Article
Cell Biology
Maxence Wisztorski, Soulaimane Aboulouard, Lucas Roussel, Marie Duhamel, Philippe Saudemont, Tristan Cardon, Fabrice Narducci, Yves-Marie Robin, Anne-Sophie Lemaire, Delphine Bertin, Nawale Hajjaji, Firas Kobeissy, Eric Leblanc, Isabelle Fournier, Michel Salzet
Summary: This study conducted an in-depth proteomic analysis of pre-neoplastic epithelial lesions in ovarian cancer using mass spectrometry imaging and immunohistochemistry techniques. Specific lesion markers were identified, and a lipidomic analysis confirmed the presence of specific lipid signatures in these lesions. The study provides new insights into the molecular mechanisms underlying the progression of ovarian cancer and confirms the fimbria origin of high-grade serous carcinoma.
CELL DEATH & DISEASE
(2023)
Article
Cell Biology
Tova M. Bergsten, Sarah E. Levy, Katherine E. Zink, Hannah J. Lusk, Melissa R. Pergande, Stephanie M. Cologna, Joanna E. Burdette, Laura M. Sanchez
Summary: This study discovered that a secreted protein called SPARC, produced by tumorigenic fallopian tube epithelial cells, enhances the release of norepinephrine (NE) from the ovary, influencing the primary metastasis of high grade serous ovarian cancer (HGSOC).
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Cell Biology
Pamoda Galhenage, Yunlan Zhou, Erica Perry, Brenda Loc, Kelly Fietz, Sonia Iyer, Ferenc Reinhardt, Tiego Da Silva, Vladimir Botchkarev, Jie Chen, Christopher P. Crum, Robert A. Weinberg, Shailja Pathania
Summary: Clinical and molecular evidence suggests that high-grade serous ovarian cancer primarily originates from the fallopian tube due to distinct differences between fallopian tube epithelial cells and ovarian surface epithelial cells. Fallopian tube cells exhibit heightened replication stress, impaired repair mechanisms, defective checkpoint functionality, and increased tumorigenicity compared to ovarian surface cells. BRCA1 heterozygosity exacerbates these defects and leads to an aggressive tumor phenotype.
Article
Oncology
Phyllis van der Ploeg, Aniek Uittenboogaard, Steven L. Bosch, Paul J. van Diest, Yvonne J. W. Wesseling-Rozendaal, Anja van de Stolpe, Sandrina Lambrechts, Ruud L. M. Bekkers, Jurgen M. J. Piek
Summary: This study investigated the activity of key signal transduction pathways in serous tubal intraepithelial carcinoma (STIC) and high-grade serous carcinoma (HGSC) and compared them to normal Fallopian tube epithelium (FTE). The results showed that the ER pathway activity was lower, while the PI3K and HH pathway activity was higher in STIC and HGSC compared to FTE. This suggests that these pathways may play a crucial role in the neoplastic transformation of FTE into STIC.
GYNECOLOGIC ONCOLOGY
(2022)
Article
Reproductive Biology
Maho Shimizu, Keitaro Yamanaka, Maho Azumi, Masako Tomimoto, Keiichi Washio, Ryosuke Takahashi, Satoshi Nagamata, Yuka Murata, Yui Yamasaki, Yoshito Terai
Summary: The case presented a patient with SEIC accompanied by serous ovarian carcinoma and lymph node metastasis. The difficulty in identifying the primary lesion was highlighted as both tumors were serous carcinomas. Further development of methods for differentiation between the diseases is needed due to controversial histological diagnostic criteria.
JOURNAL OF OVARIAN RESEARCH
(2021)
Article
Obstetrics & Gynecology
Jung Mi Byun, Hwa Jin Cho, Dae Sim Lee, Hye Kyoung Yoon, Young Nam Kim, Do Hwa Im, Da Hyun Kim, Kyung Bok Lee, Moon Su Sung, Dae Hoon Jeong
Summary: This study aimed to evaluate the proportion of STIC in patients with HGSOC and analyze the STIC-related prognosis. The results showed that 11 out of 76 cases were STIC. BRCA mutations were found in 16.9% of patients with HGSOC. The incidence of STIC in patients with BRCA mutations was higher than in patients without BRCA mutations, but the difference was not statistically significant. There was no significant difference in survival rates with or without STIC. Prophylactic salpingectomy may be useful for prevention of HGSOC.
