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Adjeroud M, Kecha M, Escuder-Rodríguez JJ, Becerra M, González-Siso MI. AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer. Appl Microbiol Biotechnol 2024; 108:114. [PMID: 38204131 PMCID: PMC10781878 DOI: 10.1007/s00253-023-12844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/12/2024]
Abstract
A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.
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Affiliation(s)
- Moussa Adjeroud
- Laboratoire de Mycologie, Département de Biologie Appliquée, de Biotechnologie Et de L'Activité Microbienne (LaMyBAM), Faculté Des Sciences de La Nature Et de La Vie, Université Des Frères Mentouri Constantine 1, 25000, Constantine, Algeria
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université de Bejaia, Campus Targa Ouzemmour, 6000, Bejaia, Algeria
| | - Juan-José Escuder-Rodríguez
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Manuel Becerra
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
| | - María-Isabel González-Siso
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
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Yunus A, Mokhtar NM, Raja Ali RA, Ahmad Kendong SM, Ahmad HF. Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues. MethodsX 2024; 12:102623. [PMID: 38435637 PMCID: PMC10907193 DOI: 10.1016/j.mex.2024.102623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a putative biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To characterize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis revealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Expanding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer.•Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing.•Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening.•Contribution to the advancement of innovative colorectal cancer diagnostic methods and targeted therapies by applying gut mycobiome knowledge.
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Affiliation(s)
- Aisyah Yunus
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah (UMPSA), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), 56000 Kuala Lumpur, Malaysia
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
- School of Medical and Life Sciences, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
| | - Siti Maryam Ahmad Kendong
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), 56000 Kuala Lumpur, Malaysia
- Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah (UMPSA), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
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Yang L, Su J, Zhuo C. A case of intracranial infection caused by Aspergillus flavus originating from chronic otitis media. Med Mycol Case Rep 2024; 44:100637. [PMID: 38585188 PMCID: PMC10997898 DOI: 10.1016/j.mmcr.2024.100637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/09/2024] Open
Abstract
Central nervous system (CNS) aspergillosis is uncommon in immunocompetent patients. We present a 64-year-old man with chronic otitis media and uncontrolled diabetes. Aspergillus flavus was identified in cerebrospinal fluid via metagenomics next-generation sequencing technology. Initial voriconazole treatment offered limited relief, but personalized dosage adjustments, guided by drug concentration, led to remission. This case underscores the importance of diverse diagnostic approaches and tailored therapy for CNS Aspergillus infections.
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Affiliation(s)
- Ling Yang
- Department of Infection, The First Hospital of Guangzhou Medical University, Guangzhou, 510000, China
| | - Jiacun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Chao Zhuo
- Department of Infection, The First Hospital of Guangzhou Medical University, Guangzhou, 510000, China
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Mat-Hussin NH, Siew SW, Maghpor MN, Gan HM, Ahmad HF. Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing. MethodsX 2024; 12:102636. [PMID: 38439930 PMCID: PMC10909749 DOI: 10.1016/j.mex.2024.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
The exposure of the air microbiome in indoor air posed a detrimental health effect to the building occupants compared to the outdoor air. Indoor air in hospitals has been identified as a reservoir for various pathogenic microbes. The conventional culture-dependent method has been widely used to access the microbial community in the air. However, it has limited capability in enumerating the complex air microbiome communities, as some of the air microbiomes are uncultivable, slow-growers, and require specific media for cultivation. Here, we utilized a culture-independent method via amplicon sequencing to target the V3 region of 16S rRNA from the pool of total genomic DNA extracted from the dust samples taken from hospital interiors. This method will help occupational health practitioners, researchers, and health authorities to efficiently and comprehensively monitor the presence of harmful air microbiome thus take appropriate action in controlling and minimizing the health risks to the hospital occupants. Key features;•Culture-independent methods offer fast, comprehensive, and unbias profiles of pathogenic and non-pathogenic bacteria from the air microbiomes.•Unlike the culture-dependent method, amplicon sequencing allows bacteria identification to the lowest taxonomy levels.
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Affiliation(s)
- Nor Husna Mat-Hussin
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
| | - Shing Wei Siew
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
| | - Mohd Norhafsam Maghpor
- Laboratory Division, Consultation and Research Department, National Institute of Occupational Safety and Health (NIOSH), Seksyen 15, Bandar Baru Bangi, Selangor 43650, Malaysia
| | - Han Ming Gan
- Patriot Biotech Sdn. Bhd., Bandar Sunway, Subang Jaya, Selangor 47500, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
- Group of Environment, Microbiology and Bioprocessing (GERMS), Universiti Malaysia Pahang, Lebuhraya Persiaran Tun Khalil Yaakob, Gambang, Kuantan, Pahang 26300, Malaysia
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Roy S, Mukhopadhyay A. A randomized optimal k-mer indexing approach for efficient parallel genome sequence compression. Gene 2024; 907:148235. [PMID: 38342250 DOI: 10.1016/j.gene.2024.148235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/13/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
Next Generation Sequencing (NGS) technology generates massive amounts of genome sequence that increases rapidly over time. As a result, there is a growing need for efficient compression algorithms to facilitate the processing, storage, transmission, and analysis of large-scale genome sequences. Over the past 31 years, numerous state-of-the-art compression algorithms have been developed. The performance of any compression algorithm is measured by three main compression metrics: compression ratio, time, and memory usage. Existing k-mer hash indexing systems take more time, due to the decision-making process based on compression results. In this paper, we propose a two-phase reference genome compression algorithm using optimal k-mer length (RGCOK). Reference-based compression takes advantage of the inter-similarity between chromosomes of the same species. RGCOK achieves this by finding the optimal k-mer length for matching, using a randomization method and hashing. The performance of RGCOK was evaluated on three different benchmark data sets: novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Homo sapiens, and other species sequences using an Amazon AWS virtual cloud machine. Experiments showed that the optimal k-mer finding time by RGCOK is around 45.28 min, whereas the time for existing state-of-the-art algorithms HiRGC, SCCG, and HRCM ranges from 58 min to 8.97 h.
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Affiliation(s)
- Subhankar Roy
- Department of Computer Science and Engineering, Academy of Technology, Adisaptagram, Hooghly 712121, West Bengal, India.
| | - Anirban Mukhopadhyay
- Department of Computer Science and Engineering, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
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Li Q, Jiang M, Hong S, Yang J, Wu X, Pang J, Chen Y, Zhao X, Ding X. Comprehensive genomic and clinical analyses identify APOBEC mutational signatures as a brain metastasis risk factor in lung adenocarcinoma patients. Transl Oncol 2024; 43:101921. [PMID: 38402722 PMCID: PMC10904272 DOI: 10.1016/j.tranon.2024.101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma is the most common source of brain metastasis (BM), resulting in significant morbidity and mortality. We aimed to identify patients with high BM risk who possibly benefit from brain-penetrant drugs, prophylactic cranial irradiation, or close brain magnetic resonance imaging surveillance. METHODS Metastatic lung adenocarcinoma patients with extracranial tumor samples profiled by a next-generation sequencing panel targeting 425 tumor-related genes were retrospectively enrolled between February 2008 and July 2021. We compared BM and non-BM patients' genomic and clinical features and studied their associations with BM risk. Two external cohorts were used for result validation and molecular mechanisms investigation, respectively. RESULTS We included 174 eligible patients, including 90 having developed BM by the end of follow-up. Age≤60, EGFR activating mutations, and high-level apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) mutational signatures were associated with elevated BM risk. Similar findings in BM-free survival were obtained by fitting Fine-Gray subdistribution hazard models addressing competing risks. Increased BM risk related to APOBEC mutational signatures was validated in an external cohort (N = 440). RNA sequencing data analyses performed in another external cohort (N = 230) revealed that expressions of metastasis-related pathways such as transforming growth factor (TGF)β and epithelial-mesenchymal transition (EMT) were upregulated in the patients with high-level APOBEC mutational signatures. CONCLUSION APOBEC mutational signatures related to upregulated TGFβ and EMT, could serve as an independent risk factor for BM and BM-free survival in metastatic lung adenocarcinoma patients. Further investigations are warranted to tailor personalized treatments to improve the susceptible patient's outcomes.
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Affiliation(s)
- Qiang Li
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Meng Jiang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Department of Neurosurgery, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Shiqiang Hong
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Jing Yang
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China
| | - Xiaoying Wu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Yedan Chen
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Xiaotian Zhao
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, China
| | - Xiao Ding
- Cancer Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China; Cancer Center, Shandong Provincial Hospital, Shandong University, Jinan, 250021, China.
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Khan R, Sunthankar KI, Yasinzai AQK, Tareen B, Zarak MS, Khan J, Nasir H, Nakasaki M, Jahangir E, Heneidi S, Ullah A. Primary cardiac sarcoma: demographics, genomic study correlation, and survival benefits of surgery with adjuvant therapy in U.S. population. Clin Res Cardiol 2024; 113:694-705. [PMID: 37246988 DOI: 10.1007/s00392-023-02236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/17/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Cardiac sarcomas are rare and aggressive tumors with little known about the demographics, genetics, or treatment outcomes. OBJECTIVES The objectives of this study were to characterize the demographics, treatment modality, and survival associated with cardiac sarcomas and evaluate the potential for mutation-directed therapies. METHODS All cases from 2000 to 2018 of cardiac sarcoma were extracted from the SEER database. Genomic comparison utilized The Cancer Genome Atlas (TCGA) database, as well as reviews and re-analysis of past applicable genomic studies. RESULTS Cardiac sarcomas occurred most often in White patients, compared with national census data cardiac sarcomas occurred at a significantly higher rate in Asians. The majority of cases were undifferentiated (61.7%) and without distant metastases (71%). Surgery was the most common primary treatment modality and offered survival benefit (HR 0.391 (p = 0.001) that was most pronounced and sustained as compared to patients who received chemotherapy (HR 0.423 (p = 0.001) or radiation (HR 0.826 (p = 0.241) monotherapy. There was no difference in survival when stratified by race or sex; however, younger patients (< 50) had better survival. Genomics data on histologically undifferentiated cardiac sarcomas revealed a significant number were likely poorly differentiated pulmonary intimal sarcomas and angiosarcomas. CONCLUSIONS Cardiac sarcoma is a rare disease with surgery continuing to be a cornerstone of therapy followed by traditional chemotherapy. Case studies have indicated the potential for therapies directed to specific genetic aberrations to improve survival for these patients and utilization of next-generation sequencing (NGS) will help improve both classification and these therapies for cardiac sarcoma patients.
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Affiliation(s)
- Rozi Khan
- Department of Medicine, Medical University of South Carolina, Florence, SC, USA
| | - Kathryn I Sunthankar
- Division of Cardiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Jaffar Khan
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hassan Nasir
- St. George's University, School of Medicine, University Centre Grenada, West Indies, Grenada
| | - Manando Nakasaki
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eiman Jahangir
- Division of Cardiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Saleh Heneidi
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Asad Ullah
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
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Sánchez-Beato M, Méndez M, Guirado M, Pedrosa L, Sequero S, Yanguas-Casás N, de la Cruz-Merino L, Gálvez L, Llanos M, García JF, Provencio M. A genetic profiling guideline to support diagnosis and clinical management of lymphomas. Clin Transl Oncol 2024; 26:1043-1062. [PMID: 37672206 PMCID: PMC11026206 DOI: 10.1007/s12094-023-03307-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
The new lymphoma classifications (International Consensus Classification of Mature Lymphoid Neoplasms, and 5th World Health Organization Classification of Lymphoid Neoplasms) include genetics as an integral part of lymphoma diagnosis, allowing better lymphoma subclassification, patient risk stratification, and prediction of treatment response. Lymphomas are characterized by very few recurrent and disease-specific mutations, and most entities have a heterogenous genetic landscape with a long tail of recurrently mutated genes. Most of these occur at low frequencies, reflecting the clinical heterogeneity of lymphomas. Multiple studies have identified genetic markers that improve diagnostics and prognostication, and next-generation sequencing is becoming an essential tool in the clinical laboratory. This review provides a "next-generation sequencing" guide for lymphomas. It discusses the genetic alterations of the most frequent mature lymphoma entities with diagnostic, prognostic, and predictive potential and proposes targeted sequencing panels to detect mutations and copy-number alterations for B- and NK/T-cell lymphomas.
