Review
Biochemistry & Molecular Biology
Tanzila Khan, Therese M. Becker, Joseph W. Po, Wei Chua, Yafeng Ma
Summary: The field of single-cell analysis has advanced rapidly in the last decade and is providing new insights into the characterization of intercellular genetic heterogeneity and complexity, especially in human cancer. Analyzing single circulating tumor cells (CTCs) is becoming particularly attractive due to the easy access to CTCs from simple blood samples called liquid biopsies. Whole genome amplification (WGA) techniques have emerged as a key step, enabling single-cell downstream molecular analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Sushmaa Chandralekha Selvakumar, K. Auxzilia Preethi, Kehinde Ross, Deusdedit Tusubira, Mohd Wajid Ali Khan, Panagal Mani, Tentu Nageswara Rao, Durairaj Sekar
Summary: Personalized or precision medicine combines genetic information with phenotypic and environmental characteristics to tailor healthcare to individuals, enabled by cancer genome sequencing. The advantages of NGS, such as limited sample requirements and the development of biomarkers, have accelerated personalized medicine.
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Article
Medicine, General & Internal
Cienne Morton, Debashis Sarker, Paul Ross
Summary: Cancers contain numerous mutations, but only a few are critical for malignancy. Targeted therapies and immunotherapy have shown great success in various cancer types. Next-generation sequencing enables the detection of potentially actionable mutations and contributes to the identification of new biomarkers. However, technical challenges and the development of targeted therapies against common genomic aberrations need to be overcome for personalized medicine to become more widely available.
Article
Virology
Laila Sara Arroyo Muhr, Daniel Guerendiain, Kate Cuschieri, Karin Sundstrom
Summary: NGS technology provides powerful opportunities for HPV genomics research, but rigorous validation and quality assurance procedures are essential to ensure reliable interpretation of results. Recommendations for optimizing sequencing data yield and curated bioinformatical procedures are crucial for robust analysis of HPV genotypes and mutations. International standards for quality assurance in HPV NGS should be developed to enhance testing and diagnostics in global efforts.
Review
Oncology
Paul Hofman
Summary: Liquid biopsy (LB) has become the only option to detect molecular targets for first-line treatment in treatment-naive NSCLC patients. Despite not being commonly used in diagnosis currently, Next-Generation Sequencing (NGS) shows the most promise for assessing genetic abnormalities.
Article
Immunology
Chengxin Liu, Juhua Yang, Huiting Huang, Shaofeng Zhan, Xintian Xia
Summary: Infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis, usually occurring in patients with immune deficiency. We report a case of a 23-year-old female with a 10-year history of cough and sputum production, diagnosed with bronchiectasis. The infection was identified using metagenomic next-generation sequencing and whole genome sequencing, and was controlled with appropriate medication.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Martin Hoenigl, Matthias Egger, Jessica Price, Robert Krause, Juergen Prattes, P. Lewis White
Summary: Timely diagnosis remains an unmet need in non-neutropenic patients at risk for aspergillosis, including those with COVID-19-associated pulmonary aspergillosis (CAPA). Currently available mycological tests show limited sensitivity when testing blood specimens. Metagenomic next-generation sequencing (mNGS) to detect microbial cell-free DNA (mcfDNA) in plasma might overcome some of the limitations of conventional diagnostics.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Hematology
Amanda M. Casto, David N. Fredricks, Joshua A. Hill
Summary: The diagnosis of infectious diseases in immunocompromised hosts is challenging, and metagenomic next generation sequencing (mNGS) based diagnostics have shown potential in identifying causative organisms. However, current studies have limitations, and further research is needed to assess its performance and clinical impact.
Article
Parasitology
Banucicek Yucesan, Dilek Guldemir, Cahit Babur, Selcuk Kilic, Ayse Cakmak
Summary: This study successfully conducted whole-genome sequencing of T. gondii for the first time in Turkey, providing important data for better understanding this pathogen.
Review
Medicine, General & Internal
Antonio Santisteban-Espejo, Irene Bernal-Florindo, Jose Perez-Requena, Lidia Atienza-Cuevas, Julia Moran-Sanchez, Maria del Carmen Fernandez-Valle, Raquel Romero-Garcia, Marcial Garcia-Rojo
Summary: This study systematically reviews the current state of NGS studies of cHL, emphasizing the need for standardization in candidate genes and bioinformatic pipelines. Comparing and reviewing the major findings of this ongoing research area could be valuable for centers that routinely perform diagnostic, monitoring, and genotyping strategies in cHL samples.
