bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic relevance of 3q amplification (AMP) in a racially diverse patient population with advanced squamous cell carcinoma of the lung.
Authors: Abu Rous Fawzi , Li Pin , Carskadon Shannon , Gutta Radhika , Potugari Bindu Rani , Gadgeel Shirish M. , Palanisamy Nallasivam 
Published: June 2023

e15142 Background: Amplification (AMP) of 3q is the most common genetic alteration in squamous cell carcinoma of the lung (LUSC) with the most frequently amplified region being 3q26-3q28. It represents one of the most striking molecular differences between LUSC and adenocarcinoma. We identified a minimal common region (MCR) of AMP constituted by 25 genes within a large amplicon on chromosome 3q by analyzing data of 476 patients with LUSC from The Cancer Genome Atlas (TCGA) and extracting copy number alteration data from cBioPortal. Full 25-gene MCR AMP was detected in 46.4% of the cases and was associated with better disease-specific survival (NR vs 9.25 years, 95% CI [5.24-NR]; p = 0.011) and progression-free interval (8 vs 4.9 years, 95% [3.5-NR]; p = 0.020). The TCGA cohort was mainly comprised of Caucasians (69.7%) and patients with early-stage disease (98.7%). We conducted a retrospective pilot analysis to validate the prognostic value of MCR AMP using a racially diverse cohort with advanced LUSC. Methods: We retrieved tissue samples for 33 patients with stage III or stage IV LUSC and collected retrospective data from Electronic Medical Records. The pathologist reviewed the slides to ensure the adequacy of tumor tissue. MCR AMP was evaluated via laboratory- developed FISH probe spanning MCR region. FISH test that showed a cluster of signals with more than 4 copies was regarded as positive; we used a control probe for the 3p arm which is typically not amplified in LUSC. Results: The mean age of the cohort was 69.1 years, 57.6% were males, 39.4% were African Americans (AA) and 54.5% were Caucasians, 66.7% had stage 3, and 33.3% had stage 4. Only 6.1% were never smokers and 84.8% were former smokers. MCR AMP was detected in 54.5% (n = 18) of the cases. PD-L1 status was available for 21 (63%) cases, 6 cases (3 had MCR AMP) were PD-L1 negative (TPS < 1%), and 15 cases (9 had MCR AMP) were PD-L1 positive (TPS > 1%). Consistent with the results observed in the TCGA cohort, MCR amplified cases had a trend towards better overall survival (OS) compared to non-amplified cases (1.74 vs 0.91 years; HR = 0.57, 95% CI [0.26-1.24], p = 0.15) as well as a trend towards better progression-free survival (PFS) (0.90 vs 0.74 years; HR = 0.88, 95% CI [0.43-1.81], p = 0.73). Conclusions: This pilot analysis shows that MCR AMP carries a prognostic value in a racially diverse patient population with advanced LUSC, similar to our observations in the TCGA cohort. Further validation in a large cohort is in progress.
Copy number variation (CNV) calling of MET, MYC, and ERBB2 using PiVAT bioinformatic platform.