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Affiliation(s)
- Margarita Sánchez-Beato
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain.
| | - Miriam Méndez
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - María Guirado
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital General Universitario de Elche, Alicante, Spain
| | - Lucía Pedrosa
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Silvia Sequero
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario San Cecilio, Granada, Spain
| | - Natalia Yanguas-Casás
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Luis de la Cruz-Merino
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Facultad de Medicina, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBID)/CSIC, Seville, Spain
| | - Laura Gálvez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Marta Llanos
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario de Canarias, La Laguna, Sta. Cruz de Tenerife, Spain
| | - Juan Fernando García
- Servicio de Anatomía Patológica, Hospital MD Anderson Cancer Center, Madrid, Spain
| | - Mariano Provencio
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Departamento de Medicina, Facultad de Medicina, Hospital Universitario Puerta de Hierro-Majadahonda, Universidad Autónoma de Madrid, IDIPHISA, Madrid, Spain
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Flory A, Wilson-Robles H. Noninvasive Blood-Based Cancer Detection in Veterinary Medicine. Vet Clin North Am Small Anim Pract 2024; 54:541-558. [PMID: 38195361 DOI: 10.1016/j.cvsm.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The past decade has seen incredible advances in blood-based cancer detection in people and in dogs - yet this represents only a glimpse of the benefits these tests can provide to patients. The clinical uses of this technology range from screening asymptomatic individuals for early detection to use as an aid in diagnosis when cancer is suspected, to cancer monitoring both during and after treatment. This article summarizes the benefits of early cancer detection and examines use cases and methods of blood-based cancer detection in dogs, including quantitative, qualitative, and alternative approaches.
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Affiliation(s)
- Andi Flory
- PetDx, 9310 Athena Circle, Suite 230, La Jolla, CA 92037, USA.
| | - Heather Wilson-Robles
- Volition Veterinary Diagnostics Development, LLC 1489 West Warm Springs Road Suite 110, Henderson, NV 89014, USA; Ethos Discovery, 10435 Sorrento Valley Road, San Diego, CA 92121, USA; The Oncology Service, United Veterinary Health, 6651 Backlick Road, Springfield, VA 22150, USA
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Fontana D, Zambrotta GPM, Scannella A, Piazza R, Gambacorti-Passerini C. Late relapse of chronic myeloid leukemia after allogeneic bone marrow transplantation points to KANSARL (KANSL1::ARL17A) alteration: a case report with insights on the molecular landscape. Ann Hematol 2024; 103:1561-1568. [PMID: 38321229 PMCID: PMC11009776 DOI: 10.1007/s00277-024-05649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/31/2024] [Indexed: 02/08/2024]
Abstract
Chronic myeloid leukemia is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome and the consequent BCR::ABL1 oncoprotein. In the era before the introduction of tyrosine kinase inhibitors (TKIs), the only potentially curative treatment was allogeneic hematopoietic stem cell transplantation (HSCT). Here, we present the case of a patient affected by CML who experienced a relapse 20 years after allogeneic HSCT. Following relapse, the patient was treated with imatinib and bosutinib, resulting in a deep molecular response and successfully discontinued treatment. Additional analysis including whole-exome sequencing and RNA sequencing provided some insights on the molecular mechanisms of the relapse: the identification of the fusion transcript KANSL1::ARL17A (KANSARL), a cancer predisposition fusion gene, could justify a condition of genomic instability which may be associated with the onset and/or probably the late relapse of his CML.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy.
| | - Giovanni Paolo Maria Zambrotta
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - Antonio Scannella
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
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Triono A, Herini ES, Gunadi. Genetic exploration of Dravet syndrome: two case report. J Med Case Rep 2024; 18:215. [PMID: 38649973 DOI: 10.1186/s13256-024-04514-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Dravet syndrome is an infantile-onset developmental and epileptic encephalopathy (DEE) characterized by drug resistance, intractable seizures, and developmental comorbidities. This article focuses on manifestations in two Indonesian children with Javanese ethnicity who experienced Dravet syndrome with an SCN1A gene mutation, presenting genetic analysis findings using next-generation sequencing. CASE PRESENTATION We present a case series involving two Indonesian children with Javanese ethnicity whom had their first febrile seizure at the age of 3 months, triggered after immunization. Both patients had global developmental delay and intractable seizures. We observed distinct genetic findings in both our cases. The first patient revealed heterozygous deletion mutation in three genes (TTC21B, SCN1A, and SCN9A). In our second patient, previously unreported mutation was discovered at canonical splice site upstream of exon 24 of the SCN1A gene. Our patient's outcomes improved after therapeutic evaluation based on mutation findings When comparing clinical manifestations in our first and second patients, we found that the more severe the genetic mutation discovered, the more severe the patient's clinical manifestations. CONCLUSION These findings emphasize the importance of comprehensive genetic testing beyond SCN1A, providing valuable insights for personalized management and tailored therapeutic interventions in patients with Dravet syndrome. Our study underscores the potential of next-generation sequencing in advancing genotype-phenotype correlations and enhancing diagnostic precision for effective disease management.
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Affiliation(s)
- Agung Triono
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Elisabeth Siti Herini
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
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12
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Ono S, Hirose K, Sukegawa S, Obata K, Masui M, Hasegawa K, Fujimura A, Shimada K, Nakamura S, Teramoto A, Hori Y, Morii E, Motooka D, Igawa T, Tanaka T, Nagatsuka H, Toyosawa S, Yamamoto H. Squamous cell carcinoma initially occurring on the tongue dorsum: a case series report with molecular analysis. Diagn Pathol 2024; 19:63. [PMID: 38650013 DOI: 10.1186/s13000-024-01487-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/13/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Squamous cell carcinoma (SCC) of the dorsum of the tongue is extremely rare, and it clinically resembles various benign lesions. Somatic mutations in TP53 and some driver genes were implicated in the development of SCC; however, the somatic genetic characteristics of dorsal tongue SCC remain unknown. With a detailed analysis of gene mutations in dorsal tongue SCC, we aimed to better understand its biology. METHODS Four cases of SCC initially occurring on the tongue dorsum were evaluated for clinical and histological findings and immunohistochemical expression of p53 and p16. Gene mutations were analyzed using next-generation sequencing with a custom panel of driver genes. RESULTS We retrospectively investigated 557 cases of tongue SCC, and only four cases of SCC initially occurred on the tongue dorsum. The four patients (cases 1-4) were one woman and three men with a mean age of 53.75 years (range: 15-74 years). Histological analysis revealed well-differentiated SCC. Through molecular analysis, we identified pathogenic somatic mutations, namely, TP53 p.C176F (c.527G > T) in case 3 and TP53 p.R282W (c.844 C > T) in case 4. No pathogenic variants were identified in the PI3K/AKT or RAS/RAF pathways. The p53 immunohistochemical examination revealed a wild-type expression pattern in cases 1-3 and strong expression in case 4. The results of p16 immunostaining were negative in all cases. CONCLUSIONS We described four previously unreported genetic characteristics of dorsal tongue SCC. Somatic TP53 mutations may contribute to the development of a subset of dorsal tongue SCC; however, more cases with genetic analysis need to be accumulated.
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Affiliation(s)
- Sawako Ono
- Department of Pathology and Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
| | - Katsutoshi Hirose
- Department of Oral and Maxillofacial Pathology, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Shintaro Sukegawa
- Department of Oral and Maxillofacial Surgery, Kagawa University Faculty of Medicine, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Kyoichi Obata
- Department of Oral and Maxillofacial Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
| | - Masanori Masui
- Department of Oral and Maxillofacial Surgery, Kagawa Prefectural Central Hospital, 1-2-1 Asahimachi, Takamatsu, Kagawa, 760-8557, Japan
| | - Kazuaki Hasegawa
- Department of Oral and Maxillofacial Surgery, Kagawa Prefectural Central Hospital, 1-2-1 Asahimachi, Takamatsu, Kagawa, 760-8557, Japan
| | - Ai Fujimura
- Department of Oral and Maxillofacial Surgery, Kagawa Prefectural Central Hospital, 1-2-1 Asahimachi, Takamatsu, Kagawa, 760-8557, Japan
| | - Katsumitsu Shimada
- Department of Clinical Pathophysiology, Matsumoto Dental University Graduate School of Oral Medicine, 1780 Gobara Hirooka, Shiojiri, Nagano, 399-0781, Japan
| | - Satoko Nakamura
- Department of Pathology, Kagawa Prefectural Central Hospital, 1-2-1 Asahimachi, Takamatsu, Kagawa, 760-8557, Japan
| | - Akari Teramoto
- Department of Oral and Maxillofacial Pathology, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumiko Hori
- Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Central Laboratory and Surgical Pathology, NHO Osaka National Hospital, 2-1-14 Hoenzaka, Chuo-ku, Osaka, Osaka, 540-0006, Japan
| | - Eiichi Morii
- Department of Pathology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuro Igawa
- Department of Pathology and Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
| | - Takehiro Tanaka
- Department of Pathology and Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
| | - Hitoshi Nagatsuka
- Department of Oral Pathology and Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
| | - Satoru Toyosawa
- Department of Oral and Maxillofacial Pathology, Osaka University Graduate School of Dentistry, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidetaka Yamamoto
- Department of Pathology and Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 700-8558, Japan
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13
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Aykut A, Durmaz A, Karaca N, Gulez N, Genel F, Celmeli F, Cogurlu MT, Akcan M, Cicek D, Cipe FE, Kiykim A, Yıldıran A, Unluhizarci K, Kilic SS, Aksu G, Ardeniz O, Kutukculer N. Primary immune regulatory disorders (PIRD): expanding the mutation spectrum in Turkey and identification of sixteen novel variants. Immunol Res 2024:10.1007/s12026-024-09477-6. [PMID: 38644452 DOI: 10.1007/s12026-024-09477-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
Human Inborn Errors of Immunity (IEIs) encompass a clinically and genetically heterogeneous group of disorders, ranging from mild cases to severe, life-threatening types. Among these, Primary Immune Regulatory Disorders (PIRDs) constitute a subset of IEIs characterized by diverse clinical phenotypes, prominently featuring severe atopy, autoimmunity, lymphoproliferation, hyperinflammation, autoinflammation, and susceptibility to malignancies. According to the latest report from the International Union of Immunological Societies (IUIS), PIRDs arise from mutations in various genes including LYST, RAB27A, AP3B1, AP3D1, PRF1, UNC13D, STX11, STXBP2, FAAP24, SLC7A7, RASGRP1, CD70, CTPS1, RLTPR, ITK, MAGT1, PRKCD, TNFRSF9, SH2DIA, XIAP, CD27 (TNFRSF7), FAS (TNFRSF6), FASLG (TNFSF6), CASP10, CASP8, FADD, LRBA, STAT3, AIRE, ITCH, ZAP70, TPP2, JAK1, PEPD, FOXP3, IL2RA, CTLA4, BACH2, IL2RB, DEF6, FERMT1, IL10, IL10RA, IL10RB, NFAT5, TGFB1, and RIPK1 genes. We designed a targeted next-generation sequencing (TNGS) workflow using the Ion AmpliSeq™ Primary Immune Deficiency Research Panel to sequence 264 genes associated with IEIs on the Ion S5™ Sequencer. In this study, we report the identification of 38 disease-causing variants, including 16 novel ones, detected in 40 patients across 15 distinct PIRD genes. The application of next-generation sequencing enabled rapid and precise diagnosis of patients with PIRDs.
