Article
Biotechnology & Applied Microbiology
Nida Anwar, Faheem Ahmed Memon, Saba Shahid, Muhammad Shakeel, Muhammad Irfan, Aisha Arshad, Arshi Naz, Ikram Din Ujjan, Tahir Shamsi
Summary: Sequencing studies on MDS patients in Pakistan revealed various genetic mutations associated with myeloid malignancies, including mutations not previously observed in MDS or AML. These findings highlight the importance of molecular profiling in diagnosis and treatment of MDS patients in countries with limited resources like Pakistan. Further research with larger sample sizes is necessary to compare molecular characteristics between Asian and global populations.
Article
Immunology
Gregoire Martin de Fremont, Pierre Hirsch, Santiago Gimenez de Mestral, Philippe Moguelet, Yoan Ditchi, Jean-Francois Emile, Patricia Senet, Sophie Georgin-Lavialle, Thomas Hanslik, Francois Maurier, Amir Adedjouma, Noemie Abisror, Thibault Mahevas, Florent Malard, Lionel Ades, Pierre Fenaux, Olivier Fain, Francois Chasset, Arsene Mekinian
Summary: In most cases of MDS/CMML, skin lesions are characterized by a clonal myeloid infiltrate, and there is generally a similar mutational profile between blood/bone marrow and skin.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Yucong Li, Rui Chen, Mingming Yuan, Dong Wang, Chunling Fu, Rongrong Chen, Cuirong Lei, Qi Zhou
Summary: This study investigates the feasibility of molecular classification using comprehensive next-generation sequencing techniques and its relationship with survival outcomes in patients with endometrial cancer. The results show that comprehensive next-generation sequencing is a reliable method for stratifying the prognosis of endometrial cancer and has the potential to guide the treatment of patients in clinical practice.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Genetics & Heredity
Yongzhi Feng, Xialin Chen, Keran Jiang, Ding Zhang, Feng Tao, Dan Ni, Jun Zhang, Lixin Wu, Jinping Cai, Libin Jiang, GenHua Yu, Lin Shi
Summary: This case report describes a non-small cell lung cancer (NSCLC) patient who developed secondary myelodysplastic syndrome (MDS) due to long-term exposure to chemicals, diagnosed through next-generation sequencing (NGS) analysis. The NGS analysis may serve as supplementary for the diagnosis of secondary MDS and provide useful information for treatment.
BMC MEDICAL GENOMICS
(2021)
Review
Oncology
Lamia Madaci, Laure Farnault, Norman Abbou, Jean Gabert, Geoffroy Venton, Regis Costello
Summary: Cytological approaches have been used for the diagnosis, prognosis, and management of acute myeloid leukemia (AML) and myelodysplastic neoplasms. Technological advances in molecular biology, particularly next-generation sequencing (NGS), have made it possible to quickly identify gene mutations in AML and MDS. The combination of cytological approaches and NGS enables better clinical management and improved prognosis for patients with acute leukemia and myelodysplastic neoplasms.
Article
Hematology
Weerapat Owattanapanich, Julia Herzig, Nikolaus Jahn, Ekaterina Panina, Theera Ruchutrakool, Smith Kungwankiattichai, Surapol Issaragrisil, Hartmut Doehner, Konstanze Doehner
Summary: This study investigated the molecular genetic aberrations in Thai patients with AML and MDS-EB using NGS, revealing FLT3-ITD, DNMT3A, and WT1 as the most frequent mutations. Patients aged over 65 years and those with TP53 mutations were found to have inferior survival outcomes.
ANNALS OF HEMATOLOGY
(2021)
Article
Immunology
Shilei Wang, Lihua Xing
Summary: Metagenomics next-generation sequencing (mNGS) is a promising method for detecting pathogenic infections, especially Non-Tuberculous Mycobacterial (NTM) and tuberculosis (TB). In this study, mNGS analysis successfully identified six distinct NTM species, primarily Mycobacterium avium complex (MAC). Conventional culture methods faced challenges, resulting in negative results, while qPCR testing showed positive results for the NTM infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Oncology
Annika Kasprzak, Kathrin Nachtkamp, Norbert Gattermann, Ulrich Germing
Summary: This article discusses the prognostic scoring systems for myelodysplastic syndromes (MDS) and chronic myelomonocytic leukemia (CMML). It highlights the limitations of current scoring systems and emphasizes the importance of patient and disease-related parameters in assessing prognosis. The article also identifies areas for further investigation.
Review
Genetics & Heredity
Chiara Chiereghin, Erica Travaglino, Matteo Zampini, Elena Saba, Claudia Saitta, Elena Riva, Matteo Bersanelli, Matteo Giovanni Della Porta
Summary: Myelodysplastic syndromes (MDS) are clonal diseases driven by a complex combination of genetic mutations, resulting in ineffective hematopoiesis and an increased risk of progression to acute myeloid leukemia. These mutations can be categorized into a limited number of cellular pathways, influencing clinical phenotype, disease progression, and prognosis.