Article
Biology
Yumi Yoshii, Shunsuke Okazaki, Masayuki Takeda
Summary: Next-generation sequencing-based comprehensive genome profiling (CGP) testing has been covered by the Japanese national health insurance system, but faces limitations such as deteriorating patient condition during analysis and a limited number of ongoing clinical trials. Despite approval of tumor-agnostic therapies in Japan, performing CGP using DNA derived from tumor tissue poses challenges in cases with insufficient tissue.
Article
Oncology
Masato Kojima, Takanori Harada, Takahiro Fukazawa, Sho Kurihara, Ryo Touge, Isamu Saeki, Shinya Takahashi, Eiso Hiyama
Summary: In this study, single-cell next-generation sequencing of circulating tumor cells (CTCs) from neuroblastoma (NB) patients was performed. The findings showed that the isolation rate of CTCs was associated with disease progression, and single-cell RNA sequencing revealed upregulated genes related to angiogenesis and cell cycle in CTCs. These results indicate the utility of single-cell CTC sequencing in characterizing NB tumor biology and metastasis mechanisms.
Article
Oncology
Chunming Wang, Qiong Luo, Wenbin Huang, Cheng Zhang, Hangyu Liao, Kunling Chen, MingXin Pan
Summary: Liquid biopsy as a method for real-time monitoring of cancer patients is gaining attention. A new method combining CTC enrichment technology with NGS was explored to analyze genetic variations in hepatocellular carcinoma patients. The number of CTCs and CTC-WBC clusters in peripheral blood of patients with liver cancer was found to be related to specific genomic profiles.
FRONTIERS IN ONCOLOGY
(2021)
Review
Biochemical Research Methods
Francesca Salvianti, Stefania Gelmini, Filomena Costanza, Irene Mancini, Gemma Sonnati, Lisa Simi, Mario Pazzagli, Pamela Pinzani
Article
Medical Laboratory Technology
Rita Lampignano, Martin H. D. Neumann, Sabrina Weber, Vera Kloten, Andrei Herdean, Thorsten Voss, Daniel Groelz, Anna Babayan, Marco Tibbesma, Martin Schlumpberger, Francesca Chemi, Dominic G. Rothwell, Harriet Wikman, Jean-Pierre Galizzi, Inger Riise Bergheim, Hege Russnes, Benedetta Mussolin, Serena Bonin, Christine Voigt, Hanny Musa, Pamela Pinzani, Evi Lianidou, Ged Brady, Michael R. Speicher, Klaus Pantel, Fotini Betsou, Ed Schuuring, Mikael Kubista, Wim Ammerlaan, Markus Sprenger-Haussels, Thomas Schlange, Ellen Heitzer
CLINICAL CHEMISTRY
(2020)
Correction
Biochemical Research Methods
F. Salvianti, S. Gelmini, F. Costanza, I. Mancini, G. Sonnati, L. Simi, M. Pazzagli, P. Pinzani
Article
Andrology
Gianmartin Cito, Maria Elisabetta Coccia, Francesca Salvianti, Rossella Fucci, Rita Picone, Claudia Giachini, Andrea Cocci, Patrizia Falcone, Elisabetta Micelli, Pierangelo Verrienti, Andrea Minervini, Marco Carini, Pamela Pinzani, Alessandro Natali
Meeting Abstract
Oncology
G. Francolini, V. Salvestrini, M. Loi, M. Mangoni, B. Detti, P. Pinzani, F. Salvianti, I. Desideri, M. Aquilano, M. Mariotti, P. Garlatti, G. Stocchi, L. P. Ciccone, S. Lucidi, G. Salvatore, M. Sottili, I. Meattini, L. Livi
ANNALS OF ONCOLOGY
(2020)
Article
Urology & Nephrology
Donata Villari, Francesca Salvianti, Maria Zanazzi, Alberto Martini, Pietro Spatafora, Simone Caroassai Grisanti, Arcangelo Sebastianelli, Giulio Nicita, Sergio Serni, Pamela Pinzani
UROLOGIA INTERNATIONALIS
(2020)
Article
Biochemical Research Methods
Enrico Baria, Riccardo Cicchi, Francesca Malentacchi, Irene Mancini, Pamela Pinzani, Marco Pazzagli, Francesco S. Pavone
Summary: Malignant melanoma is a deadly form of skin cancer caused by genetic mutations in melanocytes, with BRAF and NRAS being the most frequent genes involved. This study utilized Raman spectroscopy to examine melanoma cell lines with specific mutations, developing accurate classification algorithms based on the obtained molecular information. The results suggest that Raman spectroscopy could be an effective tool for detecting molecular differences between melanoma mutations, with high accuracy in discriminating different cell types.