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Affiliation(s)
- Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey.
| | - Asude Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey
| | - Neslihan Karaca
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Nesrin Gulez
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Ferah Genel
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Fatih Celmeli
- Immunology and Allergy Diseases, Saglık Bilimleri University, Antalya Training and Research Hospital Pediatric, Antalya, Turkey
| | - M Tuba Cogurlu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Saglık Bilimleri University, Kocaeli Derince Training and Research Hospital, Kocaeli, Turkey
| | - Mediha Akcan
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Dilek Cicek
- Department of Pediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Funda Erol Cipe
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ayca Kiykim
- Department of Pediatric Health and Diseases, Cerrahpasa Faculty of Medicine, Pediatric Allergy Immunology, Istanbul, Turkey
| | - Alisan Yıldıran
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Kursad Unluhizarci
- Department of Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Sara Sebnem Kilic
- Department of Pediatric Immunology and Rheumatology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Guzide Aksu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Omur Ardeniz
- Department of Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Necil Kutukculer
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
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14
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Tokiwa T, Fushimi M, Chou S, Yoshida A, Kinoshita K, Hikima A, Kikuchi T, Ozaki K. Aberrant sparganosis in cat caused by Spirometra mansoni (Cestoda: Diphyllobothriidae): a case report. BMC Vet Res 2024; 20:148. [PMID: 38643141 PMCID: PMC11031918 DOI: 10.1186/s12917-024-03995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/27/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Sparganosis is a rare zoonotic disease caused by plerocercoid larvae of the genera Spirometra or Sparganum (Cestoda: Diphyllobothriidae). The larvae of Spirometra generally do not undergo asexual reproduction, whereas those of Sparganum can induce proliferative lesions in infected tissues. This paper presents an unusual case of proliferative sparganosis due to infection with Spirometra mansoni in a cat, normally considered a definitive host of the species. CASE PRESENTATION A 9-year-old male domestic cat was presented with a mass on the right side of the face that underwent progressive enlargement for 1 month. The morphological and histopathological examinations revealed multiple asexual proliferative cestode larvae in the lesions, suggestive of proliferative sparganosis. Next-generation sequencing analysis of formalin-fixed and paraffin-embedded specimens of surgically excised tissue indicated that the worm was Spirometra mansoni. CONCLUSION Although S. mansoni a common tapeworm species found in the small intestine of domestic cats and dogs in Japan, proliferative sparganosis is extremely rare. This is the first confirmed case of proliferative sparganosis due to infection with S. mansoni in cat.
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Affiliation(s)
- Toshihiro Tokiwa
- Laboratory of Veterinary Parasitology, Nippon Veterinary and Life Science University, Kyonancho, Musashino, Tokyo, Japan.
| | - Momo Fushimi
- Fushimi Animal Hospital, Hanawa, Mashikomachi, Hagagun, Tochigi, Japan
| | - Shyun Chou
- Laboratory of Veterinary Parasitology, Nippon Veterinary and Life Science University, Kyonancho, Musashino, Tokyo, Japan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Xing Da Road, Taichung, Taiwan
| | - Akemi Yoshida
- Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Kensei Kinoshita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Atsushi Hikima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kiyokazu Ozaki
- Laboratory of Pathology, Setsunan University, Nagaotohgecho, Hirakata, Osaka, Japan
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15
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Hu J, Luo S, Tian M, Ye AY. TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing. BMC Bioinformatics 2024; 25:154. [PMID: 38637756 PMCID: PMC11025179 DOI: 10.1186/s12859-024-05775-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently. RESULTS Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base 'N's, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. CONCLUSIONS The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.
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Affiliation(s)
- Jianqiao Hu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Sai Luo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- School of Basic Medical Science, Tsinghua University, Beijing, China
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Adam Yongxin Ye
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
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16
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Chen H, Xu Z, Zhou Y, Jiang YH, Chen J, Xiong Y, Zhou M, Wu X, Hong D. Rituximab-induced gut microbiota changes in Chinese neuromyelitis optica spectrum disorders. Mult Scler Relat Disord 2024; 86:105606. [PMID: 38636269 DOI: 10.1016/j.msard.2024.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Recent evidence shows that immunosuppressive agents can affect the gut microbiota in autoimmune diseases. However, the relationship between the gut microbiome and B-cell depletion immunotherapy in neuromyelitis optica spectrum disorder (NMOSD) remains poorly understood. OBJECTIVES To evaluate the distinct intestinal microbial patterns and serum cytokine levels after short-term rituximab treatment (three months) in patients with NMOSD. METHODS Firstly, we conducted a cross-sectional study involving 46 treatment-naïve NMOSD patients and 48 matched healthy controls. We collected fecal specimens, which were then analyzed using next-generation sequencing, and quantified serum cytokines. Subsequently, fecal and serum samples were re-collected and re-evaluated in 31 of the 46 treatment-naïve NMOSD patients after RTX treatment. RESULTS Comparing the gut microbiome of treatment-naïve NMOSD patients to that of healthy controls revealed low α-diversity and distinct microbial compositions in the former. The microbial composition in NMOSD patients underwent changes following three months of RTX treatment. Specifically, the levels of IL-17F and IL-6 decreased, while those of IL-10 and TNFα increased after RTX treatment. LEfSe analysis identified 27 KEGG categories with significantly differential abundances between NMOSD patients and RTX treatment group. CONCLUSIONS Our study provides a comprehensive understanding of the gut microbiota landscape in the context of B-cell depletion immunotherapy. We observed dysbiosis in the gut microbiome of NMOSD patients, which was partially alleviated by three months of RTX treatment. This suggests that B-cell depletion may play a crucial role in driving changes in the gastrointestinal environment.
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Affiliation(s)
- Hao Chen
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Zubing Xu
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yu Zhou
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yu-Huan Jiang
- Medical Laborotary, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Jin Chen
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yingqiong Xiong
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Meihong Zhou
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Xiaomu Wu
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China.
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital Nanchang University, Nanchang, Jiangxi Province, 330006, China.
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Cheng B, Xu L, Zhang Y, Yang H, Liu S, Ding S, Zhao H, Sui Y, Wang C, Quan L, Liu J, Liu Y, Wang H, Zheng Z, Wu X, Guo J, Wen Z, Zhang R, Wang F, Liu H, Sun S. Correlation between NGS panel-based mutation results and clinical information in colorectal cancer patients. Heliyon 2024; 10:e29299. [PMID: 38623252 PMCID: PMC11016705 DOI: 10.1016/j.heliyon.2024.e29299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Early mutation identification guides patients with colorectal cancer (CRC) toward targeted therapies. In the present study, 414 patients with CRC were enrolled, and amplicon-based targeted next-generation sequencing (NGS) was then performed to detect genomic alterations within the 73 cancer-related genes in the OncoAim panel. The overall mutation rate was 91.5 % (379/414). Gene mutations were detected in 38/73 genes tested. The most frequently mutated genes were TP53 (60.9 %), KRAS (46.6 %), APC (30.4 %), PIK3CA (15.9 %), FBXW7 (8.2 %), SMAD4 (6.8 %), BRAF (6.5 %), and NRAS (3.9 %). Compared with the wild type, TP53 mutations were associated with low microsatellite instability/microsatellite stability (MSI-L/MSS) (P = 0.007), tumor location (P = 0.043), and histological grade (P = 0.0009); KRAS mutations were associated with female gender (P = 0.026), distant metastasis (P = 0.023), TNM stage (P = 0.013), and histological grade (P = 0.004); APC mutations were associated with patients <64 years of age at diagnosis (P = 0.04); PIK3CA mutations were associated with tumor location (P = 4.97e-06) and female gender (P = 0.018); SMAD4 mutations were associated with tumor location (P = 0.033); BRAF mutations were associated with high MSI (MSI-H; P = 6.968e-07), tumor location (P = 1.58e-06), and histological grade (P = 0.04). Mutations in 164 individuals were found to be pathogenic or likely pathogenic. A total of 26 patients harbored MSI-H tumors and they all had at least one detected gene mutation. Mutated genes were enriched in signaling pathways associated with CRC. The present findings have important implications for improving the personalized treatment of patients with CRC in China.
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Affiliation(s)
- Bo Cheng
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Lin Xu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Yunzhi Zhang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huimin Yang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Shan Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Shanshan Ding
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Huan Zhao
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Yi Sui
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Chan Wang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Lanju Quan
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Jinhong Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Ye Liu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Hongming Wang
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Zhaoqing Zheng
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Xizhao Wu
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Jing Guo
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Zhaohong Wen
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Ruya Zhang
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Fei Wang
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
| | - Hongmei Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai 201318, China
| | - Suozhu Sun
- Department of Pathology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing 100037, China
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18
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Liu S, Graves N, Tan AC. The cost-effectiveness of including liquid biopsy into molecular profiling strategies for newly diagnosed advanced non-squamous non-small cell lung cancer in an Asian population. Lung Cancer 2024; 191:107794. [PMID: 38636314 DOI: 10.1016/j.lungcan.2024.107794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/23/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
OBJECTIVES Liquid biopsy is complementary to tissue biopsy for lung cancer profiling, yet evidence of the cost-effectiveness is limited. This could retard implementation and reimbursement in clinical practice. The aim of this study is to estimate the cost-effectiveness of profiling strategies that include liquid biopsy and to identify the optimal profiling approach for newly diagnosed advanced non-squamous non-small cell lung cancer (NSCLC) in an Asian population using Singapore as an example. MATERIALS AND METHODS A decision tree and partitioned-survival model was developed from the Singapore healthcare system's perspective to evaluate the cost-effectiveness of five molecular profiling strategies: either tissue or plasma next-generation sequencing (NGS) alone, a concurrent, and two sequential approaches. Model inputs were informed by local data or published literature. Sensitivity analyses and scenario analyses were undertaken to understand the robustness of the conclusions for decision making. The optimal strategy at different willingness-to-pay (WTP) thresholds was presented by cost-effectiveness acceptability frontier and the expected loss curve. RESULTS The sequential tissue-plasma NGS approach revealed an additional 0.0981 quality adjusted life years (QALYs) for an extra cost of S$3,074 over a 20-year time horizon compared to tissue NGS alone, resulting in an incremental cost-effectiveness ratio (ICER) of S$31,318/QALY and an incremental net monetary benefit of S$1,343 per patient. The findings were sensitive to the costs of pembrolizumab and osimertinib and the probabilities of re-biopsy after tissue NGS. Sequential plasma-tissue NGS and plasma NGS alone were more costly and less effective than alternatives. CONCLUSION The sequential tissue-plasma NGS approach generated the highest net monetary benefit and was the optimal testing strategy when WTP was S$45,000/QALY. It retained superiority but understandably with a higher ICER when expensive, non-first line treatments were included. Overall, its routine clinical practice should be proactively considered for newly diagnosed advanced non-squamous NSCLC in an Asian population.