TAIWANESE JOURNAL OF OBSTETRICS & GYNECOLOGY
(2023)
Article
Oncology
Thomas Boerner, Henry S. Walch, Bastien Nguyen, Alexia Iasonos, Qin C. Zhou, Nikolaus Schultz, M. Herman Chui, Rachel N. Grisham, William P. Tew, Roisin E. O'Cearbhaill, Carol Aghajanian, Oliver Zivanovic, Nadeem R. Abu-Rustum, Ginger J. Gardner, Yukio Sonoda, Dennis S. Chi, Kara Long Roche
Summary: This study evaluated the clinical significance and genomic associations of concurrent STIC and HGSC in women undergoing PDS. Findings revealed no significant clinical or genetic differences between +STIC and no-STIC patients, suggesting a comparable, if not identical, disease process. The study provides important insights into the relationship between HGSC and STIC.
GYNECOLOGIC ONCOLOGY
(2021)
Article
Medicine, General & Internal
Yiying Wang, Qiyan Li, Ruijiao Zhao, Jerry Y. Wang, Yan Wang, Wanrun Lin, Zeng Yuan, Jing Zhang, Oluwole Fadare, Yue Wang, Wenxin Zheng
Summary: This study examined the expression of FOLR1 and FRA in different tissue samples and confirmed the contribution of the fallopian tube to the development of ovarian endometriosis. Understanding the role of the fallopian tube in endometriosis can help identify new ways to prevent and treat this condition.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, Research & Experimental
Hyunjin Kim, Go Eun Bae, Yoon Yang Jung, Hyun-Soo Kim
Summary: This is a rare case of ovarian mesonephric-like adenocarcinoma (MLA) involving the fimbria and mimicking serous tubal intraepithelial carcinoma (STIC). Immunostaining played a crucial role in differential diagnosis, especially between MLA and high-grade serous carcinoma.
Article
Oncology
Jinping Lai, Caili Tong, Jeremy R. Chien
Summary: Ovarian carcinoma is the fifth leading cause of cancer-related deaths in women in the United States. Serous papillary carcinoma is the most common histological type of ovarian carcinoma. The patient in this case report was found to have mutations in BRCA1, BRCA2, TP53, and HSP90AB1, as well as low PD-L1 expression, which may guide targeted therapy options like PARP inhibitors and immune checkpoint inhibitors.
ANTICANCER RESEARCH
(2021)
Article
Oncology
Angela Russo, Zizhao Yang, Georgette Moyle Heyrman, Brian P. Cain, Alfredo Lopez Carrero, Brett C. Isenberg, Matthew J. Dean, Jonathan Coppeta, Joanna E. Burdette
Summary: High grade serous ovarian cancers (HGSOC) mainly originate from the fallopian tube epithelium (FTE) and colonize the ovary before further metastasis. The ovary secretes specific factors during ovulation that attract tumor cells from the fallopian tube. A secreted protein of 50-100kDa in size was identified to enhance the migration of FTE cells through the Epidermal Growth Factor Receptor (EGFR). This protein, called Versican, was found to be correlated with ovulation and enhanced the adhesion and invasion of FTE cells to the ovary in an EGFR-dependent manner.
Article
Biochemistry & Molecular Biology
Yazmin Brown, Susan Hua, Pradeep S. Tanwar
Summary: High-grade serous ovarian cancer (HGSOC) is a deadly gynaecological cancer with insidious progression. It is now widely accepted that HGSOC originates from the fallopian tube epithelium. This review explores the involvement of the extracellular matrix (ECM) in HGSOC development, including its role in tumourigenesis, metastasis, and drug resistance.
Review
Obstetrics & Gynecology
Lin Zhang, Miriam Velazquez, Xiaohong Wang, Ramya Masand, Michael Deavers, Songlin Zhang
Summary: Seromucinous carcinoma of the ovary is a rare entity with overlapping morphologic and immunophenotypic features of other types of ovarian carcinoma. There is debate whether it is a distinct entity or a histologic variant of established entities. The presentation of a case with variable differentiation and morphology in different sites highlights the complexity of this tumor.
INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY
(2021)
Article
Oncology
Jingni Wu, Yael Raz, Maria Sol Recouvreux, Marcio Augusto Diniz, Jenny Lester, Beth Y. Karlan, Ann E. Walts, Arkadiusz Gertych, Sandra Orsulic
Summary: This study aimed to investigate the global visual and subvisual microenvironmental differences between fallopian tubes with and without STIC lesions. The results showed differences in stromal and epithelial cells, and also a correlation between age and cell type changes.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Che-Fang Hsu, Vaishnavi Seenan, Liang-Yuan Wang, Tang-Yuan Chu
Summary: This study examines the effect of superovulation on the metastasis of transformed human tubal epithelial cells in the peritoneum and ovaries using a bursa-free mouse model. The results show that superovulation increases the number of transformed human tubal epithelial cell seedlings in the peritoneum. Additionally, ovaries without a bursa structure are more susceptible to external tumor seeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Wendell D. Jones, Chad M. Michener, Charles Biscotti, Iona Braicu, Jalid Sehouli, Mahrukh K. Ganapathi, Ram N. Ganapathi
Letter
Oncology
Eric J. Norris, Yogin C. Patel, Kaitlin E. Klotz, Nury Steuerwald, Wendell D. Jones, Jaroslaw P. Maciejewski, Ram N. Ganapathi, Mahrukh K. Ganapathi
LEUKEMIA & LYMPHOMA
(2021)
Article
Biotechnology & Applied Microbiology
Ira W. Deveson, Binsheng Gong, Kevin Lai, Jennifer S. LoCoco, Todd A. Richmond, Jeoffrey Schageman, Zhihong Zhang, Natalia Novoradovskaya, James C. Willey, Wendell Jones, Rebecca Kusko, Guangchun Chen, Bindu Swapna Madala, James Blackburn, Igor Stevanovski, Ambica Bhandari, Devin Close, Jeffrey Conroy, Michael Hubank, Narasimha Marella, Piotr A. Mieczkowski, Fujun Qiu, Robert Sebra, Daniel Stetson, Lihyun Sun, Philippe Szankasi, Haowen Tan, Lin-ya Tang, Hanane Arib, Hunter Best, Blake Burgher, Pierre R. Bushel, Fergal Casey, Simon Cawley, Chia-Jung Chang, Jonathan Choi, Jorge Dinis, Daniel Duncan, Agda Karina Eterovic, Liang Feng, Abhisek Ghosal, Kristina Giorda, Sean Glenn, Scott Happe, Nathan Haseley, Kyle Horvath, Li-Yuan Hung, Mirna Jarosz, Garima Kushwaha, Dan Li, Quan-Zhen Li, Zhiguang Li, Liang-Chun Liu, Zhichao Liu, Charles Ma, Christopher E. Mason, Dalila B. Megherbi, Tom Morrison, Carlos Pabon-Pena, Mehdi Pirooznia, Paula Z. Proszek, Amelia Raymond, Paul Rindler, Rebecca Ringler, Andreas Scherer, Rita Shaknovich, Tieliu Shi, Melissa Smith, Ping Song, Maya Strahl, Venkat J. Thodima, Nikola Tom, Suman Verma, Jiashi Wang, Leihong Wu, Wenzhong Xiao, Chang Xu, Mary Yang, Guangliang Zhang, Sa Zhang, Yilin Zhang, Leming Shi, Weida Tong, Donald J. Johann, Timothy R. Mercer, Joshua Xu
Summary: This study evaluated the performance of five industry-leading ctDNA assays and found that all assays showed high sensitivity, precision, and reproducibility above 0.5% variant allele frequency. However, below this limit, detection became unreliable, especially when input material was limited. The key challenge for ctDNA assays is the reliable sampling of rare ctDNA fragments, with missed mutations being more common than erroneous candidates.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Wenming Xiao, Luyao Ren, Zhong Chen, Li Tai Fang, Yongmei Zhao, Justin Lack, Meijian Guan, Bin Zhu, Erich Jaeger, Liz Kerrigan, Thomas M. Blomquist, Tiffany Hung, Marc Sultan, Kenneth Idler, Charles Lu, Andreas Scherer, Rebecca Kusko, Malcolm Moos, Chunlin Xiao, Stephen T. Sherry, Ogan D. Abaan, Wanqiu Chen, Xin Chen, Jessica Nordlund, Ulrika Liljedahl, Roberta Maestro, Maurizio Polano, Jiri Drabek, Petr Vojta, Sulev Koks, Ene Reimann, Bindu Swapna Madala, Timothy Mercer, Chris Miller, Howard Jacob, Tiffany Truong, Ali Moshrefi, Aparna Natarajan, Ana Granat, Gary P. Schroth, Rasika Kalamegham, Eric Peters, Virginie Petitjean, Ashley Walton, Tsai-Wei