Article
Biochemical Research Methods
Jace Webster, Ha X. Dang, Pradeep S. Chauhan, Wenjia Feng, Alex Shiang, Peter K. Harris, Russell K. Pachynski, Aadel A. Chaudhuri, Christopher A. Maher
Summary: The detection of genomic alterations in ctDNA is important for clinical monitoring of cancer. However, strategies for detecting SVs in ctDNA are limited, and the analysis of different classes of variants is challenging. We developed a unified pipeline called PACT for accurate and consistent analysis of ctDNA, which outperformed similar tools in various datasets.
Article
Oncology
Irene Jimenez, Eleonore Frouin, Mathieu Chicard, Catherine Dehainault, Jessica Le Gall, Camille Benoist, Arnaud Gauthier, Eve Lapouble, Claude Houdayer, Francois Radvanyi, Virginie Bernard, Herve J. Brisse, Marion Gauthier-Villars, Dominique Stoppa-Lyonnet, Sylvain Baulande, Nathalie Cassoux, Livia Lumbroso, Alexandre Matet, Isabelle Aerts, Victor Renault, Francois Doz, Lisa Golmard, Olivier Delattre, Gudrun Schleiermacher
Summary: The analysis of circulating tumor DNA from non-hereditary retinoblastoma patients showed promising results in detecting ctDNA in plasma, despite challenges such as small tumor size and limited plasma sample volumes. This method may be beneficial for diagnosis, genetic counseling, and monitoring of residual intraocular disease.
EUROPEAN JOURNAL OF CANCER
(2021)
Article
Oncology
Sungun Bang, Dongju Won, Saeam Shin, Kang Su Cho, Jae Won Park, Jongsoo Lee, Young Deuk Choi, Suwan Kang, Seung-Tae Lee, Jong Rak Choi, Hyunho Han
Summary: In our study, we discovered genetic mutations in the DNA of cancer cells obtained from the blood of metastatic prostate cancer patients. These mutations were more common in patients with aggressive and progressing cancer that did not respond to conventional treatment. Compared to the traditional method of measuring prostate-specific antigen (PSA) levels, these genetic mutations were more sensitive in detecting prostate cancer progression. This suggests that a simple blood test could be used to track genetic mutations, identify aggressive cancer subtypes, monitor disease progression, and improve the management of advanced prostate cancer.
Review
Chemistry, Analytical
Yi-Hui Wang, Zhen Song, Xin-Yuan Hu, Huai-Song Wang
Summary: Tumor, an abnormal organism generated by cell proliferation and differentiation under various factors, involves gene mutations during tumorigenesis for diagnosis. Early diagnosis is crucial to improve cure rates and reduce mortality.
Review
Biochemistry & Molecular Biology
Oleg Tutanov, Svetlana Tamkovich
Summary: Circulating DNA has been proven to be a valuable tool in translational medicine. This review aims to shed light on the association of circulating DNA with different proteins, its origins and forms of circulation, biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Clinical Neurology
James Tanner McMahon, Matthew Studer, Bryan Ulrich, Juan Revuelta M. Barbero, Ivan Pradilla, Maria A. Palacios-Ariza, Gustavo Pradilla
Summary: ctDNA appears to be a highly sensitive and specific noninvasive biomarker among adults with gliomas. The performance of ctDNA is better in cerebrospinal fluid (CSF) compared to plasma, although the difference is not statistically significant. Targeted genetic analysis platforms improve ctDNA detection, particularly in high-grade gliomas.
Article
Biophysics
Ya Bin Cui, Hang Yan, Zhe Sun, Yu Ling, Hong Qun Luo, Nian Bing Li
Summary: Researchers have designed a bipedal DNA walker with multiple recognition sites, which undergoes a transition from dumbbell-shaped DNA nanostructure to an annular bipedal DNA walker. This design enables dual amplification of the signal and achieves ultrasensitive photoelectrochemical (PEC) detection of circulating tumor DNA (ctDNA).
