Article
Oncology
Maria Gabriela O. Fernandes, Natalia Cruz-Martins, Conceicao Souto Moura, Susana Guimaraes, Joana Pereira Reis, Ana Justino, Maria Joao Pina, Adriana Magalhaes, Henrique Queiroga, Jose Carlos Machado, Venceslau Hespanhol, Jose Luis Costa
Summary: Plasma ctDNA testing showed high accuracy and clinical relevance in newly diagnosed advanced NSCLC patients, highlighting its potential as a valuable tool for mutation detection in clinical practice.
Article
Infectious Diseases
Chunhui Xu, Xin Chen, Guoqing Zhu, Huiming Yi, Shulian Chen, Yuetian Yu, Erlie Jiang, Yizhou Zheng, Fengkui Zhang, Jianxiang Wang, Sizhou Feng
Summary: Plasma cell-free DNA Next-Generation Sequencing is a valuable tool for the diagnosis and treatment of infectious diseases in patients with hematological disorders, especially those with neutropenia.
JOURNAL OF INFECTION
(2023)
Article
Immunology
Esther Benamu, Kiran Gajurel, Jill N. Anderson, Tullia Lieb, Carlos A. Gomez, Hon Seng, Romielle Aquino, Desiree Hollemon, David K. Hong, Timothy A. Blauwkamp, Mickey Kertesz, Lily Blair, Paul L. Bollyky, Bruno C. Medeiros, Steven Coutre, Simona Zompi, Jose G. Montoya, Stan Deresinski
Summary: This study evaluated the ability of Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies in patients with febrile neutropenia (FN) and its impact on antimicrobial treatment. The results showed that KT was able to detect organisms that were not identified by conventional microbiological tests, and it had the potential to improve the diagnosis and optimize the antimicrobial therapy for FN.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Oncology
Tonje Bjornetro, Paula A. A. Bousquet, Kathrine Roe Redalen, Anne-Marie Siebke Troseid, Torben Luders, Espen Stang, Adriana M. M. Sanabria, Christin Johansen, Anniken Jorlo Fuglestad, Christian Kersten, Sebastian Meltzer, Anne Hansen Ree
Summary: Recent studies have found that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological characteristics of this cell-free mitochondrial DNA (mtDNA) are not well understood. In this study, the mtDNA derived from plasma EVs of colorectal cancer patients was compared to that of whole blood, peripheral blood mononuclear cells, and tumor tissue. The results showed that EV mtDNA had more variants and low-level heteroplasmy compared to whole blood mtDNA. The EV mtDNA variants were mainly located in the coding regions and had a higher proportion of missense mutations compared to whole blood and tumor tissue.
Article
Immunology
Joshua A. Hill, Sudeb C. Dalai, David K. Hong, Asim A. Ahmed, Carine Ho, Desiree Hollemon, Lily Blair, Joyce Maalouf, Jacob Keane-Candib, Terry Stevens-Ayers, Michael Boeckh, Timothy A. Blauwkamp, Cynthia E. Fisher
Summary: The study evaluated the performance of plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary invasive mold infections (IMIs) after hematopoietic cell transplant (HCT). The mcfDNA-Seq test showed moderate sensitivity and high specificity, positive predictive value (PPV), and negative predictive value (NPV) for pulmonary IMI, especially for non-Aspergillus species after HCT.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Oncology
Chul Seung Lee, Hoon Seok Kim, Jeoffrey Schageman, In Kyu Lee, Myungshin Kim, Yonggoo Kim
Summary: Circulating tumor DNA (ctDNA) is a minimally invasive biomarker that can be analyzed using next-generation sequencing (NGS) to evaluate its clinical and analytical performance in colorectal cancer (CRC) patients. Postoperative ctDNA detection can serve as a valuable marker for identifying the risk of recurrence or persistent tumor lesions in patients with CRC.