Authors: Yu Yao , Zou ShiPing , Wang Jing , Wang Bo , Sun Jing , Zhao Dan , Shi Xinyi 
Published: June 2023

e15145 Background: CNV in tumor-associated genes such as MET, MYC and ERBB2 amplification can lead to cancer progression and poor survival in multiple cancers, and is associated with treatment regimen decision. Whole genome sequencing (WGS) and comprehensive genomic profiling (CGP) panels covering hundreds of genes are currently used to detect CNV in hospitals and CLIA-accredited laboratories. However, cost and complex workflow of WGS/CGP restrict their application in clinical molecular diagnostics. CGP panel covering dozens of genes based on targeted amplicon sequencing (TAS) method is preferred, but it is not ideal to detect CNV accurately due to unique methodology. Here we established a CNV calling toolkit in PiVAT bioinformatic platform to solve CNV calling problems in small-size TAS panel. Methods: 46 CNV positive (CNV+) and 14 CNV negative (CNV-) samples were sequenced using MGISEQ-2000 with a paired end, 2x100 read length protocol and adapter sequences were trimmed from 3’ ends of each read. PiVAT’s CNV calling method is based on double coverage normalization, including one per-sample normalization and one per-amplicon normalization. CNV- samples were used as normalization references. MET, MYC and ERBB2 copy number was investigated to determine sensitivity, specificity, precision, and accuracy of the overall test. Copy number deletion is defined as ratio < 0.8 and amplification is defined as ratio > 1.2. PiVAT CNV output calls were compared against excepted copy number to calculate and plot the concordance. CNVkit and Control-FREEC, 2 other CNV calling tools, were chosen as comparators to compare ERBB2, MET and MYC copy number levels with PiVAT’s CNV caller. Results: Sequencing results from all 46 CNV+ samples showed high coverage uniformity, with > 90% of sites having base coverage depth > 20% of mean coverage for all samples. Average mapping rate and on-target rate of sequencing run, analyzed by PiVAT, were 98.98±0.41% and 98.39±0.45%. Results from PiVAT showed a sensitivity of 97.83% and a specificity of 100% for MET, MYC, ERBB2 amplifications. PiVAT estimated copy number more accurately compared with CNVkit and Control-FREEC. PiVAT’s R2, measuring degree of difference from expected copy number, was greater than CNVkit and Control-FREEC for MET, MYC and ERBB2, with values at 0.78, 0.69 and 0.96, respectively. In contrast, CNVkit and Control-FREEC were on average 77.38% and 164.04% worse. For CNVkit and Control-FREEC, many of MET, MYC and ERBB2 CNV calls were seen at a much lower magnitude than expected. Conclusions: Our studies have shown that PiVAT is a reliable tool for calling CNVs. PiVAT’s sensitivity and accuracy were calculated to be > 97%. And PiVAT outperformed other CNV calling tools, CNVkit and Control-FREEC. This demonstrates that PiVAT’s CNV caller can be used to provide CNV results from TAS panel, and guide relevant cancer diagnosis and clinical decision more accurately.
The landscape of ATM alteration in Chinese solid tumor patients.
Authors: Li Yan , Li Qingcong , Zhang Yaxuan , Lai Yuqing , Yang Zhouchao , Li Yueqin , Liao Yuehan , Yin Lu , Wu Huiting , Zhang Zhengqiong , Hu Libo , Li Ling 
Published: June 2023

e15147 Background: The Ataxia-telangiectasia mutated (ATM) gene is an oncosuppressor, which plays an important role in the repair of DNA double-strand breaks (DSBs). The mutation profiles of ATM gene in Chinese solid tumor patients can help understand pathogenesis, prognosis, and identify targets for therapy. Methods: Using commercial NGS assays, we retrospectively analyzed genomic DNA alterations in normal-paired samples from 1351 patients with malignancies from January 2021 to October 2022, and alterations including single base substitution, short and long insertion/deletions, copy number variations, gene fusions and rearrangements. Results: ATM gene was altered in 6.8% (92 of 1351) of all solid tumors. The frequency of ATM variations was assessed in multiple cancer types, including non-small cell lung cancer 22% (35/159), endometrial carcinoma 15% (2/13), biliary tract tumor 12.1% (7/58), gastric cancer 10.7% (3/28), prostatic cancer 8.3% (1/12), breast cancer 6.7% (2/30), colorectal cancer 6.5% (11/168), thyroid cancer 6.2% (5/80), cervical carcinoma 5.7% (2/35), prostatic cancer 3.9% (2/51), liver cancer 3% (2/66). A total 102 genetic alterations were identified in 92 patients, including 70 missense mutations (69%), 14 nonsense (14%), 9 splicing (9%), 3 frameshift (3%), 2 deletion (2%), 2 copy number variation (2%). Among these patients, 2 had pathogenic germline ATM heterozygous mutations, including one lung adenocarcinoma and one pancreatic cancer. Furthermore, in our cohort, ATM mutation carriers also owned other actionable mutation, the most frequent one was TP53 (41%), followed by APC (29%), KRAS (23%), MLL3 (22%) and BRCA2 (20%). Conclusions: Our findings indicate that ATM alterations are widely mutated in Chinese multiple cancer types, with specific mutations differing largely among different tumor types. ATM alterations warrant further investigation as predictive biomarkers of response to PARP inhibitors or platinum-based therapy.
Frequency of somatic mutations in solid tumor malignancies from inner city minorities: A single center study.