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Cell Biology
Pei Wang, Qianqian Song, Jie Ren, Weilong Zhang, Yuting Wang, Lin Zhou, Dongmei Wang, Kun Chen, Liping Jiang, Bochao Zhang, Wanqing Chen, Chunfeng Qu, Hong Zhao, Yuchen Jiao
Summary: The study developed the Mutation Capsule Plus (MCP) technology for multiplex profiling of cfDNA samples, enabling simultaneous detection of genetic and epigenetic alterations and genome-wide discovery of methylation markers. The MCP technology showed potential for the noninvasive detection of hepatocellular carcinoma (HCC) and achieved high sensitivity and specificity. The study also provided a comprehensive database of genetic and epigenetic alterations in the cfDNA of HCC cases and high-risk non-HCC individuals.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Review
Oncology
Morten Borg, Sara Witting Christensen Wen, Rikke Fredslund Andersen, Signe Timm, Torben Frostrup Hansen, Ole Hilberg
Summary: Lung cancer is the leading cause of cancer-related deaths, and early detection is crucial for improving patient outcomes. Non-invasive diagnostic tools, such as methylated circulating tumor DNA (ctDNA), show potential for lung cancer diagnosis. This systematic review and meta-analysis evaluated the current evidence on the use of methylated ctDNA in blood samples as a diagnostic tool for lung cancer.
Article
Oncology
Jeanne Tie, Joshua D. Cohen, Serigne N. Lo, Yuxuan Wang, Lu Li, Michael Christie, Margaret Lee, Rachel Wong, Suzanne Kosmider, Iain Skinner, Hui Li Wong, Belinda Lee, Matthew E. Burge, Desmond Yip, Christos S. Karapetis, Timothy J. Price, Niall C. Tebbutt, Andrew M. Haydon, Janine Ptak, Mary J. Schaeffer, Natalie Silliman, Lisa Dobbyn, Maria Popoli, Cristian Tomasetti, Nickolas Papadopoulos, Kenneth W. Kinzler, Bert Vogelstein, Peter Gibbs
Summary: Studies have shown that postoperative ctDNA analysis is prognostically significant in nonmetastatic CRC patients, with higher predictive accuracy for recurrence compared to clinicopathologic risk factors, and increasing mutant allele frequency (MAF) further stratifying recurrence risk.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Review
Medicine, Research & Experimental
Laiyu Yao, Hong Xu, Jinshan Wo, Meiqing Zhao, Zhihe Liu, Tieying Dong, Shuxin Xiao
Summary: This meta-analysis demonstrated that high levels of ctDNA were associated with poor prognosis in patients with lymphoma, especially in those with DLBCL.
CLINICAL AND EXPERIMENTAL MEDICINE
(2022)
Article
Engineering, Environmental
Guangxing Liu, Hua Chai, Zhenzhen Guo, Zhaoyin Wang, Yuguo Tang, Peng Miao
Summary: This study extended the concept of common molecular beacon to fabricate novel DNA nanostructures. By using hairpin fuel strands and hand-in-hand pattern, highly selective and reliable detection of the target was achieved through dual-mode analysis. This method holds great potential for DNA analysis and clinical diagnosis.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Oncology
Caroline Brenner Thomsen, Amanda Dandanell Juul, Anna Cecilie Lefevre, Christina Glismand Truelsen, Edina Dizdarevic, Heidi Ryssel, Ina Mathilde Kjaer, Karen Lycke Wind, Louise Bach Callesen, Louise Faaborg Larsen, Malene Stochkel Frank, Rikke Fredslund Andersen, Karen-Lise Garm Spindler, Anders Jakobsen
Summary: This commentary discusses the importance of standardizing circulating tumor DNA (ctDNA) analyses for monitoring metastatic solid tumors, aiming to improve its clinical validity.
Article
Oncology
Xiaoyuan Tian, Dongcen Ge, Feng Zhang, Bocheng Zhang, Wanting Bai, Xiaoying Xu, Zongjuan Li, Ying Cao, Peiying Li, Kun Zou, Lijuan Zou
Summary: The study showed that mutant genes identified in plasma DNA samples from MRCC patients influence treatment outcomes, with a decrease in mutations after chemotherapy associated with better response. Longitudinal monitoring with ctDNA in liquid biopsy samples provides predictive and prognostic information during treatment.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Surgery
Carlos S. Cabalag, Michael Yates, Mariana Benitez Corrales, Paul Yeh, Stephen Q. Wong, Bonnie Z. Zhang, Kenji M. Fujihara, Lynn Chong, Michael W. Hii, Sarah-Jane Dawson, Wayne A. Phillips, Cuong P. Duong, Nicholas J. Clemons
Summary: The study demonstrates the clinical utility of ctDNA in predicting disease status and treatment response in esophageal adenocarcinoma patients. It shows that ctDNA can provide additional prognostication over conventional staging investigations and may be a useful biomarker for surveillance of recurrent disease.
