Article
Microbiology
Thomas Sondergaard Stenum, Mette Kongstad, Erik Holmqvist, Birgitte Kallipolitis, Sine Lo Svenningsen, Michael Askvad Sorensen
Summary: Three out of seven ribosomal RNA operons in Escherichia coli end in dual terminator structures, with sRNA genes (rrA, rrB, rrF) between the terminators showing high sequence similarity and interacting with Hfq and CsrA. Deletion or overexpression of these sRNAs has modest effects on known CsrA-regulated phenotypes, indicating their potential role in fine-tuning growth-phase-dependent processes in the cell. The conserved primary and secondary structure of these small RNAs across different genera of Enterobacteriales suggests a common functional significance.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Sulev Koks, Abigail L. Pfaff, Vivien J. Bubb, John P. Quinn
Summary: This study identified the association between ApoE and MAPT haplotypes with the gene expression related to neurodegeneration using transcriptome data from the PPMI cohort. The ApoE e4 haplotype showed a significant effect on TOMM40 transcripts, while MAPT haplotypes had differential impact on various transcripts, including the largest up-regulating and down-regulating effect sizes on LRRC37A2 transcripts. This research provides insights into the molecular mechanisms underlying genetic variations in neurogenerative diseases.
Article
Medicine, Research & Experimental
Runrun Zhang, Cen Chang, Yehua Jin, Lingxia Xu, Ping Jiang, Kai Wei, Linshuai Xu, Shicheng Guo, Songtao Sun, Dongyi He
Summary: This study identified novel DNA methylation-regulated differentially expressed genes (MeDEGs) in rheumatoid arthritis (RA) through integrated analysis of DNA methylation and RNA-Seq data. The results suggest that RGS1 could serve as a potential methylated biomarker for RA.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Genetics & Heredity
Shalini Rajagopal, Akanksha Sharma, Anita Simlot, Praveen Mathur, Sudhir Mehta, Sumita Mehta, Jalaja Naravula, Krishna Mohan Medicherla, Anil Kumar, Uma Kanga, Renuka Suravajhala, Ramji Kumar Bhandari, Bipin G. Nair, P. B. Kavi Kishor, Prashanth Suravajhala
Summary: This study focuses on exploring differentially expressed genes (DEGs) and variants associated with Vitamin K (VK) disease phenotypes (such as myocardial infarction, renal failure, and prostate cancer), aiming to find common pathogenic variants and discussing the role of long noncoding RNAs (lncRNAs) in the biogenesis of VK deficiencies.
Article
Multidisciplinary Sciences
Changsheng Guo, Yuanqing Hua, Zuanhao Qian
Summary: This study identified differentially expressed lncRNAs and genes in Kawasaki disease (KD), as well as constructed ceRNA networks involving miRNAs and mRNAs. The study found specific lncRNAs (PSORS1C3, LINC00999, SNHG5) and genes (GATA3, SOD2, MAPK14, PPARG) that may play a key role in the pathogenesis and development of KD. Validation in a separate dataset showed that intravenous immunoglobulin treatment alleviated the deregulated RNA profiles in KD patients.
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Cell Biology
Wei Tian, Kegong Chen, Guangcan Yan, Xinhao Han, Yanlong Liu, Qiuju Zhang, Meina Liu
Summary: This study identified eRNA-regulated immune-related genes (IRGs) in gliomas and constructed a novel prognostic model. The regulation of these IRGs by eRNAs was associated with immune-related dysfunctions in the tumor microenvironment. Targeting these IRGs could improve immunotherapeutic/therapeutic outcomes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Zimo Huang, Jun Wang, Zhongmin Yan, Maozu Guo
Summary: This paper proposes a Multiple Self-Attention (Epi-MSA) model for predicting differentially expressed genes (DEGs) from epigenetic data. The model uses convolutional neural networks for information embedding and multiple self-attention encoders to learn important gene locations. Experimental results show that Epi-MSA outperforms existing methods in performance and stability, and has good interpretability.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Hai-Bo Zhang, Xiao-Bao Ding, Jie Jin, Wen-Ping Guo, Qiao-Lei Yang, Peng-Cheng Chen, Heng Yao, Li Ruan, Yu-Tian Tao, Xin Chen
Summary: The house mouse is a valuable mammalian model for genetic research, offering insights into human diseases. To facilitate molecular mechanism studies in mice, researchers have developed the Mouse Interactome Database and a gene set linkage analysis web tool.
