bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genes CNV features in the tumor cells in patients with ovarian serous adenocarcinoma.
Authors: Tsandekova Marieta R. , Porkhanova Natalya V. , Kit Oleg Ivanovich , Kutilin Denis S. 
Published: May 2020

e13641 Background: Serous adenocarcinoma is the most common subtype of ovarian cancer. Early diagnosis of this disease can significantly improve the prognosis. Development of more effective methods for early diagnosis and identification of more reliable markers require understanding the molecular mechanisms underlying the malignant behavior of ovarian epithelial cells. The aim of the study was to analyze the copy number variation (CNV) of genes that regulate apoptosis, DNA repair, cell proliferation, metabolism and estrogen reception in tumor and normal ovarian cells. Methods: For the study, we used tissue sections from FFPE blocks of 65 patients with serous ovarian adenocarcinoma diagnosis. Tumor and normal ovarian epithelial cells were isolated using laser microdissection with non-contact capture (Palm MicroBeam, Carl Zeiss). DNA was extracted from cells using the phenol-chloroform method. CNV of 33 genes (BRAF, KRAS, EGFR, PIK3CA, PTEN, TP53, BRCA1, BRCA2, PRKCI, NOTCH1, AKT1, BAX, CASP7, CASP3, CASP8, CASP9, MDM2, BCL2, CYP1A1, CYP1A1, CYP1A2, CYP1A2, CYP1A2, CYP1A1, CYP1A2, CYP1, ESR2, GPER, STS, SULT1A, SULT1E1, OCT4, SOX2, C-MYC, SOX18, SCNN1A) were determined by Real-Time qPCR method (reference B2M, GAPDH). Statistical analysis was performed using the Mann-Whitney test. For cluster analysis (Hierarchical Clustering, Euclidean distance) scripts in R were used. Results: A statistically significant (p < 0.005) increase in the CNV of PTEN, MDM2, SOX2, CYP1B1, ESR1, and SULT1E1 by 2.0, 2.0, 1.8, 2.5, 3.0 and 2.0 times, respectively, was found, as well as a 2.0-fold decrease in the CNV of CASP3 and CASP8 in tumor cells relatively to normal ones. Cluster analysis allowed us to distinguish 2 groups of serous adenocarcinoma samples that differed in gene CNV (p < 0.005): in group 1 (n = 40), the copy number of the SOX2, MDM2, ESR1, CYP1B1 and SULT1E1 genes was increased and the copy number of the TP53 and BRCA2 genes was reduced, in group 2 (n = 25), copy number of PTEN, PIK3CA, BCL2 was increased and copy number of BAX, CASP3 and CASP8 was lower. Conclusions: CNV analysis revealed the most characteristic markers of ovarian serous adenocarcinoma cells. Based on the differential CNV, 2 molecular subtypes of serous adenocarcinoma were distinguished.
Analysis of germline mutations in Chinese colorectal cancer patients with next-generation sequencing.
Authors: Gao Jing , Ren Hua , Liao Haiyan , Hai Luo , Cong Yuwei , Zhao Xiaochen , Bai Yuezong 
Published: May 2020

e13651 Background: Colorectal cancer (CRC) remains one of the leading causes of morbidity and mortality around the world. Familial cancer syndromes are common in CRC, inherited syndromes including Lynch syndrome (LS), familial adenomatous polyposis (FAP), and MutY human homolog (MUTYH)-associated polyposis (MAP) were well defined. But still, there are not well-established evidence between other several genes and CRC risk. Expanded multi-gene testing may be an alternative to find out the underlying mechanism for genetic susceptibility. Our study aims to assess the germline alternation landscape of Chinese CRC patients. Methods: We performed hybrid capture-based next-generation sequencing (NGS) of 381 genes on tissues from patients with CRC between January 01, 2017 and December 02, 2019 in 3D Medicines database. Genomic alterations including single nucleotide variation (SNV), insertions/deletions, copy number variations, gene rearrangement and fusions were assessed. Results: 1360 CRC patients were included for analysis, in which 95 (7.0%) patients harbored pathogenic (80/95) and likely pathogenic (15/95) germline mutations in 28 cancer predisposition genes. 33 subjects had pathogenic variants associated with Lynch syndrome (15 mutations in MLH1, 9 mutations in MSH2, 6 mutations in MSH6, 3 mutations in PMS2, respectively). 8 subjects had pathogenic variants associated with FAP (3 APC), MAP (3 MUTYH) and Li-Fraumeni syndrome (2 TP53). In addition, 14 pathogenic mutations in moderate penetrance genes (5 ATM, 3 BLM and 6 CHEK2) were found. The frequency of pathogenic BRCA mutations were 1 alternation in BRCA1 and 3 alternations in BRCA2. Conclusions: 7.0 % of patients with Chinese CRC carried germline cancer susceptibility gene mutations. Multi-gene testing would provide references for assessing genetic susceptibility and managing increased surveillance.
The alteration of TERT in 10,000 Chinese patients with solid tumors.
Authors: Lin Jie , Li Yuehua , Zou Hao , Zhang Li , Xiao Yanbin , Pan Qi , Tang Bo , Wu Huan , Shi Jiaochun , Wang Weifeng 
Published: May 2020