Article
Oncology
Jiajia Zhang, Zhicheng Ji, Justina X. Caushi, Margueritta El Asmar, Valsamo Anagnostou, Tricia R. Cottrell, Hok Yee Chan, Prerna Suri, Haidan Guo, Taha Merghoub, Jamie E. Chaft, Joshua E. Reuss, Ada J. Tam, Richard L. Blosser, Mohsen Abu-Akeel, John-William Sidhom, Ni Zhao, Jinny S. Ha, David R. Jones, Kristen A. Marrone, Jarushka Naidoo, Edward Gabrielson, Janis M. Taube, Victor E. Velculescu, Julie R. Brahmer, Franck Housseau, Matthew D. Hellmann, Patrick M. Forde, Drew M. Pardoll, Hongkai Ji, Kellie N. Smith
CLINICAL CANCER RESEARCH
(2020)
Article
Multidisciplinary Sciences
Alessandro Leal, Nicole C. T. van Grieken, Doreen N. Palsgrove, Jillian Phallen, Jamie E. Medina, Carolyn Hruban, Mark A. M. Broeckaert, Valsamo Anagnostou, Vilmos Adleff, Daniel C. Bruhm, Jenna Canzoniero, Jacob Fiksel, Marianne Nordsmark, Fabienne A. R. M. Warmerdam, Henk M. W. Verheul, Dick Johan van Spronsen, Laurens Beerepoot, Maud M. Geenen, Johanneke E. A. Portielje, Edwin P. M. Jansen, Johanna van Sandick, Elma Meershoek-Klein Kranenbarg, Hanneke W. M. van Laarhoven, Donald L. van der Peet, Cornelis J. H. van de Velde, Marcel Verheij, Remond Fijneman, Robert B. Scharpf, Gerrit A. Meijer, Annemieke Cats, Victor E. Velculescu
NATURE COMMUNICATIONS
(2020)
Article
Oncology
Xiaoshan M. Shao, Rohit Bhattacharya, Justin Huang, I. K. Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, Benjamin Kaminow, Ashton Omdahl, Maria Bonsack, Angelika B. Riemer, Victor E. Velculescu, Valsamo Anagnostou, Kymberleigh A. Pagel, Rachel Karchin
CANCER IMMUNOLOGY RESEARCH
(2020)
Article
Multidisciplinary Sciences
Hyoung Kim, Haineng Xu, Erin George, Dorothy Hallberg, Sushil Kumar, Veena Jagannathan, Sergey Medvedev, Yasuto Kinose, Kyle Devins, Priyanka Verma, Kevin Ly, Yifan Wang, Roger A. Greenberg, Lauren Schwartz, Neil Johnson, Robert B. Scharpf, Gordon B. Mills, Rugang Zhang, Victor E. Velculescu, Eric J. Brown, Fiona Simpkins
NATURE COMMUNICATIONS
(2020)
Article
Computer Science, Interdisciplinary Applications
Julie Fortin, Bjarne Bartlett, Michael Kantar, Michelle Tseng, Zia Mehrabi
Summary: Science attempts to be a meritocracy, but evidence shows systematic gender bias against women in the field. However, a new metric called Altmetric Attention Score suggests equal attention is given to articles by both male and female authors in major journals, except for the journal Science which displays marked gender bias against women.
Article
Surgery
Rebecca S. Steinberg, Aditi Nayak, Michael A. Burke, Morgan Aldridge, S. Raja Laskar, Kunal Bhatt, Lakshmi Sridharan, Mahmoud Abdou, Tamer Attia, Andrew Smith, Mani Daneshmand, J. David Vega, Divya Gupta, Alanna A. Morris
Summary: Caregiver support is crucial for patients after heart transplant and left ventricular assist device placement. Studies showed that women and Black patients were less likely to have spouses as their support person, affecting their eligibility for advanced therapies. However, the type of caregiver did not explain the differences in eligibility by gender and race.
CLINICAL TRANSPLANTATION
(2022)
Article
Oncology
Mark D. Stewart, Diana Merino Vega, Rebecca C. Arend, Jonathan F. Baden, Olena Barbash, Nike Beaubier, Grace Collins, Tim French, Negar Ghahramani, Patsy Hinson, Petar Jelinic, Matthew J. Marton, Kimberly McGregor, Jerod Parsons, Lakshman Ramamurthy, Mark Sausen, Ethan S. Sokol, Albrecht Stenzinger, Hillary Stires, Kirsten M. Timms, Diana Turco, Iris Wang, J. Andrew Williams, Elaine Wong-Ho, Jeff Allen
Summary: Homologous recombination deficiency (HRD) is a tumor phenotype characterized by the inability of cells to repair DNA double-strand breaks effectively. Research has identified opportunities to improve the consistency in defining HRD and measuring homologous repair status parameters, benefiting the broader cancer community.