Authors: Cuartas Mesa Maria Cristina , Bemis Thomas Stiles , Tamkus Deimante , Gupta Shweta 
Published: June 2023

e15149 Background: The treatment landscape for solid tumor malignancies continues to change with identification of predictive biomarker targets by next generation sequencing (NGS). However, data from individuals from racial and ethnic minorities are often underrepresented. To bridge this gap, we examined the frequency of actionable biomarker findings with a treatment target outlined in NCCN guidelines in our inner city minority population at John H. Stroger, Jr. Hospital of Cook County. Methods: We examined patients who had FoundationOne CDx or FoundationOne Liquid CDx reports for our adult patients with a solid tumor malignancy between July 2021 through December 2022. We categorized patients as having an actionable biomarker finding if there was a finding reported with a treatment target with indication in a patient’s tumor type as outlined in NCCN guidelines. Statistics were done using t-test, z-test, and chi square tests. Results: A total of 313 patients had a FoundationOne CDx or FoundationOne Liquid CDx report for a solid tumor malignancy. Median age for the population was 64.6 years (range 20-89 years). The majority of patients were African American (50%), followed by Hispanic (31%), Caucasian (13%) and Asian (6%). There were 149 patients (47.6%) that had an actionable biomarker target in their tumor type. Among the 50 total lung adenocarcinoma patients, 20 (40%) had a driver mutation, with 12 (60%) being African American. In 43 colorectal tumors were tested, 16 (37.2%) were KRAS WT, with 6 being African American, 6 Hispanic, and 4 white. Among 27 prostate cancer samples tested, 7 (25.9%) harbored a homologous recombination repair (HRR) gene mutation. Of the patients without an actionable biomarker in their tumor type, 47 patients (15%) had an actionable biomarker finding approved in another tumor type. Of the patients with biomarker targets in another tumor type, mutations in PIK3CA and HRR genes were among the most frequent findings. There were no statistically significant differences in frequency of actionable biomarkers in patient tumor type between gender (P = 0.31) or race (P = 0.63). Conclusions: Our findings showed that nearly half of our patients had a targetable somatic mutation in their tumor type. Even in patients without an actionable biomarker in their specific cancer, those patients may harbor a biomarker finding with an approved target in another cancer. While sample sizes were small to investigate mutational profiles for specific tumor types, future analysis with more samples will allow for better characterization. These findings support increasing NGS testing to better characterize the tumor mutational profiles for our racially underrepresented population, as well as for identifying potential biomarkers for future studies in other tumor types.
PD-L1 expression in patients with multiple tumors and their correlation with genomic mutations.
Authors: Lin Guomin , Yuan Shaohua , Pang Fei 
Published: June 2023

e15152 Background: Immune checkpoint inhibitors (ICIs) is effective in treating tumors expressing PD-L1, however, the reported response rate was low. Inter-tumoral heterogeneity might be one of the reasons for the insensitive of ICIs. In patients with multiple tumors (defined as co-occurrence of more than one malignant lesion in a single or multiple sites), the situation is more complicated. Methods: A total of 67 patients who provided tumor tissues from at least two anatomical sites for assessment of PD-L1 expression by immunohistochemistry (22C3 and/or 28-8 antibodies) was enrolled in this study. Cells with ≥1% staining was defined as a positive result. The sequencing data of 61 patients was also retrospectively reviewed. Targeted sequencing was performed with panels of up to 450 cancer-related genes (at least 47 genes in common). Matched peripheral blood samples were also tested as control to exclude germline mutations. Results: At sample level, the PD-L1 positivity by cancer type was as follow: cervical cancer/melanoma/adrenal gland carcinoma (100% [1/1]), thymic cancer (100% [5/5]), colorectal cancer (80% [8/10]), esophageal squamous cell carcinoma (62% [8/13]), ovarian cancer (57% [4/7]), biliary tract cancer (50% [3/6]), lymph node metastasis (50% [1/2]), pancreatic cancer (50% [2/4]), lung squamous cell carcinoma (43% [3/7]), endometrial cancer (40% [4/10]), breast cancer (29% [2/7]), gastric cancer (25% [2/8]), lung adenocarcinoma (15% [4/26]) and liver cancer (14% [1/7]). All the provided tissues were positive or negative for PD-L1 in 42 patients and were partly positive and partly negative in 25 patients. At patient level, differentially mutated genes between the two above-mentioned groups of patients included CCND1 (10.5% vs 39.1%, P = 0.0116), FGF19 (7.9% vs 30.4%, P = 0.0324), FGF3/4 (7.9% vs 34.8%, P = 0.0143) and TERT (21.1% vs 0%, P = 0.0199). Tumor mutation burden and microsatellite instability status were comparable between the two groups. Consistent with previously reported (not specifically recruiting patients with multiple tumors), EGFR exon 19 deletion was preferentially mutated in PD-L1 negative tumors (16.7% [4/24] vs 0% [0/7], P = 0.5497) in non-small-cell lung cancer, and PD-L1 expression was correlated with EGFR wild-type (wild-type: 75% [3/4] vs mutated: 45% [9/20], P = 0.5901) and ALK mutation (mutated: 25% [1/4] vs wild-type: 5% [1/20], P = 0.3116) in lung adenocarcinoma, although statistical significance was not reached. Conclusions: For patients with multiple tumors, inter-tumoral heterogeneity of PD-L1 expression is common. Several actionable gene mutations were found to be more commonly occurred in PD-L1-heterogenous tumors. Physicians should carefully consider PD-L1 and genomic assessments by case in order to select appropriate patients for ICI treatments.