Shen, Keyur Talsania, Cristobal Juan Vera, Kurt Langenbach, Maryellen de Mars, Jennifer A. Hipp, James C. Willey, Jing Wang, Jyoti Shetty, Yuliya Kriga, Arati Raziuddin, Bao Tran, Yuanting Zheng, Ying Yu, Margaret Cam, Parthav Jailwala, Cu Nguyen, Daoud Meerzaman, Qingrong Chen, Chunhua Yan, Ben Ernest, Urvashi Mehra, Roderick Jensen, Wendell Jones, Jian-Liang Li, Brian N. Papas, Mehdi Pirooznia, Yun-Ching Chen, Fayaz Seifuddin, Zhipan Li, Xuelu Liu, Wolfgang Resch, Jingya Wang, Leihong Wu, Gokhan Yavas, Corey Miles, Baitang Ning, Weida Tong, Christopher E. Mason, Eric Donaldson, Samir Lababidi, Louis M. Staudt, Zivana Tezak, Huixiao Hong, Charles Wang, Leming Shi
Summary: This study systematically investigates factors affecting detection reproducibility and accuracy of somatic mutations in paired tumor-normal cell lines at six different centers. It evaluates the reproducibility of whole-genome sequencing (WGS) and whole-exome sequencing (WES) for different sample types, input amounts, tumor purity, and library construction protocols with nine bioinformatics pipelines. The study found that read coverage and callers affected both WGS and WES reproducibility, with WES performance also affected by insert fragment size, genomic copy content, and the global imbalance score.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Tiantian Liu, Zhong Chen, Wanqiu Chen, Xin Chen, Maryam Hosseini, Zhaowei Yang, Jing Li, Diana Ho, David Turay, Ciprian P. Gheorghe, Wendell Jones, Charles Wang
Summary: The research compared seven different SARS-CoV-2 WGS library protocols and found significant differences in mappability, genome coverage, sensitivity, reproducibility, and precision, with certain protocols requiring important trimming steps for accurate variant calling. The study results provide guidance for choosing appropriate WGS protocols to study SARS-CoV-2 and its evolution.
Article
Biochemistry & Molecular Biology
Chloe Mirzayi, Audrey Renson, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J. Kasselman, Kelly Eckenrode, Janneke van de Wijgert, Amy Loughman, Francine Z. Marques, David A. MacIntyre, Manimozhiyan Arumugam, Rimsha Azhar, Francesco Beghini, Kirk Bergstrom, Ami Bhatt, Jordan E. Bisanz, Jonathan Braun, Hector Corrada Bravo, Gregory A. Buck, Frederic Bushman, David Casero, Gerard Clarke, Maria Carmen Collado, Paul D. Cotter, John F. Cryan, Ryan T. Demmer, Suzanne Devkota, Eran Elinav, Juan S. Escobar, Jennifer Fettweis, Robert D. Finn, Anthony A. Fodor, Sofia Forslund, Andre Franke, Cesare Furlanello, Jack Gilbert, Elizabeth Grice, Benjamin Haibe-Kains, Scott Handley, Pamela Herd, Susan Holmes, Jonathan P. Jacobs, Lisa Karstens, Rob Knight, Dan Knights, Omry Koren, Douglas S. Kwon, Morgan Langille, Brianna Lindsay, Dermot McGovern, Alice C. McHardy, Shannon McWeeney, Noel T. Mueller, Luigi Nezi, Matthew Olm, Noah Palm, Edoardo Pasolli, Jeroen Raes, Matthew R. Redinbo, Malte Ruhlemann, R. Balfour Sartor, Patrick D. Schloss, Lynn Schriml, Eran Segal, Michelle Shardell, Thomas Sharpton, Ekaterina Smirnova, Harry Sokol, Justin L. Sonnenburg, Sujatha Srinivasan, Louise B. Thingholm, Peter J. Turnbaugh, Vaibhav Upadhyay, Ramona L. Walls, Paul Wilmes, Takuji Yamada, Georg Zeller, Mingyu Zhang, Ni Zhao, Liping Zhao, Wenjun Bao, Aedin Culhane, Viswanath Devanarayan, Joaquin Dopazo, Xiaohui Fan, Matthias Fischer, Wendell Jones, Rebecca Kusko, Christopher E. Mason, Tim R. Mercer, Susanna-Assunta Sansone, Andreas Scherer, Leming Shi, Shraddha Thakkar, Weida Tong, Russ Wolfinger, Christopher Hunter, Nicola Segata, Curtis Huttenhower, Jennifer B. Dowd, Heidi E. Jones, Levi Waldron
Summary: The STORMS tool is a reporting guideline for human microbiome studies, consisting of a 17-item checklist to help researchers report study results concisely and completely, facilitating manuscript preparation, peer review, and reader comprehension.