Article
Biology
Rachel Knoener, Edward Evans, Jordan T. Becker, Mark Scalf, Bayleigh Benner, Nathan M. Sherer, Lloyd M. Smith
Summary: HIV-1 generates different classes of RNA that play distinct roles in viral replication, and understanding their interactions with host proteins is crucial. The HyPR-MSSV technique can isolate different types of HIV-1 RNA and identify their protein interactomes, revealing factors that impact HIV-1 gene expression.
Article
Microbiology
Yiyan Yang, Keith Dufault-Thompson, Rafaela Salgado Fontenele, Xiaofang Jiang
Summary: This study demonstrates the formation of viral-host chimeric RNAs in SARS-CoV-2-infected cells and identifies two genomic insertions derived from human rRNA regions. These findings provide direct evidence for the significance of host-derived insertions in viral evolution.
Article
Endocrinology & Metabolism
Yongjin Li, Chao Kong, Baobao Wang, Wenzhi Sun, Xiaolong Chen, Weiguo Zhu, Junzhe Ding, Shibao Lu
Summary: Lower back pain is a common reason for dyskinesia, with paraspinal muscle degeneration identified as a contributing factor. Muscle atrophy, oxidative stress, reactive oxygen species, and inflammation are all associated with this degeneration. Research on the molecular mechanisms behind paraspinal muscle degeneration could provide important insights into potential treatments.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Genetics & Heredity
Alexandra N. Nail, Brett T. Spear, Martha L. Peterson
Summary: The mammalian Cytochrome P450 (Cyp) gene superfamily encodes enzymes involved in metabolic pathways and are frequently expressed in the liver. Despite high sequence similarity, Cyp2a4 and Cyp2a5 genes exhibit differential expression in adult mouse liver, potentially regulated by unique antisense long noncoding RNAs. These antisense transcripts, found in different liver zones, show sex-biased expression patterns earlier than their corresponding sense mRNAs, providing insights into transcriptional and post-transcriptional mechanisms governing Cyp2a4 and Cyp2a5 expression.
Article
Biochemistry & Molecular Biology
Dong Hwan Ho, Hyejung Kim, Daleum Nam, Jinju Heo, Ilhong Son
Summary: This study found that nuclear alpha-Synuclein (alpha Syn) plays an important role in the pathogenesis of Parkinson's disease (PD). Overexpression of alpha Syn conjugated with a nuclear localization signal (NLS) increased cytotoxicity and apoptotic markers in mouse embryonic fibroblasts (MEF). The presence of NLS-alpha Syn also led to changes in nucleolar structure and abnormal ribosomal RNA processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Sizhong Guan, Linge Jian, Ye He, Yanna Su, Liping Zhou
Summary: This study identified key methylation-regulated genes in glioblastoma and investigated their functions. The hyper-methylation of CASP1, CFH and TTLL7 was found to be significantly correlated with patient prognosis, and their methylation levels were negatively correlated with mRNA levels in GBM cell lines.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2022)
Article
Neurosciences
Qunxi Dong, Jie Zhang, Qingyang Li, Junwen Wang, Natasha Lepore, Paul M. Thompson, Richard J. Caselli, Jieping Ye, Yalin Wang
JOURNAL OF ALZHEIMERS DISEASE
(2020)
Article
Oncology
Bingjue Li, Chaohong Zhu, Lihua Dong, Jing Qin, Wenyu Xiang, Alan J. Davidson, Shi Feng, Yucheng Wang, Xiujin Shen, Chunhua Weng, Cuili Wang, Tingting Zhu, Lisha Teng, Junwen Wang, Christoph Englert, Jianghua Chen, Hong Jiang
JOURNAL OF PATHOLOGY
(2020)
Article
Multidisciplinary Sciences
Md Mahmudul Hasan, Sumi Sukumaran Nair, Jacqueline G. O'Leary, LuAnn Thompson-Snipes, Verah Nyarige, Junwen Wang, Walter Park, Mark Stegall, Raymond Heilman, Goran B. Klintmalm, HyeMee Joo, SangKon Oh
