorated, remained stable, or chose other therapies. Many patients were presented after multiple lines of treatment or at a time of declining clinical status, which limited the clinical impact of MTB discussion. Evaluation of inherited mutations in patients and family members were difficult to complete when care was dispersed across multiple health systems. Conclusions: The MTB provided valuable updates on new molecular findings and targeted therapies. Incorporation of tumor genomic testing and MTB discussion at an earlier point in the clinical care continuum could improve overall patient outcomes. Challenges in the structure and utility of the conference will be discussed.
A novel molecular subtype of hepatocellular carcinoma based on the tumor purity and tumor microenvironment-related polygenic risk scores.
Authors: Lin Yan , Liang Rong , Gao Xing , He Ziqin , Lu Lu , Luo Min , Li Qian , Wang Xiaobo , Li Yongqiang , Wu Guobin , Luo Xiaoling , Ye Jiazhou 
Published: June 2022

e15040 Background: The molecular classification of hepatocellular carcinoma (HCC) plays a vital role in the management of precision therapy. Several molecular classification systems, mainly focusing on the tumor cells, were developed according to distinct omics features of HCC. Heterogeneous tumor microenvironment (TME) in HCC is recognized as a crucial part of inter-tumor heterogeneity. Few molecular classifications of HCC have so far taken into account both the related molecules of tumor cells and TME. Methods: Wefirstly identified the tumor purity (TP)-related and TME-related genes in the differentially expressed genes in HCC using GSE14520 data set, and separately constructed the TP-related and TME-related polygenic risk score (PRS). Secondly, according to the TP-related and TME-related PRSs, we proposed the TP-TME risk classification which was validated in two external data sets from The Cancer Genome Atlas Program and International Cancer Genome Consortium database. We also performed functional enrichment and drug repositioning analysis to reveal the potential biological heterogeneity among different subtypes. Results: The three TP-TME risk subtypes of HCC had significantly different prognosis and biological characteristics. The TP-TME low risk subtype had the best prognosis and was characterized by well-differentiated, the TP-TME high risk subtype had the worst prognosis and was characterized by aberrant activation of TGFβ and WNT pathways, and the TP-TME high risk subtype had the moderate prognosis and was characterized by exhibited activated MYC targets and proliferation-related gene sets. We also found that these three TP-TME risk subtypes may respond differently to immunotherapy (e.g., immune checkpoint inhibitors and chimeric antigen receptor-modified T cells) or other drug therapies. Conclusions: By combining separately constructed TP-related PRS and TME-related PRS, we proposed and validated a novel molecular classification system, the TP-TME risk subtyping system, to divide patients with HCC into three subtypes with distinct biological characteristics and prognosis. These findings highlight the significant clinical implications of the TP-TME risk subtyping system and provide potential personalized immunotherapy strategies for patients with HCC.
Detection of multiple types of cancer driver mutations using targeted RNA sequencing in NSCLC.
Authors: Hong Yuanyuan , Wang Xiaoqing , Mu Weina , Zeng Xuexia , Su Lin , Lin Xiaojing , Zhang Zhuo , Zhang Qi , Chen Weizhi 
Published: June 2022