e13655 Background: The reactivation of telomerase reverse transcriptase ( TERT) is one of the characters that make cancer cells immortal. TERT expression has been shown in various human cancers.However, the landscape of TERT alterations in Chinese patients with solid tumors still remains unclear. Here, we illustrated the profile of TERT variations of Chinese solid tumor patients by using next generation sequencing (NGS)-based targeted sequencing. Methods: Formalin fixed, paraffin embedded (FFPE) tumor tissues and matching blood samples were collected from 9874 Chinese patients and subjected to a NGS-based panel at a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. All classes of alterations were assessed. Results: FFPE samples from 9874 Chinese solid tumor patients included lung cancers (39.7%), liver cancers (12.5%), colorectal cancers (10.8%), gastric cancers (5.7%), pancreatic cancers (4.9%), biliary tract tumors (4.6%), and other 18 cancer types (21.7%) were assessed. And 1187 (12.0%) out of 9874 cancer samples had TERT variations. TERT variations occurred in all types of cancer with various frequencies: urothelial neoplasms (52.0%), central nervous system tumors (40.0%), melanomas (38.9%), liver cancers (30.7%), thyroid tumors (24.3%), cervical cancers (20.6%), biliary tract tumors (16.3%), head and neck tumors (14.6%), soft tissue tumors (12.2%) and lung cancers (10.3%). Substitution was the most common variation of TERT and accounted for 58.7% of all the alterations, followed by gene amplification (38.8%) and fusions (2.4%). There were 86.8% of substitution variations presented in TERT promoter region comprising of c.-124C > T (70.7%) and c.-146C > T (13.1%). Patients with TERT alterations included 414 females and 773 males with a median age of 59 years old (range: 8-88). Tumors included stage IV (34.0%), stage III (22.2%), stage II (12.7%), stage I (18.7%) and stage 0 (12.3%). TERT variations were correlated with patients’ age (p = 0.00083) and gender (p = 5.59×10−7). There was no significant correlation of TERT alterations with the highly mutated TP53. The frequencies of TERT alterations were similar in patients with mutated and wild type TP53 (12.7% vs 11.1%). Conclusions: Our study revealed that 12.0% Chinese solid tumor patients harbored TERT alterations, especially two hotspots mutations (c.-124C > T and c.-146C > T) in the promoter region. TERT variations had a correlation with patients’ age and gender, but no correlation with hotspot TP53 mutations.
Genomic comparisons between different radiological features in ground glass nodules under 20 mm in diameter.
Authors: Peng Muyun , Zhang Bingyu , Xing Guanlan , Xu Yaping , Yu Fenglei 
Published: May 2020

e13664 Background: Radiological features still matters in the management of ground glass nodules (GGNs). The 20 mm in maximum diameter and consolidation tumor ratio (CTR) under 0.5 are pivotal indexes from the lobectomy to segmentectomy decision. However, the feasibility of limited resection remains controversial. Understanding the relationship between genomic characteristics and radiological features of GGNs will provide critical insights to theoretical basis of surgical method decision and expand a novel perspective to risk-stratify patients. Methods: In total, 297 surgically resected GGNs (≤ 20 mm in maximum diameter) were consecutively collected in the study. The summarized radiological features are shown (Table). In order to obtain their comprehensive genomic profiling, these tumor samples were performed using customized panels of 1021 genes. Fisher's exact test, Mann Whitney test and Kruskal-Wallis test were used for statistical analysis. Results: Higher TMB was found in subgroups with the maximum diameter > 10 mm, the volume > 0.40 mL, the CT value > -500 HU, and the mass > 200 mg ( p < 0.05). However, TMB was not associated with the increase of CTR. These data suggested that enlarged nodules occurred with increased mutation events. EGFR, RET, TP53 and RBM10 mutations were significantly enriched in groups with maximum diameter > 10 mm, volume > 0.40 mL, and mass > 0.200 g ( p < 0.05), and significant enrichment in p53-pathway and Myc-pathway were also found ( q < 0.05). ERBB2 and BRAF mutations were significantly enriched in the subgroups with maximum diameter ≤ 10 mm, volume ≤ 0.40 mL, or mass ≤ 0.200 g ( p < 0.05). As compared to the cohort of CTR ≤ 0.5 in all nodules, mutation frequencies of EGFR, RBM10 were similar, those of RET, ALK and TP53 were relatively higher ( p < 0.05), and that of ERBB2 was lower ( p = 1.7×10−5) in the cohort of CTR > 0.5. Conclusions: Our study provides the comprehensive description of the mutational landscape and radio-genomic features of GGNs under 20 mm in diameter. [Table: see text]
Development CRISPR-Cas12-based rapid EGFR mutation detection kit.
Authors: Kunimasa Kei , Bando Yuya , Shiraishi Miyako , Aizawa Emi , Nishino Kazumi , Tamiya Motohiro , Inoue Takako , Kuhara Hanako , Kawachi Hayato , Kuno Kika , Imamura Fumio , Iwai Shigenori , Kumagai Toru , Suzuki Keiichiro 
Published: May 2020