Summary: The expression of TIGIT in memory B cells plays a critical role in immune regulation. Regulatory B cells have been shown to modulate the immune system effectively.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Leland S. Hu, Lujia Wang, Andrea Hawkins-Daarud, Jennifer M. Eschbacher, Kyle W. Singleton, Pamela R. Jackson, Kamala Clark-Swanson, Christopher P. Sereduk, Sen Peng, Panwen Wang, Junwen Wang, Leslie C. Baxter, Kris A. Smith, Gina L. Mazza, Ashley M. Stokes, Bernard R. Bendok, Richard S. Zimmerman, Chandan Krishna, Alyx B. Porter, Maciej M. Mrugala, Joseph M. Hoxworth, Teresa Wu, Nhan L. Tran, Kristin R. Swanson, Jing Li
Summary: The study developed a radiogenomics machine learning model to quantify uncertainty and predict EGFR amplification status, aiming to address intratumoral genetic heterogeneity and improve personalized therapeutic paradigms. The model used probability distributions to quantify uncertainty for each sample prediction and implemented transductive learning to reduce overall uncertainty.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Jing Qin, Yaohua Hu, Jen-Chih Yao, Ricky Wai Tak Leung, Yongqiang Zhou, Yiming Qin, Junwen Wang
Summary: Cell fate conversion by overexpressing defined factors is a powerful tool in regenerative medicine, but identifying key factors for efficient conversion is challenging. Utilizing various OMICs data and computational methods can help predict master transcription factors for successful and complete cell fate conversion, ultimately improving the effectiveness and reducing costs of experimental processes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Xinyi Tang, Zhi-Zhang Yang, Hyo Jin Kim, Theodora Anagnostou, Yue Yu, Xiaosheng Wu, Jun Chen, Jordan E. Krull, Kerstin Wenzl, Patrizia Mondello, Vaishali Bhardwaj, Junwen Wang, Anne J. Novak, Stephen M. Ansell
Summary: This study found that regulatory T-cells (Treg) are more abundant in the spleens of patients with splenic marginal zone lymphoma (SMZL) compared to reactive spleens. These Tregs can be separated into CD161(+)Treg and CD26(+)Treg subsets. CD161(+)Tregs are increased in SMZL but have dysregulated immune function. CD161(+)Tregs are associated with a favorable prognosis in SMZL, while CD26(+)Tregs are associated with a poor prognosis. Activation of the IL2/STAT5 pathway contributes to the expansion of CD26(+)Tregs and may lead to a poor clinical outcome in SMZL.
CLINICAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Navid Ahmadinejad, Shayna Troftgruben, Junwen Wang, Pramod B. Chandrashekar, Valentin Dinu, Carlo Maley, Li Liu
Summary: Understanding intratumor heterogeneity is crucial for studying tumorigenesis and designing personalized treatments. This study presents a novel algorithm, MAGOS, that successfully identifies subclones in tumors sequenced at low depths and outperforms existing methods in terms of decomposition accuracy, minimum sequencing depth, and computation efficiency. The analysis of late-stage liver cancers using MAGOS revealed that a high subclone count in a tumor is a significant risk factor for poor prognosis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Letter
Pediatrics
Juan M. Farina, Yanxi Chen, Dawn E. Jaroszewski, Peter Bostoros, Junwen Wang
JOURNAL OF PEDIATRIC SURGERY
(2023)
Article
Immunology
Qixia Shen, Lisha Teng, Yucheng Wang, Luying Guo, Feng Xu, Hongfeng Huang, Wenqing Xie, Qin Zhou, Ying Chen, Junwen Wang, Youying Mao, Jianghua Chen, Hong Jiang
Summary: This study identifies novel genes related to the recurrence of FSGS after kidney transplantation, with MDH2 being a susceptibility gene for FSGS recurrence. The MDH2 c.26C >T mutation may contribute to progressive podocyte injury in these patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Neurosciences
Jianfeng Wu, Yi Su, Yanxi Chen, Wenhui Zhu, Eric M. Reiman, Richard J. Caselli, Kewei Chen, Paul M. Thompson, Junwen Wang, Yalin Wang
Summary: The study aims to build a surface-based model to detect differences in tau deposition patterns and hippocampal atrophy between APOE subgroups, and to use the extracted features to predict cognitive decline. The results illustrate that APOE-specific morphometry features are correlated with AD progression and can better predict future AD conversion compared to other MRI biomarkers.