Article
Infectious Diseases
Amy Oreskovic, Adam Waalkes, Elizabeth A. Holmes, Christopher A. Rosenthal, Douglas P. K. Wilson, Adrienne E. Shapiro, Paul K. Drain, Barry R. Lutz, Stephen J. Salipante
Summary: This study characterized the size and composition of urine cell-free DNA from tuberculosis patients using next-generation sequencing, finding that MTB cfDNA is shorter and increases in abundance with shorter fragment lengths. Additionally, a larger fraction of short human genomic cfDNA was identified in urine samples, along with cfDNA fragments spanning the MTB genome.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Medical Laboratory Technology
Hyojin Chae, Pil Soo Sung, Hayoung Choi, Ahlm Kwon, Dain Kang, Yonggoo Kim, Myungshin Kim, Seung Kew Yoon
Summary: The study identified pathogenic variants of TP53 and CTNNB1 genes in cfDNA from HCC patients through deep sequencing, highlighting the utility of cfDNA analysis in identifying genetic variants in HCC patients.
ANNALS OF LABORATORY MEDICINE
(2021)
Article
Oncology
Wanyuan Cui, Charlotte Milner-Watts, Hazel O'Sullivan, Hannah Lyons, Anna Minchom, Jaishree Bhosle, Michael Davidson, Nadia Yousaf, Sophie Scott, Iris Faull, Marina Kushnir, Rebecca Nagy, Mary O'Brien, Sanjay Popat
Summary: The study compared the clinical utility of upfront cfDNA-NGS with routine tissue testing in patients with aNSCLC, finding that cfDNA-NGS can increase the detection rate of tier-1 variants, show high concordance with tissue results, and halve time-to-treatment.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Oncology
Raquel Carrasco, Mercedes Ingelmo-Torres, Josep Oriola, Fiorella L. Roldan, Leonardo Rodriguez-Carunchio, Sandra Herranz, Begona Mellado, Antonio Alcaraz, Laura Izquierdo, Lourdes Mengual
Summary: BC patients show genetic heterogeneity, yet mutations in TERT, ATM, RB1, and FGFR3 were found in primary tumors and metastases of all patients. These mutations were also detected in cfDNA at various follow-up time points, allowing us to track tumor evolution in response to treatment. The analysis of BC mutations in plasma cfDNA could serve as a valuable tool for monitoring tumor evolution and improving clinical management.
FRONTIERS IN ONCOLOGY
(2023)
Article
Medicine, General & Internal
Ami Patel, Erika Hissong, Lucelina Rosado, Robert Burkhardt, Lin Cong, Susan A. Alperstein, Momin T. Siddiqui, Hyeon Jin Park, Wei Song, Priya D. Velu, Hanna Rennert, Jonas J. Heymann
Summary: This study characterized the analytical and pre-analytical challenges encountered in the utilization of cfDNA extracted from pleural effusion supernatant in patients with metastatic NSCLC for molecular tumor profiling. Despite some technical challenges, PES was shown to be a robust source of DNA for NGS analysis.
FRONTIERS IN MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Li-Han Lin, Kuo-Wei Chang, Hui-Wen Cheng, Chung-Ji Liu
Summary: Accurate diagnosis and treatment of oral squamous cell carcinoma (OSCC) relies on understanding its genomic alterations. Liquid biopsies, specifically cell-free DNA (cfDNA) analysis, provide minimally invasive genomic profiling. By conducting whole-exome sequencing (WES) on paired OSCC plasma and whole blood samples, we identified frequently mutated genes in OSCC, correlated mutation burden with clinical parameters, and associated pathways with OSCC prognosis and distant metastasis. These findings have implications for designing targeted therapies and stratifying OSCC patients based on therapeutic efficacy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Infectious Diseases
Drew T. Bell
Summary: This article provides a review on the commercially available Karius Test, aiming to help readers understand the complexities of cf-mNGS in order to make informed test utilization policies and better interpret results.