Identifying anatomopathological factors associated with a Oncotype DX 21-gene recurrence score higher than 25 in menopaused women.
Authors: Guerif Clara , Jamelot Mathieu , Kebir Fatima , Zilberman Sonia , Seknazi Lauren , Barthere Xavier , De Forceville Louise , Theodore Claire , Touboul Cyril , Buob David , Gligorov Joseph , Benderra Marc Antoine 
Published: June 2023

e15156 Background: Oncotype DX recurrence score is a predictive assay clinically used to estimate the risk of distant recurrence for patients with hormone receptor positive (HR+) early breast cancer (EBC) and to predict the benefit of adjuvant chemotherapy, based on molecular factors of the tumor itself. This retrospective study examines the factors that are linked to a Recurrent score (RS) higher than 25, indicating adjuvant chemotherapy for menopaused women with hormone receptor positive early breast cancer. Methods: 157 patients diagnosed with HR+, HER 2 negative early breast cancer who underwent Oncotype DX testing during their treatment between November 2018 and December 2022 were included in the study. Of these 157 patients, 114 were older than 50 years old and with complete data. Univariate and multivariate logistic regression analysis were used to select pathological factors associated with a RS higher than 25. The receiver operating characteristic (ROC) curve was used to assess the optimal threshold of Estrogen receptor (ER), Progesterone receptor (RP) and Ki67. Results: Median age was 65 years (IQR: 59-71). 57 patients (47.5%) had a T1 tumor and 48% of patients had negative lymph nodes. Most of the patients had a Scarff-Bloom-Richardson (SBR) grade 1 (12%) or grade 2 tumor (70%), and 18% of the patients had grade 3 breast cancer. The cell proliferation marker Ki67 was higher than 30 % for 28 patients (23%). The RS was higher than 25 for 17 patients out of 120 patients. Multivariate logistic regression analysis showed that Ki67 higher than 30% was significant associated with RS > 25 (p = 0.01). To predict a RS > 25, the optimal threshold were respectively 80% for the PR, 90% for the ER and 30% for the Ki67. The area under the ROC curve (AUC) were respectively 0.70, 0.60 and 0.88. With the threshold of 30% for Ki67, the sensitivity was 0.76 and specificity 0.89. Conclusions: The use of the Oncotype DX test is validated and useful to better decide the absence of chemotherapy indication in adjuvant situation in some patients with HR+ cancers. However, access to it remains difficult and expensive in some countries with limited resources. Ki67 and SBR grade could be used as an indication for adjuvant chemotherapy but cannot replace Oncotype DX.
Comprehensive genomic profiling and therapeutic implications for patients with advanced cancers: The experience of an academic hospital.