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Multidisciplinary Sciences
Jianxin Shi, Kouya Shiraishi, Jiyeon Choi, Keitaro Matsuo, Tzu-Yu Chen, Juncheng Dai, Rayjean J. Hung, Kexin Chen, Xiao-Ou Shu, Young Tae Kim, Maria Teresa Landi, Dongxin Lin, Wei Zheng, Zhihua Yin, Baosen Zhou, Bao Song, Jiucun Wang, Wei Jie Seow, Lei Song, I-Shou Chang, Wei Hu, Li-Hsin Chien, Qiuyin Cai, Yun-Chul Hong, Hee Nam Kim, Yi-Long Wu, Maria Pik Wong, Brian Douglas Richardson, Karen M. Funderburk, Shilan Li, Tongwu Zhang, Charles Breeze, Zhaoming Wang, Batel Blechter, Bryan A. Bassig, Jin Hee Kim, Demetrius Albanes, Jason Y. Y. Wong, Min-Ho Shin, Lap Ping Chung, Yang Yang, She-Juan An, Hong Zheng, Yasushi Yatabe, Xu-Chao Zhang, Young-Chul Kim, Neil E. Caporaso, Jiang Chang, James Chung Man Ho, Michiaki Kubo, Yataro Daigo, Minsun Song, Yukihide Momozawa, Yoichiro Kamatani, Masashi Kobayashi, Kenichi Okubo, Takayuki Honda, Dean H. Hosgood, Hideo Kunitoh, Harsh Patel, Shun-ichi Watanabe, Yohei Miyagi, Haruhiko Nakayama, Shingo Matsumoto, Hidehito Horinouchi, Masahiro Tsuboi, Ryuji Hamamoto, Koichi Goto, Yuichiro Ohe, Atsushi Takahashi, Akiteru Goto, Yoshihiro Minamiya, Megumi Hara, Yuichiro Nishida, Kenji Takeuchi, Kenji Wakai, Koichi Matsuda, Yoshinori Murakami, Kimihiro Shimizu, Hiroyuki Suzuki, Motonobu Saito, Yoichi Ohtaki, Kazumi Tanaka, Tangchun Wu, Fusheng Wei, Hongji Dai, Mitchell J. Machiela, Jian Su, Yeul Hong Kim, In-Jae Oh, Victor Ho Fun Lee, Gee-Chen Chang, Ying-Huang Tsai, Kuan-Yu Chen, Ming-Shyan Huang, Wu-Chou Su, Yuh-Min Chen, Adeline Seow, Jae Yong Park, Sun-Seog Kweon, Kun-Chieh Chen, Yu-Tang Gao, Biyun Qian, Chen Wu, Daru Lu, Jianjun Liu, Ann G. Schwartz, Richard Houlston, Margaret R. Spitz, Ivan P. Gorlov, Xifeng Wu, Ping Yang, Stephen Lam, Adonina Tardon, Chu Chen, Stig E. Bojesen, Mattias Johansson, Angela Risch, Heike Bickeboeller, Bu-Tian Ji, H-Erich Wichmann, David C. Christiani, Gadi Rennert, Susanne Arnold, Paul Brennan, James McKay, John K. Field, Sanjay S. Shete, Loic Le Marchand, Geoffrey Liu, Angeline Andrew, Lambertus A. Kiemeney, Shan Zienolddiny-Narui, Kjell Grankvist, Mikael Johansson, Angela Cox, Fiona Taylor, Jian-Min Yuan, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Hyo-Sung Jeon, Shih Sheng Jiang, Jae Sook Sung, Chung-Hsing Chen, Chin-Fu Hsiao, Yoo Jin Jung, Huan Guo, Zhibin Hu, Laurie Burdett, Meredith Yeager, Amy Hutchinson, Belynda Hicks, Jia Liu, Bin Zhu, Sonja I. Berndt, Wei Wu, Junwen Wang, Yuqing Li, Jin Eun