e15043 Background: DNA NGS sequencing has been widely used as a companion diagnostic method for matching NSCLC patients with appropriate personalized target therapy. RNA-based NGS has been proved to be valuable in detecting fusion and exon skipping mutations and therefore recommended by NCCN guidelines for these mutation types. It would be helpful to have a diagnostic method that suits different types of clinically actionable mutations in a single tube. Methods: We developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for detection of fusion, SNV and indel mutations, as well as gene expression quantification. Reference materials were used for analytical validation of the panel, and 1253 FFPE samples from NSCLC patients were analyzed by DNA panel sequencing and RNA panel sequencing in parallel to assess the performance of the RNA panel in detection of multiple types of clinically actionable mutations. Results: Analytical validation showed a detection specificity of 100.0% for SNVs and fusions. The targeted RNA panel achieved a 1.45-3.15 copies/ng limit of detection (LOD) for SNVs and a 0.21-6.48 copies/ng LOD for fusions. Gene expression analysis revealed a correlation greater than 0.9 between the RNA-seq and targeted RNA panel results. Among 1253 NSCLC FFPE samples, multiple mutation types were called at both DNA and RNA levels and compared between the two assays. Twenty-one fusion and six METex14 skipping events were only detected by the RNA panel. The positive percent agreement (PPA) and positive prediction value (PPV) were 98.08% and 98.62% for targetable SNVs and 98.15% and 99.38% for targetable Indels, respectively. We also explored the relationship of RNA expression with gene copy number and protein expression. The RPKM (reads per kilobase per million mapped reads) of EGFR transcripts exhibited a linear relationship with copy number, whereas MET gene expression seemed to be regulated in a more complexed manner. In IHC analysis, all MET IHC 3+ samples had significantly higher RPKM levels than samples with MET IHC level of 2+/1+. Conclusions: Parallel DNA and RNA systematic analysis demonstrated the accuracy and robustness of the RNA sequencing panel for detection of multiple types of clinically actionable mutations. The simplified experimental workflow, lowered cost and sample consumption, along with the superior performance in simultaneous detection of multiple types of mutations will make RNA panel sequencing an effective method in clinical testing for NSCLC.
A phase 1, safety and dose escalation study of BXQ-350, a nanovesicle formulation of saposin c, a modulator of sphingolipid metabolism, in patients with advanced solid malignancies.
Authors: Curry Richard Charles , Rixe Olivier , Morris John Charles , Wesolowski Robert , Yilmaz Emrullah , Villano John L. , Muller Carolyn , Wise-Draper Trisha Michel , Noonan Anne M. , Puduvalli Vinay K. , Tapolsky Gilles , Takigiku Ray 
Published: June 2022

e15059 Background: Bexion recently completed an all-comer Phase 1 clinical study of BXQ-350 in patients with advanced solid tumors including high grade gliomas to evaluate the safety profile and to determine the maximum tolerated- or biologically effective dose. BXQ-350 is a nanovesicle comprised of recombinantly expressed Saposin C (SapC) and dioleoylphosphatidylserine. SapC, a human protein encoded by the Psap gene, is an allosteric activator of several enzymes involved sphingolipid metabolism. Sphingolipids are bioactive signaling molecules implicated in multiple cellular processes including apoptosis and immune stimulation/inhibition. In nonclinical studies, BXQ-350 evidences broad anticancer activity, selectively inducing apoptosis of cancer cells by modulating sphingolipids (ceramides/S1P), and BXQ-350 acts synergistically with multiple classes of anticancer agents and treatments. Methods: In the trial (NTC02859857), performed at four US sites, BXQ-350 was administered intravenously for a minimum of 6 cycles over 28 weeks at escalating doses from 0.7 mg/kg up to 2.4 mg/kg. Multiple secondary parameters were included to characterize its pharmacokinetics, efficacy profile and identify potential biomarkers. Results: Results indicate that: i) BXQ-350 was safe and well-tolerated as no DLT was observed and an MTD was not reached; ii) treatment related adverse events leading to discontinuation were typical for this patient population and disease related; iii)* biomarker analyses suggest positive modulation of sphingolipid metabolism and stimulation of the immune system; iv)* surprisingly, some patients noted improvement of existing peripheral neuropathies. RANO or RECIST ver 1.1 criteria were used to evaluate tumor response: 13 patients reached Cycle 6 restaging (17% ORR); 8 patients (11.0% of evaluable patients) demonstrated progression free survival over more than 6 months; and 2 patients (a GBM and CRC patient) are still on study after 5 years. * subject of separate abstracts. Conclusions: In conclusion, BXQ-350 is a first-in-human and first-in-class novel biologic whose Phase 1 results suggest that it may have clinical utility either as a monotherapy or when combined with other targeted agents. Clinical trial information: 028559857.
The landscape of NRG1 fusions based on NGS in Chinese solid tumor patients.
Authors: Yuan Shaohua , Chen Hui , Wang Liwei , Dong Xiaowei , Wang Aodi , Wang Kai 
Published: June 2022