Authors: Teuwen Laure-Anne Marie Nicole , Roets Evelyne , D'Hoore Pieter , Pauwels Patrick , Prenen Hans 
Published: June 2023

e15162 Background: Next generation sequencing (NGS) can be used to detect tumor-specific genomic alterations, with the aim to identify actionable genomic alteration and provide additional treatment options for patients with advanced cancer. While smaller sequencing panels are being applied broadly, controversy exists around the routine implementation of comprehensive genomic profiling with large multigene NGS panels. Indeed, there is an ongoing discussion about the indications as well as timing of comprehensive genomic profiling in patients with advanced solid tumors. Therefore, there is a need for more data to increase understanding of the potential indications and added clinical benefit of routine implementation of broad comprehensive genomic profiling. However, available studies have often been reporting on a small patient population, which complicates the interpretation and translation to the clinical setting. This study aims to describe the feasibility of performing broad NGS panels in patients with advanced cancer in an academic hospital setting, as well as the targetable alterations detected. Methods: In this retrospective study, we analysed genomic alterations in solid tumor biopsies of 464 patients with locally advanced or metastatic cancer. Next generation sequencing was performed using the Foundation Medicine assay (FoundationOneCDx). The therapeutic implications of the genomic alterations were determined using the OncoKB classification. Results: The FoundationOne CDx was successfully applied in 464/521 patients (89%) with a range of cancer types. The most common altered genes were TP53 (61%), followed by KRAS (20%), CDKN2A (20%), TERT (16%), APC (16%), PTEN (14%), PIK3CA (14%) and CDKN2B (14%). Among 419 patients with successfully analyzed tumor mutational burden (TMB), the median TMB was 2.52 (range 0 – 67) mutations/Mb (mut/Mb). Forty-three patients presented with a high-TMB ( > = 10 mut/Mb) of which eight had microsatellite instability. Out of 126 patients with an actionable target (e.g. ERBB2, KRAS, PIK3CA, FGFR2), 40 patients received matched treatment (8.6%), of which 17 were included in clinical trials. Conclusions: This single-center retrospective study shows that broad application of NGS is feasible in an academic center, increases the detection of actionable genomic alterations, and opens opportunities to provide treatment with immune checkpoint inhibitors in case of high tumor mutational burden and microsatellite instability status regardless of tumor histology. The study brings to attention that strategies such as inclusion in clinical (basket) trials and development of new targeted drugs are necessary to improve matched treatment rates. Further research is needed to assess the possible clinical benefit of broad application of NGS and genotype matched treatment.
m6A mediated upregulation of lncRNA CASC9 in head and neck squamous cell carcinoma.
Authors: Karuvantevida Noushad , Arumugam Paramasivam 
Published: June 2023

e15165 Background: Long noncoding RNAs (lncRNAs) are dysregulated in many cancers including head and neck squamous cell carcinoma (HNSCC). Many recent studies have shown that abnormal expression of lncRNA CASC9 (CASC9) is involved in the pathophysiological processes of cancers. N6-methyladenosine (m6A) represents the most common methylation modification of lncRNAs and has been shown to play important roles in the development of different cancer types. However, the potential role of m6A mediated upregulation of CASC9 in HNSCC and its molecular mechanisms remain largely unknown. In the present study, we identified the molecular mechanisms of CASC9 in promoting the malignancy of HNSCC. Methods: We used real-time polymerase chain reaction (qPCR) to identify the level of CASC9 expression in HNSCC clinical samples and cell lines. The oncogenic role of CASC9 in HNSCC was analyzed using online tool UALCAN. RNA immunoprecipitation sequencing (MeRIP-seq) was performed to determine the m6A modification of CASC9. The relationship between CASC9 expression and patients prognosis was analysed using Kaplan-Meier plotter. Loss of function studies used to evaluate cell proliferation, viability, and migration of HNSCC cell lines. Results: Results revealed that m6A mediated CASC9 expression was significantly upregulated in HNSCC tissues than those in the paired adjacent non-tumor tissues. Similarly, m6A mediated CASC9 was significantly overexpressed in the HNSCC cell lines compared with normal cells. The upregulated CASC9 expression was significantly associated with advanced stages and closely correlated to the unfavorable prognosis. m6A was highly enriched within CASC9 and enhanced its RNA stability. Knockdown of CASC9 remarkably inhibited the proliferation, migration and promoted the apoptosis of HNSCC cells. Mechanistically, we found that IGF2BP2 (insulin-like growth factor 2 mRNA binding protein 2), m6A reader could recognize the m6A site in CASC9 and enhance its stability. Conclusions: Overall, this work highlights for the first time that m6A modification enhance CASC9 stability may serve as a potential prognostic biomarker and therapeutic target in HNSCC.