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Affiliation(s)
- Sibo Liu
- Health Services and Systems Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Nicholas Graves
- Health Services and Systems Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 168583, Singapore.
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Cao B, Sun C, Bi R, Liu Z, Jia Y, Cui W, Sun M, Yu B, Li X, Zhou X. Mutation landscape in Chinese nodal diffuse large B-cell lymphoma by targeted next generation sequencing and their relationship with clinicopathological characteristics. BMC Med Genomics 2024; 17:84. [PMID: 38609996 PMCID: PMC11015559 DOI: 10.1186/s12920-024-01866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL), an aggressive and heterogenic malignant entity, is still a challenging clinical problem, since around one-third of patients are not cured with primary treatment. Next-generation sequencing (NGS) technologies have revealed common genetic mutations in DLBCL. We devised an NGS multi-gene panel to discover genetic features of Chinese nodal DLBCL patients and provide reference information for panel-based NGS detection in clinical laboratories. METHODS A panel of 116 DLBCL genes was designed based on the literature and related databases. We analyzed 96 Chinese nodal DLBCL biopsy specimens through targeted sequencing. RESULTS The most frequently mutated genes were KMT2D (30%), PIM1 (26%), SOCS1 (24%), MYD88 (21%), BTG1 (20%), HIST1H1E (18%), CD79B (18%), SPEN (17%), and KMT2C (16%). SPEN (17%) and DDX3X (6%) mutations were highly prevalent in our study than in Western studies. Thirty-three patients (34%) were assigned as genetic classification by the LymphGen algorithm, including 12 cases MCD, five BN2, seven EZB, seven ST2, and two EZB/ST2 complex. MYD88 L265P mutation, TP53 and BCL2 pathogenic mutations were unfavorable prognostic biomarkers in DLBCL. CONCLUSIONS This study presents the mutation landscape in Chinese nodal DLBCL, highlights the genetic heterogeneity of DLBCL and shows the role of panel-based NGS to prediction of prognosis and potential molecular targeted therapy in DLBCL. More precise genetic classification needs further investigations.
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Affiliation(s)
- Bing Cao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- Fudan University Medical Library, Shanghai, China
| | - Chenbo Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Rui Bi
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Zebing Liu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yijun Jia
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Wenli Cui
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Menghong Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Baohua Yu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoqiu Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Pathology, Fudan University, Shanghai, China.
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Angulo-Aguado M, Carrillo-Martinez JC, Contreras-Bravo NC, Morel A, Parra-Abaunza K, Usaquén W, Fonseca-Mendoza DJ, Ortega-Recalde O. Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population. Sci Rep 2024; 14:8497. [PMID: 38605121 PMCID: PMC11009356 DOI: 10.1038/s41598-024-57982-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.
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Affiliation(s)
- Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Juan Camilo Carrillo-Martinez
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | | | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia.
- Departamento de Morfología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
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Trzebny A, Nahimova O, Dabert M. High temperatures and low humidity promote the occurrence of microsporidians (Microsporidia) in mosquitoes (Culicidae). Parasit Vectors 2024; 17:187. [PMID: 38605410 PMCID: PMC11008030 DOI: 10.1186/s13071-024-06254-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND In the context of climate change, a growing concern is that vector-pathogen or host-parasite interactions may be correlated with climatic factors, especially increasing temperatures. In the present study, we used a mosquito-microsporidian model to determine the impact of environmental factors such as temperature, humidity, wind and rainfall on the occurrence rates of opportunistic obligate microparasites (Microsporidia) in hosts from a family that includes important disease vectors (Culicidae). METHODS In our study, 3000 adult mosquitoes collected from the field over 3 years were analysed. Mosquitoes and microsporidia were identified using PCR and sequencing of the hypervariable V5 region of the small subunit ribosomal RNA gene and a shortened fragment of the cytochrome c oxidase subunit I gene, respectively. RESULTS DNA metabarcoding was used to identify nine mosquito species, all of which were hosts of 12 microsporidian species. The prevalence of microsporidian DNA across all mosquito samples was 34.6%. Microsporidian prevalence in mosquitoes was more frequent during warm months (> 19 °C; humidity < 65%), as was the co-occurrence of two or three microsporidian species in a single host individual. During warm months, microsporidian occurrence was noted 1.6-fold more often than during the cold periods. Among the microsporidians found in the mosquitoes, five (representing the genera Enterocytospora, Vairimorpha and Microsporidium) were positively correlated with an increase in temperature, whereas one (Hazardia sp.) was significantly correlated with a decrease in temperature. Threefold more microsporidian co-occurrences were recorded in the warm months than in the cold months. CONCLUSIONS These results suggest that the susceptibility of mosquitoes to parasite occurrence is primarily determined by environmental conditions, such as, for example, temperatures > 19 °C and humidity not exceeding 62%. Collectively, our data provide a better understanding of the effects of the environment on microsporidian-mosquito interactions.
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Affiliation(s)
- Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| | - Olena Nahimova
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- Genetics and Cytology Department, School of Biology, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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22
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Kasprzak J, Westphalen CB, Frey S, Schmitt Y, Heinemann V, Fey T, Nasseh D. Supporting the decision to perform molecular profiling for cancer patients based on routinely collected data through the use of machine learning. Clin Exp Med 2024; 24:73. [PMID: 38598013 PMCID: PMC11006770 DOI: 10.1007/s10238-024-01336-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/21/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Personalized medicine offers targeted therapy options for cancer treatment. However, the decision whether to include a patient into next-generation sequencing (NGS) testing is not standardized. This may result in some patients receiving unnecessary testing while others who could benefit from it are not tested. Typically, patients who have exhausted conventional treatment options are of interest for consideration in molecularly targeted therapy. To assist clinicians in decision-making, we developed a decision support tool using routine data from a precision oncology program. METHODS We trained a machine learning model on clinical data to determine whether molecular profiling should be performed for a patient. To validate the model, the model's predictions were compared with decisions made by a molecular tumor board (MTB) using multiple patient case vignettes with their characteristics. RESULTS The prediction model included 440 patients with molecular profiling and 13,587 patients without testing. High area under the curve (AUC) scores indicated the importance of engineered features in deciding on molecular profiling. Patient age, physical condition, tumor type, metastases, and previous therapies were the most important features. During the validation MTB experts made the same decision of recommending a patient for molecular profiling only in 10 out of 15 of their previous cases but there was agreement between the experts and the model in 9 out of 15 cases. CONCLUSION Based on a historical cohort, our predictive model has the potential to assist clinicians in deciding whether to perform molecular profiling.
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Affiliation(s)
- Julia Kasprzak
- Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Pettenkoferstraße 8a, Munich, Germany.
| | - C Benedikt Westphalen
- Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Pettenkoferstraße 8a, Munich, Germany
| | - Simon Frey
- Roche Pharma AG, Grenzach-Wyhlen, Germany
| | | | - Volker Heinemann
- Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Pettenkoferstraße 8a, Munich, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK, Partner Site Munich), Heidelberg, Germany
| | - Theres Fey
- Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Pettenkoferstraße 8a, Munich, Germany
| | - Daniel Nasseh
- Comprehensive Cancer Center (CCC Munich LMU), LMU University Hospital Munich, Pettenkoferstraße 8a, Munich, Germany
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23
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Gong B, Lababidi S, Kusko R, Bouri K, Prezek S, Thovarai V, Prasanna A, Maier EJ, Golkaram M, Sun X, Kyriakidis K, Kitajima JP, Ebrahim Sahraeian SM, Guo Y, Johanson E, Jones W, Tong W, Xu J. Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA. Sci Rep 2024; 14:8165. [PMID: 38589653 PMCID: PMC11001604 DOI: 10.1038/s41598-024-58573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.
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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Samir Lababidi
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rebecca Kusko
- Cellino Biotech, 750 Main Street, Cambridge, MA, 02143, USA
| | - Khaled Bouri
- Office of Regulatory Science and Innovation, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | | | | | | | | | | | | | | | | | - Yunfei Guo
- Roche Sequencing Solutions, Santa Clara, CA, 95050, USA
| | - Elaine Johanson
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Wendell Jones
- Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Gao S, Zhang Q, Ding Y, Wang L, Li Z, Hu F, Yao RE, Yu T, Chang G, Wang X. Molecular and phenotypic characteristics of Bardet-Biedl syndrome in Chinese patients. Orphanet J Rare Dis 2024; 19:149. [PMID: 38584252 PMCID: PMC11000329 DOI: 10.1186/s13023-024-03150-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a type of non-motile ciliopathy. To date, 26 genes have been reported to be associated with BBS. However, BBS is genetically heterogeneous, with significant clinical overlap with other ciliopathies, which complicates diagnosis. Disability and mortality rates are high in BBS patients; therefore, it is urgent to improve our understanding of BBS. Thus, our study aimed to describe the genotypic and phenotypic spectra of BBS in China and to elucidate genotype-phenotype correlations. METHODS Twenty Chinese patients diagnosed with BBS were enrolled in this study. We compared the phenotypes of Chinese BBS patients in this study with those from other countries to analyze the phenotypic differences across patients worldwide. In addition, genotype-phenotype correlations were described for our cohort. We also summarized all previously reported cases of BBS in Chinese patients (71 patients) and identified common and specific genetic variants in the Chinese population. RESULTS Twenty-eight variants, of which 10 are novel, in 5 different BBS-associated genes were identified in 20 Chinese BBS patients. By comparing the phenotypes of BBSome-coding genes (BBS2,7,9) with those of chaperonin-coding genes (BBS10,12), we found that patients with mutations in BBS10 and 12 had an earlier age of onset (1.10 Vs. 2.20, p < 0.01) and diagnosis (4.64 Vs. 13.17, p < 0.01), whereas patients with mutations in BBS2, 7, and 9 had a higher body mass index (28.35 Vs. 24.21, p < 0.05) and more vision problems (p < 0.05). Furthermore, in 91 Chinese BBS patients, mutations were predominant in BBS2 (28.89%) and BBS7 (15.56%), and the most frequent variants were in BBS2: c.534 + 1G > T (10/182 alleles) and BBS7: c.1002delT (7/182 alleles), marking a difference from the genotypic spectra of BBS reported abroad. CONCLUSIONS We recruited 20 Chinese patients with BBS for genetic and phenotypic analyses, and identified common clinical manifestations, pathogenic genes, and variants. We also described the phenotypic differences across patients worldwide and among different BBS-associated genes. This study involved the largest cohort of Chinese patients with BBS, and provides new insights into the distinctive clinical features of specific pathogenic variants.
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Affiliation(s)
- Shiyang Gao
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qianwen Zhang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yu Ding
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Libo Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhiying Li
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feihan Hu
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Ru-En Yao
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tingting Yu
- Department of Genetic Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Guoying Chang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Xiumin Wang
- Department of Endocrinology, Metabolism and Genetics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Dosbaa A, Guilbaud R, Yusti AMF, Ferré VM, Charpentier C, Descamps D, Le Hingrat Q, Coppée R. RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis. J Virol Methods 2024; 327:114938. [PMID: 38588779 DOI: 10.1016/j.jviromet.2024.114938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/17/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique. OBJECTIVE Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults. RESULTS We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies. AVAILABILITY RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.