JOURNAL OF BIOPHOTONICS
(2021)
Review
Medical Laboratory Technology
Pamela Pinzani, Valeria D'Argenio, Marzia Del Re, Cristina Pellegrini, Federico Cucchiara, Francesca Salvianti, Silvia Galbiati
Summary: Liquid biopsy is an emerging, non-invasive method for detecting and monitoring cancer in various body fluids, rather than tumor tissue. By analyzing circulating tumor cells, DNA, RNA, etc., it can reflect the disease evolution of patients.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2021)
Meeting Abstract
Oncology
Giulio Francolini, Pietro Garlatti, Mauro Loi, Beatrice Detti, Michele Aquilano, Andrea Allegra, Barbara Guerrieri, Viola Salvestrini, Pamela Pinzani, Chiara Bellini, Francesca Salvianti, Giulia Stocchi, Lucia Pia Ciccone, Giulia Salvatore, Mariangela Sottili, Vanessa Di Cataldo, Isacco Desideri, Monica Mangoni, Icro Meattini, Lorenzo Livi
JOURNAL OF CLINICAL ONCOLOGY
(2021)
Article
Oncology
Francesca Salvianti, Stefania Gelmini, Irene Mancini, Mario Pazzagli, Serena Pillozzi, Elisa Giommoni, Marco Brugia, Francesco Di Costanzo, Francesca Galardi, Francesca De Luca, Francesca Castiglione, Luca Messerini, Pamela Pinzani, Lorenzo Antonuzzo
Summary: Liquid biopsy, including cfDNA and CTCs, shows prognostic value in KRAS mutated mCRC. CTCs are a negative prognostic marker at baseline, while cfDNA is easily accessible for monitoring tumor mutations over time. In longitudinal monitoring, these two markers complement each other in assessing disease progression.
BRITISH JOURNAL OF CANCER
(2021)
Article
Oncology
G. Francolini, M. Loi, V. Salvestrini, M. Mangoni, B. Detti, V. Di Cataldo, M. Aquilano, P. Pinzani, F. Salvianti, I. Desideri, M. Mariotti, P. Garlatti, G. Stocchi, L. P. Ciccone, S. Lucidi, G. Salvatore, M. Sottili, I. Meattini, L. Livi
Summary: This study investigated the predictive value of miRNA and ARV7 mutational status in mCRPC patients, as well as the role of CTC detection in 1st line therapy. Results showed that CTC+ and ARFL+ patients had significantly reduced TTCR, indicating the important impact of CTC detection and ARFL expression on patient prognosis.
CLINICAL & EXPERIMENTAL METASTASIS
(2021)
Article
Oncology
Giulia Cantini, Letizia Canu, Roberta Armignacco, Francesca Salvianti, Giuseppina De Filpo, Tonino Ercolino, Gabriella Nesi, Mario Maggi, Massimo Mannelli, Pamela Pinzani, Michaela Luconi
Meeting Abstract
Obstetrics & Gynecology
G. Cito, P. Pinzani, R. Fucci, R. Picone, F. Salvianti, C. Giachini, P. Falcone, E. Micelli, A. Cocci, P. Verrienti, A. Minervini, M. Carini, A. Natali, M. E. Coccia
HUMAN REPRODUCTION
(2020)
Meeting Abstract
Oncology
Giulio Francolini, Mauro Loi, Beatrice Detti, Monica Mangoni, Isacco Desideri, Cristina Muntoni, Lucia Pia Ciccone, Michele Aquilano, Pamela Pinzani, Francesca Salvianti, Sara Lucidi, Matteo Mariotti, Pietro Garlatti, Giulia Salvatore, Mariangela Sottili, Lorenzo Livi
JOURNAL OF CLINICAL ONCOLOGY
(2020)