e13669 Background: Recently, several cancer gene panel tests have been developed to determine many driver mutations including lung cancer simultaneously. However, the current next-sequencing based platform is not ideal testing method in the clinical practice due to the high examination cost and the time required for the result to reach the field. By refining recently reported CRISPR-Cas-based nucleic acid detection methods, we developed a novel CRISPR-Cas12 family based rapid-detection kit for targetable EGFR mutations in non-small lung cancer (NSCLC) patients. Methods: To develop a powerful CRISPR-based testing method, we focused on unique Cas12 family proteins which contain a single RuvC nuclease domain that cleave target double-stranded DNA adjacent to protospacer adjacent motif (PAM) sequences as well as non-target single-stranded DNA (ssDNA) collaterally. We purified 6 Cas12 family proteins (Cas12a, Cas12c1, Cas12c2, Cas12g, Cas12i1, and Cas12i2) as well as two types of target-defined guide RNA for EGFR Ex.19 del(E746-A750) and L858R mutations. The target sequences including EGFR Ex.19(E746-A750) and L858R mutations were amplified from EGFR mutated cell lines, FFPE lung cancer tissues or cell free DNA (cfDNA) of NSCLC patients using PCR with PrimeSTAR GXL DNA polymerase (Takara, Shiga, Japan) or isothermal recombinase polymerase amplification (RPA) with TwistAmp Basic (TwistDx, Cambridge, UK). CRISPR-Cas12-based cleavage assay was conducted in a reaction buffer consisting of 10 nM Cas12 proteins, 10 nM purified guide RNA, 0.4nM target DNA, and 50 nM collateral ssDNA (quenched fluorescent DNA reporter) in a 20 μl volume at 37 °C for 1 h. The excited fluorescence, which is an indicator of the presence of target cancer mutation, was measured by Synergy H1 hybrid Multi-Mode Reader (BioTek, Vermont, USA). For simpler instrument-free and portable detection lateral flow readouts were also developed and tested using Milenia HybriDetect1 kit (TwistDx). Results: Cas12a, Cas12i1, Cas12i2-based assays successfully detected the EGFR Ex.19 del(E746-A750) and L858R mutations from PCR and RPA products. Lateral flow readout kit could also detect EGFR Ex.19 del (E746-A750) mutation from cfDNA derived from NSCLC patients. It took about 3 hours from plasma collection to DNA extraction, RPA, and measurement with the kit. Conclusions: CRISPR-Cas based lateral flow readout kit can detect EGFR mutation at an unprecedented pace with low cost. Our developed system will be an innovative testing tool for lung cancer patients with low cost, rapid, multiplexable, and noninvasive procedure.
Ki-67 versus MammaPrint/BluePrint for assessing luminal type breast cancer.
Authors: Tian Chen , Fu Lili , Wei Jiyu , Yin Pengfei , Zhang Henghui 
Published: May 2020