e15073 Background: Neuregulin 1 gene ( NRG1) fusions are oncogenic in various tumor types and represent an emerging potential therapeutic target. In the previous reports, NRG1 fusions are overall rare (0.12%) in the Western population, being seen most frequently in NSCLCs. The incidence of NRG1 fusions in a variety of solid tumors based on NGS has been explored limitedly in Chinese patients. Methods: FFPE samples and matched peripheral blood were collected for NGS based 450 cancer genes panel assay and RNA panel assay.Somatic variants were analyzed following CAP/CLIA-certificated workflows, including Single Nucleotide Variant (SNV), Copy Number Variation (CNV), large insertion and deletions (Lindel) and gene rearrangements. Results: A total of 47 patients harboring NRG1 fusions and four of them were detected in RNA level. Non-small cell lung cancer (NSCLC) was the most common cancer type with the incidence of 0.19% (25/13089). The followed cancer types were bone sarcoma, breast carcinoma, pancreatic adenocarcinoma and colorectal carcinoma with the frequency of 0.30% (3/973), 0.16% (3/1850), 0.14% (3/2098) and 0.07% (3/4344) respectively. CD74 (10.1%), SLC34A2 (10.1%) and WRN (4.3%) represented the most common NRG1 fusion partners, other known partners contained CDH1, HMBOX1, ADAM5 and UNC5D. In total, 76.6% of the partners were novel partners, and the most common break points of NRG1 were intron5 and intron1. The 47 NRG1 fusion patients evenly distributed in female (49%) and male (51%), and 44.7% were at advanced stage (stage ≥ III). The median age was 57 years old (range, 8-86 years old) and the median TMB was 3.3 muts/Mb (range, 0-30.5). TP53 (48.9%), CDKN2A (14.9%) and ERBB2/FGFR1/MUC16/SMAD4 (12.8%) were the most common co-occurred mutated gene. In the alterations of ERBB2, 50% were amplifications and 2 patients were breast carcinoma. Only one patient showed ALK fusion and one showed FGFR1 fusion. Among all patients, 8.5% included p.G12X mutation of KRAS and 10.6% included alterations of EGFR with two L858R and two 19del mutations. Conclusions: This study revealed NRG1 fusions in approximately 0.19% of Chinese NSCLC tumor pts and presented the frequency of same common tumors. Also the genomic and clinical feature were analysed. NGS panel sequencing and OrigiFus algorithm showed the advantage of detecting NRG1 fusion and providing structure information of partners which could potentially guide more precise treatment options.
A deep learning approach to discover cyclin-dependent kinases 12 (CDK12) inhibitors in breast cancer.
Authors: Wen Tingyu , Li Lixi , Li Yiqun , Wang Jun , Gao Peng , Xie Guotong , Ma Fei 
Published: June 2022

e15086 Background: Although anti-HER2 tyrosine kinase inhibitors (TKIs) have significantly prolonged survival and improved prognosis in HER2-positive breast cancer patients, resistance is a constant obstacle leading to TKIs treatment failure and tumor progression. Our previous research shows dual inhibition of HER2/CDK12 will prominently benefit the outcomes of patients with HER2-positive breast cancer by sensitizing the tumors to anti-HER2 TKIs treatment. Unfortunately, there is no high selective CDK12 inhibitor in clinical. This study sought to accelerate the CDK12 inhibitor discovery by a deep learning approach. Methods: We developed a large-scale self-supervised graph neural network to learn 11 million unlabelled compounds for molecular representation. And the model was trained with 233,823 kinase domain sequences by drug-target interaction datasets from the BindingDB database. Then, this transformer architecture was used to predict potential CDK12 inhibitors. The candidate hits compounds with diverse skeletons were divided into 50 clusters by clustering analysis. The representative hits with high transform scores and rational binding mode in each cluster were detected in the homogeneous time-resolved fluorescence CDK12 kinase assay. Candidate clusters with half-maximal inhibitory concentrations (IC50) lower than 200 nM were selected into expanded validation and kinase selective panel detection. xCELLigence RTCA system was adopted to monitor cell growth and sensitivity of breast cancer cells to CDK12 inhibitors in a real-time manner. Results: Our predictive transfer learning model yielded satisfactory predictions on various targets including CDK12. We screened a total of 4,527,236 compounds and recommended 50 clusters of potential CDK12 inhibitors for further enzyme activity detection. The IC50 of seven cluster representative compounds is lower than 10 uM. Expanded screening of 500 compounds in these clusters discovered a lot of hits with highly CDK12 selective inhibition. Half of the new compounds are showed promising proliferation inhibition in breast cancer cell lines. Conclusions: Our study provides a highly efficient and end-to-end deep learning approach to discover highly selective CDK12 inhibitors in breast cancer.
The landscape of RAS mutations and hotspots in Chinese patients with solid tumors.
Authors: Li Mei , Li Han 
Published: June 2022