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Affiliation(s)
- Alexandre Dosbaa
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France
| | - Romane Guilbaud
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Anna-Maria Franco Yusti
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France
| | - Valentine Marie Ferré
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Charlotte Charpentier
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Diane Descamps
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Quentin Le Hingrat
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France; Service de Virologie, AP-HP, Hôpital Bichat - Claude Bernard, Paris F-75018, France
| | - Romain Coppée
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris F-75018, France.
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Chung C, Umoru G. Prognostic and predictive biomarkers with therapeutic targets in nonsmall-cell lung cancer: A 2023 update on current development, evidence, and recommendation. J Oncol Pharm Pract 2024:10781552241242684. [PMID: 38576390 DOI: 10.1177/10781552241242684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
BACKGROUND Since the publication of the original work in 2014, significant progress has been made in the characterization of genomic alterations that drive oncogenic addiction of nonsmall cell lung cancer (NSCLC) and how the immune system can leverage non-oncogenic pathways to modulate therapeutic outcomes. This update evaluates and validates the recent and emerging data for prognostic and predictive biomarkers with therapeutic targets in NSCLC. DATA SOURCES We performed a literature search from January 2015 to October 2023 using the keywords non-small cell lung cancer, clinical practice guidelines, gene mutations, genomic assay, immune cancer therapy, circulating tumor DNA, predictive and prognostic biomarkers, and targeted therapies. STUDY SELECTION AND DATA EXTRACTION We identified, reviewed, and evaluated relevant clinical trials, meta-analyses, seminal articles, and published clinical practice guidelines in the English language. DATA SYNTHESIS Regulatory-approved targeted therapies include those somatic gene alterations of EGFR ("classic" mutations, exon 20 insertion, and rare EGFR mutations), ALK, ROS1, BRAF V600, RET, MET, NTRK, HER2, and KRAS G12C. Data for immunotherapy and circulating tumor DNA in next-generation sequencing are considered emerging, whereas the predictive role for PIK3CA gene mutation is insufficient. CONCLUSIONS Advances in sequencing and other genomic technologies have led to identifying novel oncogenic drivers, novel resistance mechanisms, and co-occurring mutations that characterize NSCLC, creating further therapeutic opportunities. The benefits associated with immunotherapy in the perioperative setting hold initial promise, with their long-term results awaiting.
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Affiliation(s)
- Clement Chung
- Department of Pharmacy, Houston Methodist West Hospital, Houston, TX, USA
| | - Godsfavour Umoru
- Department of Pharmacy, Houston Methodist Hospital, Houston, TX, USA
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Zhang Y, Talukder S, Bhuiyan MSA, He L, Sarker S. Opportunistic sampling of yellow canary (Crithagra flaviventris) has revealed a high genetic diversity of detected parvoviral sequences. Virology 2024; 595:110081. [PMID: 38599030 DOI: 10.1016/j.virol.2024.110081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Parvoviruses are known to be significant viral pathogens that infect a wide range of species globally. However, little is known about the parvoviruses circulating in Australian birds, including yellow canaries. Here, we present four parvoviral sequences including three novel parvoviruses detected from 10 yellow canaries (Crithagra flaviventris), named canary chaphamaparvovirus 1 and -2 (CaChPV1 and CaChPV2), canary dependoparvovirus 1 and -2 (CaDePV1 and CaDePV2). The whole genome sequences of CaChPV1, CaChPV2, CaDePV1, and CaDePV2 showed the highest identity with other parvoviruses at 76.4%, 75.9%, 84.0%, and 59.1%, respectively. Phylogenetic analysis demonstrated that CaChPV1 and CaChPV2 were clustered within the genus Chaphamaparvovirus. Meanwhile, CaDePV1 and CaDePV2 fall within the genus Dependoparvovirus and have the closest evolutionary relationship to the bird-associated dependoparvoviruses. Overall, this study enriched our understanding of the genetic diversity among avian parvoviruses within the Parvoviridae family.
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Affiliation(s)
- Yuhao Zhang
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Saranika Talukder
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Md Safiul Alam Bhuiyan
- Faculty of Sustainable Agriculture, Livestock Production, Universiti Malaysia Sabah, Sandakan, Sabah, Malaysia
| | - Lei He
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024:10.1007/s11096-024-01704-2. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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Banerjee S. Cost-Effectiveness and the Economics of Genomic Testing and Molecularly Matched Therapies. Surg Oncol Clin N Am 2024; 33:231-242. [PMID: 38401907 DOI: 10.1016/j.soc.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Cost-effectiveness analysis of precision oncology can help guide value-driven care. Next-generation sequencing is increasingly cost-efficient over single gene testing because diagnostic algorithms require multiple individual gene tests to determine biomarker status. Matched targeted therapy is often not cost-effective due to the high cost associated with drug treatment. However, genomic profiling can promote cost-effective care by identifying patients who are unlikely to benefit from therapy. Additional applications of genomic profiling such as universal testing for hereditary cancer syndromes and germline testing in patients with cancer may represent cost-effective approaches compared with traditional history-based diagnostic methods.
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Affiliation(s)
- Sudeep Banerjee
- Division of Colorectal Surgery, Department of General Surgery, Kaiser Permanente San Jose Medical Center, Kaiser Permanente Northern California, 280 Hospital Parkway, Building B, San Jose, CA 95119, USA.
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Huang S, Chen P, Wang L, Xu L, Wang N, Li F, Dou L, Liu D. Next-generation sequencing reveals relapse and leukemia-free survival risks in newly diagnosed acute myeloid leukemia treated with CAG regimen combined with decitabine. Cancer Pathog Ther 2024; 2:112-120. [PMID: 38601484 PMCID: PMC11002746 DOI: 10.1016/j.cpt.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 04/12/2024]
Abstract
Background Acute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy whose prognosis is associated with several biomarkers. Decitabine, a deoxyribonucleic acid (DNA) methyltransferase (DNMT) inhibitor, combined with cytarabine, aclarubicin hydrochloride, and granulocyte colony-stimulating factor (DCAG), has been used in patients newly diagnosed with AML. This regimen has been especially used in older and fragile patients who are immunocompromised or have co-morbidities, as well as those with specific gene mutations. However, the integration of molecular risk stratification and treatment guidance for the DCAG regimen has not been well defined. Therefore, this study aimed to investigate the genetic mutations associated with AML and establish appropriate treatment strategies for patients newly diagnosed with AML. Methods This study analyzed the clinical data and genetic mutations based on next-generation sequencing (NGS) in 124 newly diagnosed patients with AML who received the DCAG regimen at the People's Liberation Army (PLA) General Hospital from January 2008 to August 2020. Factors associated with the cumulative incidence of relapse (CIR) and leukemia-free survival (LFS) in patients newly diagnosed with AML were analyzed. Results The most adverse prognosis of DCAG-treated patients was observed in those with FLT3-ITD, KIT, PTPN11, GATA2, or IDH1 mutations during univariable analysis, whereas PTPN11 mutation was solely significant in multivariable analysis, with an increased likelihood of CIR (P = 0.001) and reduced LFS duration (P = 0.077). Hyperleukocytosis was maintained as an independent risk factor for increased CIR risk (P = 0.044) and decreased LFS duration (P = 0.042) in multivariable analysis. In this study, we validated the risk classification of patients with AML receiving an epigenetic modifier-based induction regimen across a broad age range. Conclusion NGS demonstrated a dismal overall outcome in patients with the rare PTPN11 mutations, indicating the need for new therapies that target this high-risk subtype of AML. These results offer a potential molecular stratification and treatment guidance for patients with AML.
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Affiliation(s)
- Sai Huang
- Department of Hematology, Senior Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
- National Clinical Research Center of Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Peng Chen
- Department of Hematology, Senior Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
- Chinese PLA Medical School, Beijing 100853, China
| | - Lu Wang
- Department of Hematology, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Lingmin Xu
- Department of Hematology, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Nan Wang
- Chinese PLA Medical School, Beijing 100853, China
- Department of Hematology, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Fei Li
- Department of Hematology, The First Medical Center of PLA General Hospital, Beijing 100853, China
| | - Liping Dou
- Department of Hematology, Senior Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
| | - Daihong Liu
- Department of Hematology, Senior Department of Hematology, The Fifth Medical Center of PLA General Hospital, Beijing 100039, China
- National Clinical Research Center of Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
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Conde E, Hernandez S, Rodriguez Carrillo JL, Martinez R, Alonso M, Curto D, Jimenez B, Caminoa A, Benito A, Garrido P, Clave S, Arriola E, Esteban-Rodriguez I, De Castro J, Sansano I, Felip E, Rojo F, Dómine M, Abdulkader I, Garcia-Gonzalez J, Teixido C, Reguart N, Compañ D, Insa A, Mancheño N, Palanca S, Juan-Vidal O, Baixeras N, Nadal E, Cebollero M, Calles A, Martin P, Salas C, Provencio M, Aranda I, Massuti B, Lopez-Vilaro L, Majem M, Paz-Ares L, Lopez-Rios F. RET Fusion Testing in Patients With NSCLC: The RETING Study. JTO Clin Res Rep 2024; 5:100653. [PMID: 38525319 PMCID: PMC10957499 DOI: 10.1016/j.jtocrr.2024.100653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction RET inhibitors with impressive overall response rates are now available for patients with NSCLC, yet the identification of RET fusions remains a difficult challenge. Most guidelines encourage the upfront use of next-generation sequencing (NGS), or alternatively, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) when NGS is not possible or available. Taken together, the suboptimal performance of single-analyte assays to detect RET fusions, although consistent with the notion of encouraging universal NGS, is currently widening some of the clinical practice gaps in the implementation of predictive biomarkers in patients with advanced NSCLC. Methods This situation prompted us to evaluate several RET assays in a large multicenter cohort of RET fusion-positive NSCLC (n = 38) to obtain real-world data. In addition to RNA-based NGS (the criterion standard method), all positive specimens underwent break-apart RET FISH with two different assays and were also tested by an RT-PCR assay. Results The most common RET partners were KIF5B (78.9%), followed by CCDC6 (15.8%). The two RET NGS-positive but FISH-negative samples contained a KIF5B(15)-RET(12) fusion. The three RET fusions not identified with RT-PCR were AKAP13(35)-RET(12), KIF5B(24)-RET(9) and KIF5B(24)-RET(11). All three false-negative RT-PCR cases were FISH-positive, exhibited a typical break-apart pattern, and contained a very high number of positive tumor cells with both FISH assays. Signet ring cells, psammoma bodies, and pleomorphic features were frequently observed (in 34.2%, 39.5%, and 39.5% of tumors, respectively). Conclusions In-depth knowledge of the advantages and disadvantages of the different RET testing methodologies could help clinical and molecular tumor boards implement and maintain sensible algorithms for the rapid and effective detection of RET fusions in patients with NSCLC. The likelihood of RET false-negative results with both FISH and RT-PCR reinforces the need for upfront NGS in patients with NSCLC.