Article
Oncology
Vijaya Kadam Maruthi, Mahyar Khazaeli, Devi Jeyachandran, Mohamed Mokhtar Desouki
Summary: Targeted therapy based on test results has high clinical utility and can improve survival for gynecologic cancer patients.
Article
Genetics & Heredity
Jifeng Zhu, Junying Zhang, Meiyan Jiang, Weirong Wang, Jianxia Jiang, Yanli Li, Liyong Yang, Xirong Zhou
Summary: Rapeseed is an important oil crop with a huge genome. Next generation sequencing technology was used to develop SSR markers in rapeseed, which were validated and tested for polymorphism, demonstrating their usefulness in genetic studies of rapeseed.
Article
Oncology
Alessandro Liquori, Ivan Lesende, Laura Palomo, Gayane Avetisyan, Mariam Ibanez, Elisa Gonzalez-Romero, Mireia Boluda-Navarro, Mireya Morote-Faubel, Cristian Garcia-Ruiz, Cristina Martinez-Valiente, Marta Santiago-Balsera, Ines Gomez-Segui, Alejandra Sanjuan-Pla, Miguel A. Sanz, Guillermo Sanz, Francesc Sole, Esperanza Such, Jose Cervera
Summary: This study introduced a novel NGS-based strategy for detecting clinically relevant genetic alterations associated with MDS and myeloid-related disorders, showing significant improvement in diagnosis and risk stratification. Validation on a large patient cohort demonstrated high concordance with standard clinical assays, highlighting the sensitivity and capability of this NGS platform in identifying key genetic alterations.
Article
Oncology
Rashmi Kanagal-Shamanna, Guillermo Montalban-Bravo, Koji Sasaki, Faezeh Darbaniyan, Elias Jabbour, Carlos Bueso-Ramos, Yue Wei, Kelly Chien, Tapan Kadia, Farhad Ravandi, Gautam Borthakur, Kelly A. Soltysiak, Mark Routbort, Keyur Patel, Sherry Pierce, L. Jeffrey Medeiros, Hagop Kantarjian, Guillermo Garcia-Manero
Summary: The subtype of SF3B1 mutation plays a key role in risk assessment and prognosis of MDS, with K700E mutation associated with a favorable outcome compared to non-K700E mutations. This highlights the importance of refining MDS subclassification based on different SF3B1 mutation subtypes.
Article
Oncology
Wan-Hsuan Lee, Chien-Chin Lin, Yu-Hung Wang, Chi-Yuan Yao, Yuan-Yeh Kuo, Mei-Hsuan Tseng, Yen-Ling Peng, Cheng-An Hsu, Hsun- Sun, Yi-Kuang Chuang, Chia-Lang Hsu, Feng-Ming Tien, Cheng-Hong Tsai, Wen-Chien Chou, Hsin-An Hou, Hwei-Fang Tien
Summary: This study compared the genetic landscape between younger and older patients with MDS and found distinct genetic characteristics and differences in the impact of mutations on survival based on age.
HEMATOLOGICAL ONCOLOGY
(2023)
Article
Pathology
Ching-Yeuh Yanga, Yi-Che Yeh, Lei-Chi Wanga, Yen-Yu Lina, Shin-Ying Lina, Shu-Ying Wanga, Ping-Yuan Chua, Zih-Yu Liua, Yu-Chi Sua, Hsiang-Ling Ho, Teh-Ying Choua
Summary: This study aimed to investigate the value of large-scale next-generation sequencing (NGS) panels in distinguishing between separate primary lung cancers (SPLCs) and intrapulmonary metastases (IPMs). With NGS and a molecular classification algorithm, 97.6% of tumor pairs can be accurately classified as SPLCs or IPMs. The molecular classification was predictive of postoperative clinical outcomes in terms of overall survival and recurrence-free interval, providing accurate risk stratification.