e15114 Background: As one of the most commonly oncogene, RAS mutations ( HRAS, NRAS, KRAS) have been confirmed closely related to the tumorgenesis and proliferation of solid tumors.Yet a comprehensive analysis of RAS mutations and hotspots in Pan-Cancers of Chinese is lacking. Herein, we firstly report the RAS mutation frequency and hotspots features based on a Chinese pan-cancers database, aiming to evaluate the correlation between RAS mutation status and the clinical implication of human cancers. Methods: This was a retrospective study in patients with solid tumors performed NGS panel based on tissue or blood samples in ChosenMed. A cohort of 5420 samples consisting of 22 solid tumor types from Chinese was analyzed to exhibit the landscape of RAS mutations and hotspots. Results: According to our database, the total mutation frequency of KRAS, NRAS, and HRAS was 17.34% (940/5429) in 22 tumor types, of which pancreatic cancer, bowel cancer and endometrial eancer occurred more commonly (with mutation frequencies of 64.04%, 46.07%, and 26.32%, respectively). The RAS mutation hotspots mainly consisted of G12, G13, and Q61, which exhibited preference in each RAS isoforms. For KRAS, G12 mutation site occupied 76.99% (619/804) of all mutations, and mutations at Q61 accounted for 52.83% (28/53) of NRAS mutations. Lastly, HRAS mutations at above three sites presented lowest proportion of 16.83% (17/101). Conclusions: This study firstly reports the RAS mutation characters in pan-cancers based on the Chinese database, which has provided RAS hotspots details for helping to screen more tumor patients who are sensitive to RAS inhibitors. Also, further investigation should be performed for the development of RAS-targeting drugs.
The landscape of NFE2L2 alteration in Chinese solid tumor patients.
Authors: Xian Xiuying , Li Chunhai , Meng Hong , Wang Lixin , Liu Chuang , Meng Fanfan , Li Ling 
Published: June 2022

e15126 Background: NFE2L2 encodes a transcription factor which is a member of a small family of basic leucine zipper (bZIP) proteins. NFE2L2 variations were detected in many tumors, such as lung cancer, esophageal cancer, renal cell carcinoma and other cancer types. The landscape of NFE2L2 gene in solid tumors of Chinese population has not been descripted. Methods: 3193 normal-paired samples from patients with solid tumors were analyzed using hybridization capture-based next generation sequencing, and alterations including single base substitution, short and long insertion/deletions, copy number variations, gene fusions and rearrangements. Results: NFE2L2 gene was altered in 2.0% (65 of 3193) of all solid tumors. The frequency of NFE2L2 variations was assessed in multiple cancer types, including lung cancer (33/1109), liver cancer (10/206), colorectal cancer (6/391), stomach cancer (3/227), cervical cancer (3/112), esophageal cancer (3/53), and other cancer types. A total of 54 variations of NFE2L2 were found, mainly in exon 2 (26/54), exon 5 (11/54), exon 3 (4/54) and exon 4 (2/54), no variation in exon 1. NFE2L2 D16G, D21H, R34_S40del, V36_E45del, F37_E45del, R42P, L48P, K53Tfs*2, L62P, E67Q and L76_E78delinsQ in exon 2 have not been reported before. In addition, we identified copy number amplifications of NFE2L2 in four patients, including three lung squamous cell carcinomas and one cervical squamous cell carcinoma patients. Furthermore, in our cohort, NFE2L2 mutation carriers also owned other actionable or driver mutation, the most frequent one was TP53 (71%), followed by PIK3CA (34%), MLL2 (28%), CDKN2A (31%), and ATR (25%). Analysis of co-mutation correlation of NFE2L2 showed that NFE2L2 variation was correlated with ATR, ACVR1B, TERC and Sox2 ( p<0.001). TERC and SOX2 were mainly copy number amplification at chromosome 3q36, and there is higher amplification frequency at 3q36 in squamous cell carcinoma. In TCGA cohort, the patients with NFE2L2 variations and 3q36 amplification had a longer median survival than those group without 3q36 amplification (63.59 vs 32.04 months, p = 0.0459). Conclusions: NFE2L2 deleterious mutations are highly diverse and present at low to moderate frequencies across many cancers. Our results revealed the potential targeted therapeutic strategies and prognostic analysis among NFE2L2 population with solid tumors should be considered in further study.