Article
Cell Biology
Bjarne Bartlett, Zitong Gao, Monique Schukking, Mark Menor, Vedbar S. Khadka, Muller Fabbri, Peiwen Fei, Youping Deng
Summary: Extrinsic factors like PD-L1 expression in tumor microenvironment, as well as intrinsic factors like MSI and TMB, have been linked to responses to checkpoint blockade therapy. MiRNAs were found to be correlated with tumor features and M1 macrophage polarization, but not with overall survival. Predicted targets of miRNAs could impact TGF-beta and potentially serve as companions to immune checkpoint blockade therapy.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Rebecca S. Steinberg, Eisha Udeshi, Neal Dickert, Arshed Quyyumi, Julio A. Chirinos, Alanna A. Morris
Summary: Arterial stiffness and early wave reflections can increase afterload and impair cardiovascular function. This study found that premature wave reflections are associated with adverse clinical outcomes in patients with heart failure with reduced ejection fraction. The results indicate that heart failure patients with reduced ejection fraction have impaired left ventricular systolic function and early wave reflections increase the left ventricular diastolic load and lead to poor clinical outcomes.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Pathology
Ellen L. Verner, Jennifer B. Jackson, Eric Severson, Kenneth C. Valkenburg, Amy E. Greer, David R. Riley, Mark Sausen, Cynthia Maddox, Paul M. McGregor, Aanavi Karandikar, Stephanie B. Hastings, Rebecca A. Previs, Venkataprasanth P. Reddy, Taylor J. Jensen, Shakti H. Ramkissoon
Summary: Genomic profiling plays a critical role in guiding treatment decisions in precision oncology. Liquid biopsy testing, such as the Labcorp Plasma Focus test, is a valuable alternative when tissue samples are not readily available. This study demonstrates the accuracy, sensitivity, and specificity of the test, showing its utility in identifying actionable variants in solid cancers. The data also highlight the high concordance and agreement with orthogonal methods for detecting different types of genomic alterations.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2023)
Article
Health Care Sciences & Services
Rebecca Steinberg, Bjorn Anderson, Ziyue Hu, Theodore M. Johnson, James B. O'Keefe, Laura C. Plantinga, Rishi Kamaleswaran, Blake Anderson
Summary: Engagement in a COVID-19 remote patient monitoring (RPM) programme or telemedicine programme was associated with better outcomes, including reduced risk of emergency department visits, hospital admissions, or intensive care unit-level care. However, these improvements were likely due to differences in baseline characteristics between engaged and non-engaged groups rather than the efficacy of the intervention alone.
Meeting Abstract
Oncology
Yasuto Kinose, Hyoung Kim, Haineng Xu, Sergey Medvedev, Erin George, Sarah Gitto, Margaret Whicker, Dorothy Hallberg, Lauren Schwartz, Gordon Mills, Victor E. Velculescu, Tian-Li Wang, Ronny Drapkin, Fiona Simpkins
CLINICAL CANCER RESEARCH
(2020)
Meeting Abstract
Oncology
Yasuto Kinose, Hyoung Kim, Haineng Xu, Sergey Medvedev, Erin George, Sarah Gitto, Margaret Whicker, Dorothy Hallberg, Lauren Schwartz, Gordon Mills, Victor E. Velculescu, Tian-Li Wang, Ronny Drapkin, Fiona Simpkins
CLINICAL CANCER RESEARCH
(2020)
Meeting Abstract
Oncology
Kristen A. Marrone, Valsamo Anagnostou, Michael J. Topper, Kellie Smith, Jiajia Zhang, Elisabeth Prophet, Joanne Reimer, Margaret Fitzpatrick, Victor Velculescu, Patrick Forde, Christine Hann, Ronan Kelly, David Ettinger, Cynthia Zahnow, Jorge Rivera, Barbara Gitlitz, Drew Pardoll, Stephen Baylin, Julie Brahmer
CANCER IMMUNOLOGY RESEARCH
(2020)
Meeting Abstract
Oncology
Xiaoshan M. Shao, Rohit Bhattacharya, Justin Huang, Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, Ben Kaminow, Ashton Omdahl, Maria Bonsack, Angelika B. Riemer, Victor E. Velculescu, Valsamo Anagnostou, Kymberleigh Pagel, Rachel Karchin
CANCER IMMUNOLOGY RESEARCH
(2020)