Article
Pathology
Lingyun Wu, Mohammad Awaji, Sugandha Saxena, Michelle L. Varney, Bhawna Sharma, Rakesh K. Singh
AMERICAN JOURNAL OF PATHOLOGY
(2020)
Article
Multidisciplinary Sciences
Xu Wang, Guohua Gan, Ling-Yun Wu
Article
Multidisciplinary Sciences
Xiao Li, Feng Xu, Ling-Yun Wu, You-Shan Zhao, Juan Guo, Qi He, Zheng Zhang, Chun-Kang Chang, Dong Wu
SCIENTIFIC REPORTS
(2020)
Letter
Hematology
Lingyun Wu, Xiao Li, Feng Xu, Dong Wu, Qi He, Luxi Song, Chao Xiao, Youshan Zhao, Zheng Zhang, Juan Guo, Liyu Zhou, Jiying Su, Chunkang Chang
BRITISH JOURNAL OF HAEMATOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Mohammad Awaji, Sugandha Saxena, Lingyun Wu, Dipakkumar R. Prajapati, Abhilasha Purohit, Michelle L. Varney, Sushil Kumar, Satyanarayana Rachagani, Quan P. Ly, Maneesh Jain, Surinder K. Batra, Rakesh K. Singh
Article
Cell Biology
Yuqian Zhu, Dandan Song, Juan Guo, Jiacheng Jin, Ying Tao, Zheng Zhang, Feng Xu, Qi He, Xiao Li, Chunkang Chang, Lingyun Wu
Summary: The study found that U2AF1 mutations are associated with poor prognosis in MDS and AML patients, significantly inhibiting cell proliferation and inducing cellular apoptosis in cell models. The results showed that U2AF1 mutations promoted FOXO3a-dependent apoptosis and NLRP3 inflammasome activation, leading to pyroptotic cell death. FOXO3a was identified as the key molecule on which these pathways converge.
CELL DEATH & DISEASE
(2021)
Article
Oncology
Xiao Li, Feng Xu, Zheng Zhang, Juan Guo, Qi He, Lu-Xi Song, Dong Wu, Li-Yu Zhou, Ji-Ying Su, Chao Xiao, Chun-Kang Chang, Ling-Yun Wu
Summary: BCOR mutations are more common in CN MDS patients, predicting a higher risk of leukemia transformation. BCORMUT patients showed a better response to decitabine and achieved longer post-CR survival.
CLINICAL EPIGENETICS
(2021)
Article
Multidisciplinary Sciences
Bo Gao, Yue Zhao, Yonghang Gao, Guojun Li, Ling-Yun Wu
Summary: High-throughput biological data has provided an opportunity to illuminate the mechanisms of tumor emergence and evolution, with the tool ComCovEx being developed to explore common cancer driver gene modules between two cancers and reveal their associations. The research results offer new insights into the pathological basis of different cancer types and provide new clues for the diagnosis and treatment of associated cancers.
Review
Operations Research & Management Science
Xu Wang, Ling-Yun Wu
Summary: Blockchain technology has rapidly developed and been applied in various scenarios beyond cryptocurrencies, with a focus on security, efficiency, and resource allocation. This paper aims to analyze blockchain technology from the perspective of operations research and address relevant issues to promote its wider application in the future.
JOURNAL OF THE OPERATIONS RESEARCH SOCIETY OF CHINA
(2022)
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: This study introduces a novel Importance-Penalized Joint Graphical Lasso method (IPJGL) for differential network inference, where the importance of genes is taken into consideration. The method is validated through simulation experiments and real datasets. Additionally, a new metric named APC2 is proposed to assess the differential levels of gene pairs.
Article
Biotechnology & Applied Microbiology
Duanchen Sun, Xiangnan Guan, Amy E. Moran, Ling-Yun Wu, David Z. Qian, Pepper Schedin, Mu-Shui Dai, Alexey Danilov, Joshi J. Alumkal, Andrew C. Adey, Paul T. Spellman, Zheng Xia
Summary: Scissor is a method that identifies cell subpopulations associated with a given phenotype from single-cell data, by quantifying the similarity between single cells and bulk samples, and optimizing a regression model with sample phenotype. Applied in lung cancer, melanoma, facioscapulohumeral muscular dystrophy, and Alzheimer's disease datasets, Scissor effectively identifies biologically and clinically relevant cell subpopulations.
NATURE BIOTECHNOLOGY
(2022)
Article
Physics, Multidisciplinary
Jiating Yu, Ling-Yun Wu
Summary: Link prediction is a classical problem in the field of complex networks, which is of great significance for understanding the evolution and dynamic development mechanisms of networks. This study proposes a novel method called MOLI, which utilizes local information from neighbors at different distances and defines a local network diffusion process via random walks on the graph, achieving better utilization of network information. The results show that MOLI outperforms other widely used link prediction methods on different types of networks.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: Gene-based transcriptome analysis can identify key factors causing disease production and cell differentiation, but basic life activities are mainly driven by gene interactions, requiring interaction-based transcriptome analysis to investigate insights into differential gene interactions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Physics, Multidisciplinary
Jiating Yu, Jiacheng Leng, Duanchen Sun, Ling-Yun Wu
Summary: Network models are widely used in various fields for their ability to represent relationships between variables. Network structure can be unclear due to factors like experimental noise and missing data, hindering downstream analyses such as community detection. Therefore, network denoising is necessary before analysis. However, the importance of network pre-processing for community detection has been neglected. In this study, a novel network denoising method, called Network Refinement (NR), was proposed to enhance the self-organization properties of complex networks through a global diffusion process. NR significantly improved the clarity of the network's mesoscale structure and boosted the performance of various community detection algorithms.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Hematology
Yuqian Zhu, Lingyun Wu