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Affiliation(s)
- Esther Conde
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Susana Hernandez
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | | | - Marta Alonso
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Daniel Curto
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | | | - Pilar Garrido
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Sergi Clave
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | | | - Javier De Castro
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigacion Sanitaria del Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Irene Sansano
- Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | | | - Federico Rojo
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Manuel Dómine
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Ihab Abdulkader
- Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Cristina Teixido
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Noemi Reguart
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | | | - Amelia Insa
- Hospital Clinico Universitario, Valencia, Spain
| | - Nuria Mancheño
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sarai Palanca
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Nuria Baixeras
- Hospital Universitari de Bellvitge, L’Hospitalet, Barcelona, Spain
| | - Ernest Nadal
- Catalan Institute of Oncology, L’Hospitalet, Barcelona, Spain
| | - Maria Cebollero
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Antonio Calles
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Paloma Martin
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Clara Salas
- Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Ignacio Aranda
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Bartomeu Massuti
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | | | | | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Fernando Lopez-Rios
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
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Oh R, Woo SJ, Joo K. Whole genome sequencing for inherited retinal diseases in the Korean National Project of Bio Big Data. Graefes Arch Clin Exp Ophthalmol 2024; 262:1351-1359. [PMID: 37947821 DOI: 10.1007/s00417-023-06309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE This study aimed to analyze the genetic results of inherited retinal diseases (IRDs) and evaluate the diagnostic usefulness of whole genome sequencing (WGS) in the Korean National Project of Bio Big Data. METHODS As part of the Korean National Project of Bio Big Data, WGS was performed on 32 individuals with IRDs with no identified pathogenic variants through whole or targeted exome sequencing. RESULTS Individuals with retinitis pigmentosa (n = 23), cone dystrophy (n = 2), cone-rod dystrophy (n = 2), familial exudative vitreoretinopathy (n = 2), pigmented paravenous chorioretinal atrophy (n = 1), North Carolina macular dystrophy (n = 1), and bull's-eye macular dystrophy (n = 1) were included. WGS revealed genetic mutations in the IQCB1, PRPF31, USH2A, and GUCY2D genes in five cases (15.6%). Two large structural variations and an intronic variant were newly detected in three cases. Two individuals had biallelic missense mutations that were not identified in previous exome sequencing. CONCLUSION With WGS, the causative variants in 15.6% of unsolved IRDs from the Korean National Project of Bio Big Data were identified. Further research with a larger cohort might unveil the diagnostic usefulness of WGS in IRDs and other diseases.
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Affiliation(s)
- Richul Oh
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620.
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Krenn M, Wagner M, Zulehner G, Weng R, Jäger F, Keritam O, Sener M, Brücke C, Milenkovic I, Langer A, Buchinger D, Habersam R, Mayerhanser K, Brugger M, Brunet T, Jacob M, Graf E, Berutti R, Cetin H, Hoefele J, Winkelmann J, Zimprich F, Rath J. Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses. J Neurol 2024; 271:1937-1946. [PMID: 38127101 DOI: 10.1007/s00415-023-12101-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Neuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes. METHODS We analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis. RESULTS Initially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21-0.82), while a positive family history (OR 5.46; 95%CI 2.60-11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11-7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies. CONCLUSION Our findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Merve Sener
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christof Brücke
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ivan Milenkovic
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Agnes Langer
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Dominic Buchinger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Richard Habersam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. Von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
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Shen G, Li W, Zhang Y, Chen L. Next-generation sequencing based newborn screening and comparative analysis with MS/MS. BMC Pediatr 2024; 24:230. [PMID: 38561707 PMCID: PMC10985934 DOI: 10.1186/s12887-024-04718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Newborn screening (NBS), such as tandem mass spectrometry (MS/MS), may yield false positive/negative results. Next-generation sequencing (NGS) has the potential to provide increased data output, efficiencies, and applications. This study aimed to analyze the types and distribution of pathogenic gene mutations in newborns in Huzhou, Zhejiang province, China and explore the applicability of NGS and MS/MS in NBS. METHODS Blood spot samples from 1263 newborns were collected. NGS was employed to screen for pathogenic variants in 542 disease-causing genes, and detected variants were validated using Sanger sequencing. Simultaneously, 26 inherited metabolic diseases (IMD) were screened using MS/MS. Positive or suspicious samples identified through MS/MS were cross-referenced with the results of NGS. RESULTS Among all newborns, 328 had no gene mutations detected. NGS revealed at least one gene mutation in 935 newborns, with a mutation rate of 74.0%. The top 5 genes were FLG, GJB2, UGT1A1, USH2A, and DUOX2. According to American College of Medical Genetics guidelines, gene mutations in 260 cases were classified as pathogenic or likely pathogenic mutation, with a positive rate of 20.6%. The top 5 genes were UGT1A1, FLG, GJB2, MEFV, and G6PD. MS/MS identified 18 positive or suspicious samples for IMD and 1245 negative samples. Verification of these cases by NGS results showed no pathogenic mutations, resulting in a false positive rate of 1.4% (18/1263). CONCLUSION NBS using NGS technology broadened the range of diseases screened, and enhanced the accuracy of diagnoses in comparison to MS/MS for screening IMD. Combining NGS and biochemical screening would improve the efficiency of current NBS.
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Affiliation(s)
- Guosong Shen
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China.
| | - Wenwen Li
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Yaqin Zhang
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Lyuyan Chen
- Institut for Neuroscience, Technical University of Munich, 80802, Munich, Germany
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Fitak RR. The magneto-microbiome: A dataset of the metagenomic distribution of magnetotactic bacteria. Data Brief 2024; 53:110073. [PMID: 38317726 PMCID: PMC10838685 DOI: 10.1016/j.dib.2024.110073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/09/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
Magnetotactic bacteria (MTB) are diverse prokaryotes characterized by their ability to generate biogenic magnetic iron crystals. MTB are ubiquitous across aquatic environments, and growing evidence has indicated they may be present in association with animal microbiomes. Unfortunately, they are difficult to culture in vitro and more studies understanding their biogeographical distribution and ecological roles are needed. To provide data regarding the patterns of diversity and distribution of MTB, we screened the entire Sequence Read Archive (SRA) from the National Center for Biotechnology Information for DNA sequencing reads matching known MTB taxa. The dataset summarizes the count of reads assigned to MTB from more than 26 million SRA accessions comprising approximately 80 petabases (7.98 × 1016) of DNA. More than 396 million DNA sequencing reads were assigned to 214 MTB taxa in 691,086 (2.65 %) SRA accessions. The final dataset can be utilized by researchers to narrow their efforts in examination of both environmental and ecological roles of specific MTB or to identify potential host organisms. These data will be instrumental to further elucidating the importance and utility of these enigmatic bacteria.
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Affiliation(s)
- Robert R. Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
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Chen H, Wang B, Cai L, Yang X, Hu Y, Zhang Y, Leng X, Liu W, Fan D, Niu B, Zhou Q. A comprehensive performance evaluation, comparison, and integration of computational methods for detecting and estimating cross-contamination of human samples in cancer next-generation sequencing analysis. J Biomed Inform 2024; 152:104625. [PMID: 38479675 DOI: 10.1016/j.jbi.2024.104625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/25/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Cross-sample contamination is one of the major issues in next-generation sequencing (NGS)-based molecular assays. This type of contamination, even at very low levels, can significantly impact the results of an analysis, especially in the detection of somatic alterations in tumor samples. Several contamination identification tools have been developed and implemented as a crucial quality-control step in the routine NGS bioinformatic pipeline. However, no study has been published to comprehensively and systematically investigate, evaluate, and compare these computational methods in the cancer NGS analysis. In this study, we comprehensively investigated nine state-of-the-art computational methods for detecting cross-sample contamination. To explore their application in cancer NGS analysis, we further compared the performance of five representative tools by qualitative and quantitative analyses using in silico and simulated experimental NGS data. The results showed that Conpair achieved the best performance for identifying contamination and predicting the level of contamination in solid tumors NGS analysis. Moreover, based on Conpair, we developed a Python script, Contamination Source Predictor (ConSPr), to identify the source of contamination. We anticipate that this comprehensive survey and the proposed tool for predicting the source of contamination will assist researchers in selecting appropriate cross-contamination detection tools in cancer NGS analysis and inspire the development of computational methods for detecting sample cross-contamination and identifying its source in the future.
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Affiliation(s)
- Huijuan Chen
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; WillingMed Technology Beijing Co. Ltd., Beijing 100176, China
| | - Bing Wang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Lili Cai
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Xiaotian Yang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Yali Hu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Yiran Zhang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Xue Leng
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Wen Liu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Dongjie Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Beifang Niu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang 311103, China.
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang 311103, China.
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Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
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Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
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da Silveira Corrêa B, De-Paris F, Viola GD, Andreis TF, Rosset C, Vianna FSL, da Rosa Rivero LF, de Oliveira FH, Ashton-Prolla P, de Souza Macedo G. Challenges to the effectiveness of next-generation sequencing in formalin-fixed paraffin-embedded tumor samples for non-small cell lung cancer. Ann Diagn Pathol 2024; 69:152249. [PMID: 38150865 DOI: 10.1016/j.anndiagpath.2023.152249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) of Formalin-Fixed and Paraffin-Embedded (FFPE) specimens is routine in precision oncology practice. However, results are not always conclusive, and it is important to identify which factors may influence FFPE tumor sequencing success. MATERIALS AND METHODS Here, we evaluated the influence of pre-analytical factors on 705 samples of non-small cell lung cancer specimens that underwent NGS testing. Factors such as tumor site, tumor cell percentage, fragment size, primary tumor or metastasis, presence of necrosis, DNA purity, DNA concentration, sample origin and year of testing. RESULTS The overall NGS success rate was 84.9 % (n = 599). Bone site specimens had a very low success rate (42.1 %), differing from lung samples (79.8 %) (P < 0.05). Samples with tumor percentages <5 % (success rate of 44.4 %) represented 14.1 % of failed sequencings. Moreover, samples with tumor percentages >10 %-20 % (82 %) did not differ from those with >30 % (88.9 %) on sequencing outcomes (P = 0.086). Specimens that provided DNA concentrations >2.0 ng/uL, 1.0-2.0 ng/uL, 0.5-1.0 ng/uL and <0.5 ng/uL had success rates of 92 %, 77.1 %, 61.3 % and 20.4 %, respectively. Small fragments (≤0.2 cm2) had a success rate of 74.7 % and were more prevalent in the unsuccessful group (P < 0.05). CONCLUSIONS Our results suggest that tumor percentage, fragment size, decalcified bone specimens, and DNA concentration are potential modifiers of NGS success rates. Interestingly, specimens with tumor percentages between 10 % and 20 % have the same sequencing outcome than specimens with >30 %. These results can strengthen the understanding of factors that lead to NGS success variability.
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Affiliation(s)
- Bruno da Silveira Corrêa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil.
| | - Fernanda De-Paris
- Serviço de Diagnóstico Laboratorial, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Guilherme Danielski Viola
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Unidade de Pesquisa Laboratorial, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda Sales Luiz Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Luis Fernando da Rosa Rivero
- Serviço de Patologia Cirúrgica - Hospital de Clínicas de Porto Alegre - Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Francine Hehn de Oliveira
- Serviço de Patologia Cirúrgica - Hospital de Clínicas de Porto Alegre - Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel de Souza Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Serviço de Diagnóstico Laboratorial, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
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Piñeros-Fernández MC, Morte B, García-Giménez JL. Utility of exome sequencing for the diagnosis of pediatric-onset neuromuscular diseases beyond diagnostic yield: a narrative review. Neurol Sci 2024; 45:1455-1464. [PMID: 37989827 PMCID: PMC10942921 DOI: 10.1007/s10072-023-07210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Diagnosis of neuromuscular diseases (NMD) can be challenging because of the heterogeneity of this group of diseases. This review aimed to describe the diagnostic yield of whole exome sequencing (WES) for pediatric-onset neuromuscular disease diagnosis, as well as other benefits of this approach in patient management since WES can contribute to appropriate treatment selection in NMD patients. WES increases the possibility of reaching a conclusive genetic diagnosis when other technologies have failed and even exploring new genes not previously associated with a specific NMD. Moreover, this strategy can be useful when a dual diagnosis is suspected in complex congenital anomalies and undiagnosed cases.