Choi, Kyong Hwa Park, Sook Whan Sung, Li Liu, Chang Hyun Kang, Wen-Chang Wang, Jun Xu, Peng Guan, Wen Tan, Chong-Jen Yu, Gong Yang, Alan Dart Loon Sihoe, Ying Chen, Yi Young Choi, Jun Suk Kim, Ho-Il Yoon, In Kyu Park, Ping Xu, Qincheng He, Chih-Liang Wang, Hsiao-Han Hung, Roel C. H. Vermeulen, Iona Cheng, Junjie Wu, Wei-Yen Lim, Fang-Yu Tsai, John K. C. Chan, Jihua Li, Hongyan Chen, Hsien-Chih Lin, Li Jin, Jie Liu, Norie Sawada, Taiki Yamaji, Kathleen Wyatt, Shengchao A. Li, Hongxia Ma, Meng Zhu, Zhehai Wang, Sensen Cheng, Xuelian Li, Yangwu Ren, Ann Chao, Motoki Iwasaki, Junjie Zhu, Gening Jiang, Ke Fei, Guoping Wu, Chih-Yi Chen, Chien-Jen Chen, Pan-Chyr Yang, Jinming Yu, Victoria L. Stevens, Joseph F. Fraumeni, Nilanjan Chatterjee, Olga Y. Gorlova, Chao Agnes Hsiung, Christopher I. Amos, Hongbing Shen, Stephen J. Chanock, Nathaniel Rothman, Takashi Kohno, Qing Lan
Summary: This study identified 12 novel susceptibility variants for lung adenocarcinoma and a total of 28 loci associated with the disease in East Asian populations. Additionally, new candidate genes were discovered, contributing to the understanding of the disease etiology. These findings have important implications for the research and translational applications of lung adenocarcinoma in individuals from East Asian populations.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Zhi-Zhang Yang, Hyo Jin Kim, Hongyan Wu, Xinyi Tang, Yue Yu, Jordan Krull, Daniel P. Larson, Raymond M. Moore, Matthew J. Maurer, Kevin D. Pavelko, Shahrzad Jalali, Joshua C. Pritchett, Rekha Mudappathi, Junwen Wang, Jose C. Villasboas, Patrizia Mondello, Anne J. Novak, Stephen M. Ansell
Summary: T-lymphocytes in the tumor microenvironment of follicular lymphoma (FL) show diverse phenotypes, which may influence tumor biology and patient survival. Our analysis of 82 FL patients revealed four immune subgroups with different T-cell phenotypes, and a higher prevalence of CD57(+) T-FH cells with a late-stage differentiation phenotype was associated with poor patient survival.
BLOOD CANCER JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Ahmad Mohamadi, Tianfan Cheng, Lijian Jin, Junwen Wang, Hongzhe Sun, Mohamad Koohi-Moghadam
Summary: In this study, a neural network method based on three-dimensional structure was developed to predict metal-binding sites in proteins. By constructing multi-channel 3D voxels and training and evaluating the model, it showed high performance in predicting various metal-binding sites.