CURRENT OPINION IN INFECTIOUS DISEASES
(2023)
Article
Pathology
Derek Hoerres, Qunsheng Dai, Sandra Elmore, Siddharth Sheth, Gaorav P. Gupta, Sunil Kumar, Margaret L. Gulley
Summary: This study proposed a new strategy to improve the accuracy of next-generation sequencing (NGS) by using spiked normalizers for calibration, which can promote standardization and harmonization of analyte concentrations. The results showed that NGS calibration achieved equivalent concentrations to droplet digital polymerase chain reaction (ddPCR), indicating the potential for a universal reference material to overcome variables hindering traditional NGS strategies for quantifying disease burden.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
(2023)
Article
Oncology
Minsuk Kwon, Bo Mi Ku, Steve Olsen, Sehhoon Park, Martina Lefterova, Justin Odegaard, Hyun-Ae Jung, Jong-Mu Sun, Se-Hoon Lee, Jin Seok Ahn, Keunchil Park, Myung-Ju Ahn
Summary: This study found that cell-free plasma DNA (cfDNA) next-generation sequencing (NGS) could detect ALK fusions and resistance mutations and predict the response and resistance to tyrosine kinase inhibitor (TKI) therapy in patients with ALK-rearranged non-small cell lung cancer (ALK+ NSCLC). Furthermore, the absence of ctDNA at baseline and clearance of ctDNA at 2 months were associated with longer progression-free survival and overall survival. Patients with co-occurring TP53 alterations and ALK fusions at baseline showed shorter progression-free survival.
Article
Surgery
Maria Posada-Gonzalez, Alejandro Villagrasa, Mariano Garcia-Arranz, Peter Vorwald, Rocio Olivera, Susana Olmedillas-Lopez, Luz Vega-Clemente, Gabriel Salcedo, Damian Garcia-Olmo
Summary: This study compared adipose-derived mesenchymal stem cells (MSCs) from healthy donors, patients with morbid obesity, and cancer, originating from omentum and subcutaneous fat depots. The cells from obese and cancer patients showed similar proliferation capacity but varied in differentiation potential and secretion of cytokines compared to healthy donor cells.
SURGICAL INNOVATION
(2022)
Letter
Cell & Tissue Engineering
Mariano Garcia-Arranz, Damian Garcia-Olmo
Article
Biochemistry & Molecular Biology
Andrea Santos, Ion Cristobal, Jaime Rubio, Cristina Carames, Melani Luque, Marta Sanz-Alvarez, Miriam Morales-Gallego, Juan Madoz-Gurpide, Federico Rojo, Jesus Garcia-Foncillas
Summary: miR-199b shows functional relevance and potential value as a novel circulating marker in locally advanced rectal cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Susana Olmedillas-Lopez, Rocio Olivera-Salazar, Mariano Garcia-Arranz, Damian Garcia-Olmo
Summary: In the era of personalized medicine and targeted therapies for cancer patients, ultrasensitive detection methods like ddPCR play a significant role in tumor genotyping. Liquid biopsy using ddPCR has seen a substantial increase in publications, providing reliable tools for detecting nucleic acid-based markers and monitoring disease progression in various cancers. Additionally, ddPCR is being investigated in a wide range of biologic fluids as alternative sources for genetic material in cancer profiling.
MOLECULAR DIAGNOSIS & THERAPY
(2022)
Article
Chemistry, Medicinal
Hector Guadalajara, Olatz Lopez-Fernandez, Miguel Leon Arellano, Victor Dominguez-Prieto, Cristina Carames, Damian Garcia-Olmo
Summary: Personalized precision medicine (PPM) advocates for the use of genomic information in personalized treatment and shared decision-making (SDM) to balance personal and clinical factors, aiming to improve the quality and value of care. However, the knowledge base for clinicians to individualize information and involve patients in the decision-making process is relatively limited. Ethical implications of SDM need to be addressed, and efforts should be made to enhance clinician and patient training, as well as the development and utilization of SDM tools in PPM.
Article
Biochemistry & Molecular Biology
Luis Javier Serrano, Mariano Garcia-Arranz, Juan A. De Pablo-Moreno, Jose Carlos Segovia, Rocio Olivera-Salazar, Damian Garcia-Olmo, Antonio Liras
Summary: Factor V deficiency is an ultra-rare congenital coagulopathy that can be modeled and potentially corrected using CRISPR/Cas9-mediated gene editing technique, which may lead to a transformation of the severe phenotype of the disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Miguel Leon Arellano, Mariano Garcia-Arranz, Hector Guadalajara, Rocio Olivera-Salazar, Teresa Valdes-Sanchez, Damian Garcia-Olmo
Summary: The methylation status of the SEPT9 gene can be used as a non-invasive and effective method to detect minimal residual disease and predict tumor recurrences in colorectal cancer. One month after surgery is the optimal time to obtain the best prediction results based on Septin 9 methylation levels.