e13673 Background: Ki-67 is widely used for risk stratification in patients with ER+/HER2- breast cancer. The multigene assay, MammaPrint/BluePrint (MP/BP) test, is validated as a good predictor of recurrence in patients with Luminal type breast cancer and a good tool of molecular subtyping classification. Previous study showed that MP/BP test was able to re-stratify 54% of patients with a Luminal-B pathological subtyping (PS) to a low-risk Luminal A-type group. But there is no study directly show the comparison between Ki67 and MP/BP test result. Here in this study, we compare Ki-67 with MP/BP test result in Chinese patients with luminal type breast cancer. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumour samples or fresh tumour samples from 1008 eligible breast cancer patients were collected from 122 hospitals in China. Tumor RNAs were isolated from samples and analyzed using RNA sequencing technology. Ki-67 protein expression were assessed in FFPE tissue blocks by IHC. The pathology subtyping of patient was categorized based on the 2013 St. Gallen. Comparison of MP/BP result with Ki-67 IHC was performed. Concordance between subtyping by the MP/BP and PS was also evaluated. Results: Of 1008 patients with ER+/HER2- breast cancer, 640 were MP Low-Risk and 368 were MP High-Risk. MammaPrint index was significantly associated with Ki-67 expression (p < 0.001). Among the patients with Ki-67 value lower than 15%, 81.11% were MP Low-Risk, while 65.12% of patients with Ki-67 value between 15%-20% and 46.67% of patients with Ki-67 value between 21%-30% were MP Low Risk. Of the patients with Ki-67 value higher than 30%, 77.24% were MP High-Risk. Among the 453 patients with PS Luminal-A tumours, 77 (17%) were categorized as Luminal-B by MP/BP test. While among the 555 patients with PS Luminal-B tumours, 265 (48%) were categorized as Luminal-A by MP/BP test. Conclusions: Our results show that for the patients with low Ki-67 value ( < 15%) or high Ki-67 value ( > 30%), the risk prediction by MP test are mostly agree with Ki-67 IHC, while for the patients with intermediate Ki-67 value (15-30%), MammaPrint test may provide more information. And compare with the traditional pathological factors, MP/BP test can help to identify a large group of patient with low risk of recurrence.
Clinical use of RNA sequencing and oncobox analytics to predict personalized targeted therapeutic efficacy.
Authors: Poddubskaya Elena , Sorokin Maxim , Garazha Andrew , Glusker Alex , Moisseev Alexey , Sekacheva Marina , Suntsova Maria , Kim Ella L , Gaifullin Nurshat , Tkachev Victor , Giese Alf , Barbara Viktoria , Borisov Nikolay , Buzdin Anton 
Published: May 2020

e13676 Background: Analysis of mutation profiles in cancer patients does not provide clinical benefits in 80-90% of cases in the US (Marquart et al., 2018). Gene expression analysis potentially complements standard detection of clinically relevant mutations. Methods: 239 adult late-stage cancer patients. RNA gene expression sequencing completed on solid tumor samples using FFPE blocks. Patient mRNA profiles were analyzed using Oncobox bioinformatics, prioritizing target drugs according to their personalized predicted efficacy. Summary reports were provided to oncologists and resulting treatment selection and outcomes were assessed. Results: As of February 2020, feedback was received from participating doctors for 224 patients; 34 patients died before therapy prescription, 52 patients received treatment other than targeted therapy (chemo, surgery, radiation, or palliative care), 75 patients received at least one targeted therapy (single or combination therapy) predicted to be effective based on Oncobox analysis (“RNAseq cohort”). 63 patients received chemo or other drug therapy predicted to be potentially ineffective from Oncobox analysis (“other cohort”). Therapeutic response was obtained on 46 patients with biopsies collected no longer than 6 months prior to analysis who had no further surgery (30 in the RNAseq cohort and 16 in the other cohort). 63% of the RNAseq cohort obtained either partial response or stable disease using Oncobox guided therapies, compared to 44% of the other cohort (19% increase of disease control). The RNAseq cohort had higher mean prior therapies (1.3) compared to the other cohort (0.8) indicating more advanced disease. The similarly designed WINTHER trial reported ~8% increase of disease control using gene expression-guided vs mutation-guided therapeutics in a cohort of advanced cancer patients averaging three prior therapies (Rodon et al., 2019). Conclusions: Collectively these data suggest that gene expression profiling provides a more clinically relevant therapeutic match, and better response rates, than mutation guided therapeutic treatments. This potentially results in improved clinical outcomes for cancer patients. Clinical trial information: NCT03724097.
Genetic testing experiences and emotional reactions among individuals with variant of uncertain significance results from cancer multiplex genetic testing.
Authors: Hamilton Jada G. , Brower Jamie , Clark Dana , Ebrahimzadeh Jessica E , Kane Sarah R. , Sanchez Pauleen , Wildman Temima , Merrill Margaret , Couch Fergus , Garber Judy Ellen , Offit Kenneth , Robson Mark E. , Domchek Susan M. 
Published: May 2020