CELL REPORTS PHYSICAL SCIENCE
(2022)
Proceedings Paper
Engineering, Biomedical
Jianfeng Wu, Yi Su, Eric M. Reiman, Richard J. Caselli, Kewei Chen, Paul M. Thompson, Junwen Wang, Yalin Wang
Summary: Alzheimer's disease, characterized by tau tangle pathology, is a common form of dementia in the aging population. Hippocampal atrophy and APOE genotypes are closely associated with the disease. This study introduces a federated chow test model to investigate the combined effects of APOE and tau on hippocampal morphometry.
2022 IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (IEEE ISBI 2022)
(2022)
Article
Biotechnology & Applied Microbiology
Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabon-Pena, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann, James C. Willey, Pierre R. Bushel, Ying Yu, Chang Xu, Guangchun Chen, Daniel Burgess, Simon Cawley, Kristina Giorda, Nathan Haseley, Fujun Qiu, Katherine Wilkins, Hanane Arib, Claire Attwooll, Kevin Babson, Longlong Bao, Wenjun Bao, Anne Bergstrom Lucas, Hunter Best, Ambica Bhandari, Halil Bisgin, James Blackburn, Thomas M. Blomquist, Lisa Boardman, Blake Burgher, Daniel J. Butler, Chia-Jung Chang, Alka Chaubey, Tao Chen, Marco Chierici, Christopher R. Chin, Devin Close, Jeffrey Conroy, Jessica Cooley Coleman, Daniel J. Craig, Erin Crawford, Angela del Pozo, Ira W. Deveson, Daniel Duncan, Agda Karina Eterovic, Xiaohui Fan, Jonathan Foox, Cesare Furlanello, Abhisek Ghosal, Sean Glenn, Meijian Guan, Christine Haag, Xinyi Hang, Scott Happe, Brittany Hennigan, Jennifer Hipp, Huixiao Hong, Kyle Horvath, Jianhong Hu, Li-Yuan Hung, Mirna Jarosz, Jennifer Kerkhof, Benjamin Kipp, David Philip Kreil, Pablo Lapunzina, Peng Li, Quan-Zhen Li, Weihua Li, Zhiguang Li, Yu Liang, Shaoqing Liu, Zhichao Liu, Charles Ma, Narasimha Marella, Ruben Martin-Arenas, Dalila B. Megherbi, Qingchang Meng, Piotr A. Mieczkowski, Tom Morrison, Donna Muzny, Baitang Ning, Barbara L. Parsons, Cloud P. Paweletz, Mehdi Pirooznia, Wubin Qu, Amelia Raymond, Paul Rindler, Rebecca Ringler, Bekim Sadikovic, Andreas Scherer, Egbert Schulze, Robert Sebra, Rita Shaknovich, Qiang Shi, Tieliu Shi, Juan Carlos Silla-Castro, Melissa Smith, Mario Solis Lopez, Ping Song, Daniel Stetson, Maya Strahl, Alan Stuart, Julianna Supplee, Philippe Szankasi, Haowen Tan, Lin-ya Tang, Yonghui Tao, Shraddha Thakkar, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkat J. Thodima, David Thomas, Boris Tichy, Nikola Tom, Elena Vallespin Garcia, Suman Verma, Kimbley Walker, Charles Wang, Junwen Wang, Yexun Wang, Zhining Wen, Valtteri Wirta, Leihong Wu, Chunlin Xiao, Wenzhong Xiao, Shibei Xu, Mary Yang, Jianming Ying, Shun H. Yip, Guangliang Zhang, Sa Zhang, Meiru Zhao, Yuanting Zheng, Xiaoyan Zhou, Christopher E. Mason, Timothy Mercer, Weida Tong, Leming Shi, Wendell Jones, Joshua Xu
Summary: All panels exhibit high sensitivity for variants within the 5-20% VAF range in high-confidence coding regions, but sensitivity decreases when using VAF thresholds due to variability in VAF measurements. Enforcing a VAF threshold for reporting reduces false positive calls, and false positive rate is higher outside high-confidence coding regions, leading to lower reproducibility. Region restriction and VAF thresholds result in low technical variability in estimating promising biomarkers and tumor mutational burden.