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Affiliation(s)
- Martha Cecilia Piñeros-Fernández
- Servicio de Neurología Pediátrica, Hospital Pediátrico, Fundación Cardio Infantil-LaCardio, Bogotá, Colombia
- Unidad Pediátrica, Los Cobos Medical Center, Bogotá, Colombia
- Consulta Externa Especializada, Virrey Solís IPS, Bogotá, Colombia
| | - Beatriz Morte
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, València, Spain.
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Colson P, Chaudet H, Delerce J, Pontarotti P, Levasseur A, Fantini J, La Scola B, Devaux C, Raoult D. Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic. J Infect 2024; 88:106150. [PMID: 38570164 DOI: 10.1016/j.jinf.2024.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
OBJECTIVES The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. METHODS We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script. RESULTS A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons). CONCLUSIONS most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Vecteurs, Infections Tropicales et Méditerranéennes (VITROME), 27 Boulevard Jean Moulin, 13005 Marseille, France; French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte Marthe, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Jacques Fantini
- "Aix-Marseille Université, INSERM UMR UA 16, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France.
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Seaby EG, Leggatt G, Cheng G, Thomas NS, Ashton JJ, Stafford I, Baralle D, Rehm HL, O'Donnell-Luria A, Ennis S. A gene pathogenicity tool "GenePy" identifies missed biallelic diagnoses in the 100,000 Genomes Project. Genet Med 2024; 26:101073. [PMID: 38245859 DOI: 10.1016/j.gim.2024.101073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
PURPOSE The 100,000 Genomes Project diagnosed a quarter of affected participants, but 26% of diagnoses were not on the applied gene panel(s); with many being de novo variants. Assessing biallelic variants without a gene panel is more challenging. METHODS We sought to identify missed biallelic diagnoses using GenePy, which incorporates allele frequency, zygosity, and a user-defined deleterious metric, generating an aggregate GenePy score per gene, per participant. We calculated GenePy scores for 2862 recessive disease genes in 78,216 100,000 Genomes Project participants. For each gene, we ranked participant GenePy scores and scrutinized affected participants without a diagnosis, whose scores ranked among the top 5 for each gene. In cases which participant phenotypes overlapped with the disease gene of interest, we extracted rare variants and applied phase, ClinVar, and ACMG classification. RESULTS 3184 affected individuals without a molecular diagnosis had a top-5-ranked GenePy score and 682 of 3184 (21%) had phenotypes overlapping with a top-ranking gene. In 122 of 669 (18%) phenotype-matched cases (excluding 13 withdrawn participants), we identified a putative missed diagnosis (2.2% of all undiagnosed participants). A further 334 of 669 (50%) cases have a possible missed diagnosis but require functional validation. CONCLUSION Applying GenePy at scale has identified 456 potential diagnoses, demonstrating the value of novel diagnostic strategies.
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Affiliation(s)
- Eleanor G Seaby
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Paediatric Infectious Diseases, Imperial College London, London, United Kingdom.
| | - Gary Leggatt
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Guo Cheng
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - N Simon Thomas
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom; Wessex Regional Genomics Laboratory, Salisbury NHS Foundation Trust, Salisbury, United Kingdom
| | - James J Ashton
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | | | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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Rophina M, Sinha A, Biswas D, Basu D, Datta SS, Scaria V. Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases. Transfus Apher Sci 2024; 63:103872. [PMID: 38272782 DOI: 10.1016/j.transci.2024.103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
The DEL phenotype represents an intriguing and challenging aspect of blood group serology. This condition is characterized by an extremely weak expression of the D antigen on red blood cells, to the extent that it often eludes detection through routine serological methods. Identifying the DEL phenotype necessitates more specialized techniques, such as adsorption and elution tests, to reveal the presence of the D antigen. This distinctive phenotype underscores the complexity and subtlety of blood group genetics and highlights the importance of using advanced methods to accurately classify individuals with this condition, as their ability to form anti-D antibodies can have clinical implications during transfusion and pregnancy scenarios. There is a paucity of data for the DEL phenotype in the Indian population, and the molecular basis has not been elucidated yet. Our investigation delves into the genetic underpinnings of two distinct DEL phenotype cases that pose challenges for resolution through conventional serological techniques. We employ next-generation amplicon sequencing to unravel the intricate genetic landscape underlying these cases. In the D-negative donor, the DEL phenotype was first identified serologically, which was subsequently confirmed by molecular analysis. In the second case, it was associated with an anti-D antibody in a D-positive patient. Initial data analysis unveiled a substantial reduction in coverage across the exonic segments of the RHD gene in both samples, suggesting the potential presence of RHD exon deletions. On both occasions, we identified a homozygous intronic RHD polymorphism that is well established to be linked to the RHD* 01EL.32/RHD*DEL32 variant.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Ayesha Sinha
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Durba Biswas
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Debapriya Basu
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Suvro Sankha Datta
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India; Vishwanath Cancer Care Foundation, B 702, Neelkanth Business Park Kirol Village, Mumbai, 400 086, India
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Rezazadeh A, Pruett J, Detzner A, Edwin N, Hamadani M, Shah NN, Fenske TS. Immunoglobulin High Throughput Sequencing (Ig-HTS) Minimal Residual Disease (MRD) Analysis is an Effective Surveillance Tool in Patients With Mantle Cell Lymphoma. Clin Lymphoma Myeloma Leuk 2024; 24:254-259. [PMID: 38195321 DOI: 10.1016/j.clml.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024]
Abstract
INTRODUCTION Mantle cell lymphoma (MCL) accounts for 4% to 6% of B-cell non-Hodgkin lymphoma with historically poor outcomes. With the advent of intensive first-line, targeted, and cellular therapies, outcomes have improved, and initial remission can be 8 to 10 years or longer. As patients experience longer remissions, this raises the question of the optimal surveillance modality. Peripheral blood minimal residual disease (MRD) analysis offers a potential alternative to surveillance imaging that is sensitive, less costly, and eliminates the risk of radiation exposure. MATERIALS AND METHODS The clonoSEQ assay (Adaptive Biotechnologies) is an FDA-cleared commercially available Ig-HTS MRD assay with a sensitivity of 1 cell in 1,000,000. We performed a retrospective analysis of 34 patients from 2015 to 2021, who underwent MRD testing after achieving remission with first-line therapy. RESULTS With a median follow-up of 6.5 years, 10-year progression free survival (PFS) was 60% and 10-year overall survival was 92% of the entire cohort. Among 12 patients who sustained a radiographic relapse, peripheral blood became MRD+ either at or prior to the time of relapse in 11 patients (92%). The first MRD+ test had a lead time of 0 to 24 months (median 34 days) prior to radiographic relapse. Only 1 patient had a MRD- result while being found to have progressive disease on imaging. Among 22 patients who sustained continuous clinical remission, 21 have remained MRD-. Several patients were able to enjoy 2 to 4-year intervals without surveillance imaging. CONCLUSIONS Our data suggest that the clonoSEQ MRD assay is an effective surveillance tool for MCL patients following first-line therapy and is predictive of relapse prior to imaging.
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Affiliation(s)
- Alexandra Rezazadeh
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI
| | - Julie Pruett
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI
| | - Amy Detzner
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI
| | | | - Mehdi Hamadani
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI; BMT & Cellular Therapy Program, Medical College of Wisconsin, Milwaukee, WI
| | - Nirav N Shah
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI; BMT & Cellular Therapy Program, Medical College of Wisconsin, Milwaukee, WI
| | - Timothy S Fenske
- Division of Hematology & Oncology, Medical College of Wisconsin, Milwaukee, WI; BMT & Cellular Therapy Program, Medical College of Wisconsin, Milwaukee, WI.
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Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L, Rosenquist R. Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med 2024; 96:101250. [PMID: 38330674 DOI: 10.1016/j.mam.2024.101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024]
Abstract
Current precision cancer medicine is dependent on the analyses of a plethora of clinically relevant genomic aberrations. During the last decade, next-generation sequencing (NGS) has gradually replaced most other methods for precision cancer diagnostics, spanning from targeted tumor-informed assays and gene panel sequencing to global whole-genome and whole-transcriptome sequencing analyses. The shift has been impelled by a clinical need to assess an increasing number of genomic alterations with diagnostic, prognostic and predictive impact, including more complex biomarkers (e.g. microsatellite instability, MSI, and homologous recombination deficiency, HRD), driven by the parallel development of novel targeted therapies and enabled by the rapid reduction in sequencing costs. This review focuses on these sequencing-based methods, puts their emergence in a historic perspective, highlights their clinical utility in diagnostics and decision-making in pediatric and adult cancer, as well as raises challenges for their clinical implementation. Finally, the importance of applying sensitive tools for longitudinal monitoring of treatment response and detection of measurable residual disease, as well as future avenues in the rapidly evolving field of sequencing-based methods are discussed.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Lund, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Lucia Cavelier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden; Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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Wu LS, Luo X, Tan M, Zhang LJ, Luo HF, Huang G, Huang P, Chen J, Chen Y. Prevalence of thalassemia-carrier couples and fertility risk assessment. Int J Hematol 2024; 119:374-382. [PMID: 38411864 DOI: 10.1007/s12185-024-03722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Thalassemia is a highly prevalent hematologic disease in Guizhou, China. This study aimed to determine the epidemiological characteristics of thalassemia in couples at childbearing age and assess the neonatal risk of thalassemia in this subpopulation. A cohort of 4481 couples at childbearing age were recruited for thalassemia carrier screening by both traditional hematological tests and next-generation sequencing. Of them, 1314 (14.66%) thalassemia carriers were identified, including 857 (9.76%) α-thalassemia, 391 (4.36%) β-thalassemia, and 48 (0.54%) composite α and β-thalassemia. A total of 12 α-globin gene alterations and 16 β-globin mutations were detected, including four novel thalassemia mutations. SEA was the most common α-thalassemia genotype (26.86%), CD41-42 the most common β-thalassemia genotype (36.57%), and αα/- α3.7 + CD41-42 the most common composite α- and β-thalassemia genotype (18.75%). Ethnically, the Zhuang had the highest rate of thalassemia gene carriers among the ethnic groups. Geographically, Qiannan had the highest rate of thalassemia gene carriers. In addition, 38 of the 48 couples with composite α- and β-thalassemia were high-risk thalassemia carriers, and 4 carrying the -SEA/αα gene needed fertility guidance.
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Affiliation(s)
- Liu-Song Wu
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Xi Luo
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Mei Tan
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Li-Jun Zhang
- Department of Pediatrics, The Qian-Nan-Zhou People's Hospital of Guizhou, Guizhou, China
| | - Hong-Fang Luo
- Department of Pediatrics, The 2nd Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Ge Huang
- Clinical Laboratory, The Qian-Dong-Nan People's Hospital of Guizhou, Guizhou, China
| | - Pei Huang
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jindong Chen
- Exploring Health, LLC., 3 Lanyue Rd., Huangpu District, Guangzhou, 510663, China.
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Yan Chen
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China.