Article
Biochemistry & Molecular Biology
Andrea Santos, Ion Cristobal, Jaime Rubio, Cristina Carames, Melani Luque, Marta Sanz-Alvarez, Sandra Zazo, Juan Madoz-Gurpide, Federico Rojo, Jesus Garcia-Foncillas
Summary: The downregulation of miR-19b enhances the antitumor effects of 5-FU treatment, and the ectopic modulation of miR-19b restores sensitivity to 5-FU treatment. Moreover, miR-19b overexpression significantly anticipates patient recurrence in LARC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Medicine, Research & Experimental
Jesus Garcia-Foncillas
ARCHIVES OF MEDICAL RESEARCH
(2022)
Article
Medicine, Research & Experimental
Juan Manuel Corral, Laura del Puerto-Nevado, Mabel Cedeno, Anxo Rio-Vilarino, Ignacio Mahillo-Fernandez, Carlos Galeano, Natalia Banos, Jesus Garcia-Foncillas, Manuel Domine, Arancha Cebrian
Summary: This study found that high levels of Gal-1 and PLR were associated with poorer prognosis in SCLC patients, supporting their utility as clinical prognostic biomarkers. Additionally, an in vivo model suggested that inhibition of Gal-1 may be a novel potential therapy for this disease with very poor prognosis.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Review
Surgery
D. Garcia-Olmo, M. Gomez-Barrera, F. de la Portilla
Summary: A systematic literature review compared the results of different techniques used in the treatment of Crohn's disease or cryptoglandular fistula. The study found that new surgical techniques had better healing rates in Crohn's disease patients compared to traditional techniques, while traditional techniques had better results in cryptoglandular fistula. The new techniques were less invasive and could improve fecal incontinence rates.
Article
Medicine, General & Internal
Weiyao Li, Miguel Gonzalez-Gonzalez, Lara Sanz-Criado, Nuria Garcia-Carbonero, Angel Celdran, Pedro Villarejo-Campos, Pablo Minguez, Roberto Pazo-Cid, Custodia Garcia-Jimenez, Alberto Orta-Ruiz, Jesus Garcia-Foncillas, Javier Martinez-Useros
Summary: Pancreatic cancer is a deadly tumor that is difficult to detect early, making the development of non-invasive biomarkers necessary. This study reveals that certain piRNAs regulated by PIWIL3 and PIWIL4 show differential expression in pancreatic cancer, and some of these piRNAs can be used as biomarkers for pancreatic cancer in liquid biopsies.
JOURNAL OF CLINICAL MEDICINE
(2022)
Editorial Material
Cell & Tissue Engineering
Rachele Ciccocioppo, Hector Guadalajara, Giuseppe Astori, Giorgio Carlino, Damian Garcia-Olmo
Article
Medicine, General & Internal
Pedro Villarejo-Campos, Mariano Garcia-Arranz, Siyuan Qian, Santos Jimenez de los Galanes, Victor Dominguez-Prieto, Juan Felipe Velez-Pinto, Ismael Guijo Castellano, Montiel Jimenez-Fuertes, Hector Guadalajara, Damian Garcia-Olmo
Summary: This study investigated the immunohistochemical and biological characteristics of mucin in patients with cellular and acellular pseudomyxoma peritonei, and found that MUC-2 and mucin-5AC were the primary components of mucin in both types. Additionally, Pseudomonas was the most common bacterial genus colonizing the mucin. These findings have significant implications for the diagnosis and treatment of pseudomyxoma peritonei.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Oncology
David Garcia-Gonzalez, Juan Medino-Munoz, Maria Romero-Elias, Jesus Garcia-Foncillas, Ana Ruiz-Casado
Summary: Cancer-related fatigue (CRF) is a multidimensional symptom affecting physical, emotional, and cognitive spheres in cancer survivors. This study aims to summarize the knowledge about the biological mechanisms that potentially drive CRF in breast cancer survivors (BCS) after treatment, and highlight the need for further research in this area.
JOURNAL OF CANCER SURVIVORSHIP
(2023)