e13680 Background: Multiplex genetic testing (MGT) simultaneously analyzes multiple cancer susceptibility genes and can reveal genetic variants of uncertain significance (VUS) that have unclear associations with cancer risks. Little is known about how people are prepared for receiving VUS results from MGT, or whether their emotional reactions differ based on the levels of cancer risk to which they may be susceptible. Methods: We recruited participants from the online Prospective Registry of Multiplex Testing (PROMPT). Those with only a VUS in a cancer predisposition gene completed a survey including measures of their MGT experience, distress (range 0-30; α = .87), uncertainty (0-45; α = .83), and positive experiences (0-20; α = .75). We used generalized linear modeling to examine how demographics, awareness of the possibility of VUS before testing, and level of cancer risks associated with their VUS gene were related to emotional outcomes. Results: Data were available from 661 individuals (40% response rate, 95% female, 90% white, 78% college graduate, 69% cancer history, age 23-93) with VUS in a gene of high risk (47%), moderate/low risk (35%) or limited evidence of risk (18%). Among the sample, 80.8% reported ever receiving cancer genetic counseling, and only 50.8% reported being aware of the possibility of VUS when deciding about testing. Participants reported low current distress ( M± SD= 3.25±5.19), uncertainty (9.18±8.35) and positive experiences (7.83±5.98). Distress was associated with younger age, less family cancer history, and being unaware of the possibility of VUS before testing; distress was also higher among those with VUS in a gene of high risk than those with VUS in a gene of moderate/low risk or limited evidence of risk ( ps≤.023). Uncertainty was associated with younger age, non-white race, less education, and being unaware of the possibility of VUS; uncertainty was also higher among those with VUS in a gene of high risk than those with VUS in a gene with limited evidence of risk ( ps≤.05). Fewer positive experiences were associated with more education and more family cancer history; those with VUS in a gene of high risk had fewer positive experiences than those with VUS in a gene with limited evidence of risk ( ps≤.03). Conclusions: Many individuals undergoing MGT may not fully understand the prospect of receiving VUS. Clinicians should consider patients’ background, preparation, and level of cancer risk to which they are potentially susceptible, as these factors may affect their emotional adaptation.
Clinical and analytical validation of FoundationOne Liquid CDx, a novel 324-gene blood-based comprehensive genomic profiling assay.
Authors: Woodhouse Ryan , Dennis Lucas , Li Meijuan , Burns Christine , Ma Pei , Meng Wei , Dewal Ninad , Vietz Christine , Hegde Priti 
Published: May 2020

e13685 Background: As the availability of precision therapies expand, a well-validated blood-based comprehensive genomic profiling (CGP) assay has the potential to provide considerable value as a complement to tissue-based testing to ensure that potentially life-extending therapies are administered to the patients most likely to benefit. Comprehensive clinical and analytical validity data for blood-based assays are crucial to enabling physicians to understand the true performance of available testing options. Methods: The FoundationOne Liquid CDx assay is a blood-based CGP assay that has been validated for a Premarket Approval (PMA) submission to the Food and Drug Administration (FDA). Validation studies included > 9,000 tests and > 30,000 unique variants across > 300 genes and > 50 cancer types, allowing for a comprehensive assessment of performance. Results: The results of these extensive studies demonstrate a 95% limit of detection (LoD) of 0.40% variant allele fraction (VAF) for select short variants (subs and indels), 0.37% VAF for select rearrangements, 21.7% tumor fraction (TF) for select copy number amplifications, and 30.4% TF for copy number losses. LoD for complex biomarkers such as microsatellite instability (MSI) and blood tumor mutational burden (bTMB) were also determined. The limit of blank (LoB) was shown to be the ideal value of zero. Reproducibility of variant calling was determined to be 99.59% with two-sided exact CI of (99.58%, 99.60%). In comparison with an orthogonal method, an overall PPA (95% CI) of 96.3% (94.8, 97.4%) and NPA (95% CI) of > 99.9% (99.9%, 100.0%) was observed. Critically, clinical validity and concordance with tissue-based CGP results across multiple tumor types were also evaluated. Conclusions: The results of these studies demonstrate that FoundationOne Liquid CDx accurately and reproducibly detects the major types of genomic alterations (short variants, rearrangements, and copy number alterations), as well as complex biomarkers, such as MSI, bTMB, and tumor fraction. These data demonstrate that the assay can identify genomic variants that may inform therapeutic decisions for cancer patients with any solid tumor using a single blood sample. Additionally, clinical validation results establish FoundationOne Liquid CDx as an additional tool for physicians in the therapeutic management of cancer patients.