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Takase K, Susa S, Sato H, Hada Y, Nagaoka K, Takakubo N, Karasawa S, Kameda W, Numakura C, Ishizawa K. Identification of causative gene variants for patients with known monogenic diabetes using a targeted next-generation sequencing panel in a single-center study. Diabetol Int 2024; 15:203-211. [PMID: 38524932 PMCID: PMC10959868 DOI: 10.1007/s13340-023-00669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/19/2023] [Indexed: 03/26/2024]
Abstract
Aims We aimed to verify the usefulness of targeted next-generation sequencing (NGS) technology for diagnosing monogenic diabetes in a single center. Methods We designed an amplicon-based NGS panel targeting 34 genes associated with known monogenic diabetes and performed resequencing in 56 patients with autoantibody-negative diabetes mellitus diagnosed at < 50 years who had not been highly obese. By bioinformatic analysis, we filtered significant variants based on allele frequency (< 0.005 in East Asians) and functional prediction. We estimated the pathogenicity of each variant upon considering the family history. Results Overall, 16 candidate causative variants were identified in 16 patients. Among them, two previously known heterozygous nonsynonymous single-nucleotide variants associated with monogenic diabetes were confirmed as causative variants: one each in the GCK and WFS1 genes. The former was found in two independent diabetes-affected families. Two novel putatively deleterious heterozygous variants were also assumed to be causative from the family history: one frameshift and one nonsynonymous single-nucleotide variant in the HNF4A gene. Twelve variants remained as candidates associated with the development of diabetes. Conclusion Targeted NGS panel testing was useful to diagnose various forms of monogenic diabetes in combination with familial analysis, but additional ingenuity would be needed for practice. Supplementary Information The online version contains supplementary material available at 10.1007/s13340-023-00669-3.
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Affiliation(s)
- Kaoru Takase
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Shinji Susa
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Hidenori Sato
- Genomic Information Analysis Unit, Department of Genomic Cohort Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Yurika Hada
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Kyoko Nagaoka
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Noe Takakubo
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
- Takakubo Clinic, 2-9-7 Kitamachi, Warabi, Saitama 335-0001 Japan
| | - Shigeru Karasawa
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Wataru Kameda
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
| | - Chikahiko Numakura
- Department of Pediatrics and Clinical Genomics, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama 350-0495 Japan
| | - Kenichi Ishizawa
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata, 990-9585 Japan
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Adashek JJ, Kato S, Sicklick JK, Lippman SM, Kurzrock R. If it's a target, it's a pan-cancer target: Tissue is not the issue. Cancer Treat Rev 2024; 125:102721. [PMID: 38522181 DOI: 10.1016/j.ctrv.2024.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
Cancer is traditionally diagnosed and treated on the basis of its organ of origin (e.g., lung or colon cancer). However, organ-of-origin diagnostics does not reveal the underlying oncogenic drivers. Fortunately, molecular diagnostics have advanced at a breathtaking pace, and it is increasingly apparent that cancer is a disease of the genome. Hence, we now have multiple genomic biomarker-based, tissue-agnostic Food and Drug Administration approvals for both gene- and immune-targeted therapies (larotrectinib/entrectinib, for NTRK fusions; selpercatinib, RET fusions; dabrafenib plus trametinib, BRAFV600E mutations; pembrolizumab/dostarlimab, microsatellite instability; and pembrolizumab for high tumor mutational burden; pemigatinib is also approved for FGFR1-rearranged myeloid/lymphoid neoplasms). There are emerging targets as well, including but not limited to ALK, BRCA and/or homologous repair deficiency, ERBB2 (HER2), IDH1/2, KIT, KRASG12C, NRG1, and VHL. Many tissue-agnostic approvals center on rare/ultra-rare biomarkers (often < 1 % of cancers), necessitating screening hundreds of tumors to find a single one harboring the cognate molecular alteration. Approval has generally been based on small single-arm studies (<30-100 patients) with high response rates (>30 % to > 75 %) of remarkable durability. Because of biomarker rarity, single-gene testing is not practical; next generation sequencing of hundreds of genes must be performed to obtain timely answers. Resistance to biomarker-driven therapeutics is often due to secondary mutations or co-driver gene defects; studies are now addressing the need for customized drug combinations matched to the complex molecular alteration portfolio in each tumor. Future investigation should expand tissue-agnostic therapeutics to encompass both hematologic and solid malignancies and include biomarkers beyond those that are DNA-based.
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Affiliation(s)
- Jacob J Adashek
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore, MD, USA.
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Jason K Sicklick
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA; Department of Surgery, Division of Surgical Oncology, University of California San Diego, UC San Diego Health, San Diego, CA, USA; Department of Pharmacology, University of California San Diego, UC San Diego Health, San Diego, CA, USA
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Razelle Kurzrock
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee Wisconsin, USA; WIN Consortium, Paris France; University of Nebraska, United States.
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Bai H, Zhou Y, Liu W, Xu WY, Cheng L, Huo Y, Ji H, Xiong L. Genetic mutation profiling reveals biomarkers for targeted therapy efficacy and prognosis in non-small cell lung cancer. Heliyon 2024; 10:e27633. [PMID: 38496877 PMCID: PMC10944256 DOI: 10.1016/j.heliyon.2024.e27633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction The genetic heterogeneity of non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations may affect clinical responses and outcomes to EGFR tyrosine kinase inhibitors (EGFR-TKIs). This study aims to investigate the genomic factors that influence the efficacy and clinical outcomes of first-line, second-line and third-line treatments in NSCLC and explore the heterogeneity of resistance mechanisms. Materials and methods This real-world study comprised 65 patients with EGFR mutant NSCLC. Molecular alterations were detected using a customized DNA panel before and after administering targeted therapy. The efficacy and prognosis of each treatment line were evaluated. Results In first-generation EGFR-TKIs treatment, gefitinib showed favorable efficacy compared to icotinib and erlotinib, particularly in patients with EGFR L858R mutations. The resistance mechanisms to first-generation EGFR-TKIs varied among different EGFR mutation cohorts and different first-generation EGFR-TKIs. In second-line EGFR-TKIs treatment, EPH receptor A3 (EPHA3), IKAROS family zinc finger 1 (IKZF1), p21 (RAC1) activated kinase 5 (PAK5), DNA polymerase epsilon, catalytic subunit (POLE), RAD21 cohesin complex component (RAD21) and RNA binding motif protein 10 (RBM10) mutations were markedly associated with poorer progression-free survival (PFS). Notably, EPHA3, IKZF1 and RBM10 were identified as independent predictors of PFS. The mechanisms of osimertinib resistance exhibited heterogeneity, with a higher proportion of non-EGFR-dependent resistant mutations. In third-line treatments, the combination of osimertinib and anlotinib demonstrated superior efficacy compared to other regimens. Glutamate ionotropic receptor NMDA type subunit 2A (GRIN2A) mutation was an independent risk indicator of shorter OS following third-line treatments. Conclusions Comprehending the tumor evolution in NSCLC is advantageous for assessing the efficacy and prognosis at each stage of treatment, providing valuable insights to guide personalized treatment decisions for patients.
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Affiliation(s)
- Hao Bai
- Department of Pulmonary and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yan Zhou
- Department of Pulmonary and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Wanting Liu
- Department of Pulmonary and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | | | - Lei Cheng
- Department of Pulmonary and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | | | - Hao Ji
- Department of Respiratory and Critical Care Medicine, Department of Healthcare Associated Infection Management, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Liwen Xiong
- Department of Pulmonary and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
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Zhu C, Tang M, Fu Y, Xun Z, Lin C, Wu S, Chen T, Zeng Y, Yang B, Ou Q, Liu C. Characterization of BCP/PreC/C region quasispecies in treatment-naive patients with different phases of HBV infection using next-generation sequencing. Int J Med Microbiol 2024; 315:151619. [PMID: 38564936 DOI: 10.1016/j.ijmm.2024.151619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To analysis of quasispecies (QS) changes and high-frequency mutations in the BCP/PreC/C region of patients at different phases of hepatitis B virus (HBV) infection and provides novel biomarkers for the diagnosis of chronic hepatitis B (CHB) patients. METHODS With the application of next-generation sequencing technology, we were able to sequence the HBV BCP/PreC/C regions in 40 patients, each at different phases of the HBV infection. The heterogeneity of QS and the frequency of mutations were calculated using MEGA 7 software. RESULTS Our results show that the complexity and diversity of the BCP/PreC/C QS in HBeAg-positive CHB patients are significantly higher than those in HBeAg-positive chronic infection patients, while HBeAg-negative chronic infection patients had significantly higher QS complexity and diversity than HBeAg-negative CHB patients. In addition, HBeAg-negative patients showed reduced complexity but increased diversity compared with HBeAg-positive patients. Receiver operating characteristic curves showed that G1764A, C2102T, dN and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-positive CHB, while the A2189C, dS and complexity of QS could be used as potential biomarkers for diagnosing HBeAg-negative chronic hepatitis. Finally, our study also found that G1896A and A2159G may be hotspot mutations affecting HBeAg seroconversion. CONCLUSION Our research elucidates the evolution of HBV by analyzing QS heterogeneity and mutation patterns, offering novel serum biomarkers for enhancing clinical diagnosis and disease prognosis. This comprehensive approach sheds light on the intricate dynamics of HBV progression and paves the way for more precise medical interventions.
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Affiliation(s)
- Chenggong Zhu
- Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Minjie Tang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ya Fu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Caorui Lin
- Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Songhang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China; Department of Laboratory Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Gene Diagnostic Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China; Fujian Clinical Research Center for Laboratory Medicine of Immunology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
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Shen J, Sun H, Zhou S, Wang L, Dong C, Ren K, Du Q, Cao J, Wang Y, Sun J. Development of a screening system of gene sets for estimating the time of early skeletal muscle injury based on second-generation sequencing technology. Int J Legal Med 2024:10.1007/s00414-024-03210-6. [PMID: 38532207 DOI: 10.1007/s00414-024-03210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The present study is aimed to address the challenge of wound age estimation in forensic science by identifying reliable genetic markers using low-cost and high-precision second-generation sequencing technology. A total of 54 Sprague-Dawley rats were randomly assigned to a control group or injury groups, with injury groups being further divided into time points (4 h, 8 h, 12 h, 16 h, 20 h, 24 h, 28 h, and 32 h after injury, n = 6) to establish rat skeletal muscle contusion models. Gene expression data were obtained using second-generation sequencing technology, and differential gene expression analysis, weighted gene co-expression network analysis (WGCNA) and time-dependent expression trend analysis were performed. A total of six sets of biomarkers were obtained: differentially expressed genes at adjacent time points (127 genes), co-expressed genes most associated with wound age (213 genes), hub genes exhibiting time-dependent expression (264 genes), and sets of transcription factors (TF) corresponding to the above sets of genes (74, 87, and 99 genes, respectively). Then, random forest (RF), support vector machine (SVM) and multilayer perceptron (MLP), were constructed for wound age estimation from the above gene sets. The results estimated by transcription factors were all superior to the corresponding hub genes, with the transcription factor group of WGCNA performed the best, with average accuracy rates of 96% for three models' internal testing, and 91.7% for the highest external validation. This study demonstrates the advantages of the indicator screening system based on second-generation sequencing technology and transcription factor level for wound age estimation.
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Affiliation(s)
- Junyi Shen
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
- Institute of Forensic Science Public Security Department of Shanxi, Taiyuan, China
| | - Hao Sun
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Shidong Zhou
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Liangliang Wang
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Chaoxiu Dong
- Institute of Forensic Science Public Security Department of Shanxi, Taiyuan, China
| | - Kang Ren
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Qiuxiang Du
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Jie Cao
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Yingyuan Wang
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China.
| | - Junhong Sun
- Department of Forensic Medicine, Shanxi Medical University, Jinzhong, China.
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