Article
Multidisciplinary Sciences
Anthony Mammoliti, Petr Smirnov, Minoru Nakano, Zhaleh Safikhani, Christopher Eeles, Heewon Seo, Sisira Kadambat Nair, Arvind S. Mer, Ian Smith, Chantal Ho, Gangesh Beri, Rebecca Kusko, Eva Lin, Yihong Yu, Scott Martin, Marc Hafner, Benjamin Haibe-Kains
Summary: Reproducibility is crucial in open science for findings to be valid and shareable. The complexity and growth of biomedical data pose challenges in processing and sharing. ORCESTRA platform tackles this by processing multimodal biomedical data and providing customizable workflows.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Binsheng Gong, Ira W. Deveson, Timothy Mercer, Donald J. Johann, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study evaluated the analytical performance of five industry-leading ctDNA assays and demonstrated their high accuracy and reproducibility. By using tailor-made reference samples and assessing multiple key variables, this study provides a valuable dataset for ultra-deep ctDNA sequencing technology.
Article
Multidisciplinary Sciences
Binsheng Gong, Rebecca Kusko, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study developed four reference samples and sequenced them with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. The resulting dataset provided valuable information for assessing the clinical applicability of oncopanels and optimizing bioinformatics pipelines and sequencing parameters.
Article
Biochemistry & Molecular Biology
Wendell Jones, David Tait, Chad Livasy, Mahrukh Ganapathi, Ram Ganapathi
Summary: This study analyzed genomic alterations in primary-metastatic tumors and found that PLK3 amplification and the tumor immune microenvironment (TIME) were associated with time-to-recurrence (TTR) risk in uterine serous carcinoma (USC). TP53 loss in metastatic tumors was associated with platinum resistance, increased recurrence, and mortality risk.
Article
Biotechnology & Applied Microbiology
Yifan Zhang, Thomas M. Blomquist, Rebecca Kusko, Daniel Stetson, Zhihong Zhang, Lihui Yin, Robert Sebra, Binsheng Gong, Jennifer S. Lococo, Vinay K. Mittal, Natalia Novoradovskaya, Ji-Youn Yeo, Nicole Dominiak, Jennifer Hipp, Amelia Raymond, Fujun Qiu, Hanane Arib, Melissa L. Smith, Jay E. Brock, Daniel H. Farkas, Daniel J. Craig, Erin L. Crawford, Dan Li, Tom Morrison, Nikola Tom, Wenzhong Xiao, Mary Yang, Christopher E. Mason, Todd A. Richmond, Wendell Jones, Donald J. Johann, Leming Shi, Weida Tong, James C. Willey, Joshua Xu
Summary: To ensure reliable results, it is recommended to avoid the block surface portion and restrict mutation detection to genomic regions of high confidence.
Article
Biochemical Research Methods
James C. Willey, Tom B. Morrison, Bradley Austermiller, Erin L. Crawford, Daniel J. Craig, Thomas M. Blomquist, Wendell D. Jones, Aminah Wali, Jennifer S. Lococo, Nathan Haseley, Todd A. Richmond, Natalia Novoradovskaya, Rebecca Kusko, Guangchun Chen, Quan-Zhen Li, Donald J. Johann, Ira W. Deveson, Timothy R. Mercer, Leihong Wu, Joshua Xu
Summary: The SEQC2 project aims to develop standard analysis protocols and quality control metrics for DNA testing. This study introduces a targeted NGS method for detecting actionable mutations in ctDNA clinical specimens, using internal standard spike-ins to improve accuracy and sensitivity.
CELL REPORTS METHODS
(2021)
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.
Article
Biotechnology & Applied Microbiology
Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas, Daniel Burgess, Daniel J. Butler, Simon Cawley, Chia-Jung Chang, Guangchun Chen, Tao Chen, Yun-Ching Chen, Daniel J. Craig, Angela Del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, Yingyi Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff Jasper, Giuseppe Jurman, David Philip Kreil, Pawel Labaj, Kevin Lai, Jianying Li, Quan-Zhen Li, Yulong Li, Zhiguang Li, Zhichao Liu, Mario Solis Lopez, Kelci Miclaus, Raymond Miller, Vinay K. Mittal, Marghoob Mohiyuddin, Carlos Pabon-Pena, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Weida Tong, Leming Shi, Joshua Xu
Summary: Through analyzing ten diverse cancer cell lines and their pool, researchers have developed a new reference sample with over 40,000 variants for evaluating oncopanel analytical performance. Additionally, by mixing with another normal reference sample, new samples with lower allele frequency can be created, enhancing the evaluation capability for liquid biopsy panels.