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Murali H, Wang P, Liao EC, Wang K. Genetic variant classification by predicted protein structure: A case study on IRF6. Comput Struct Biotechnol J 2024; 23:892-904. [PMID: 38370976 PMCID: PMC10869248 DOI: 10.1016/j.csbj.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024] Open
Abstract
Next-generation genome sequencing has revolutionized genetic testing, identifying numerous rare disease-associated gene variants. However, to impute pathogenicity, computational approaches remain inadequate and functional testing of gene variant is required to provide the highest level of evidence. The emergence of AlphaFold2 has transformed the field of protein structure determination, and here we outline a strategy that leverages predicted protein structure to enhance genetic variant classification. We used the gene IRF6 as a case study due to its clinical relevance, its critical role in cleft lip/palate malformation, and the availability of experimental data on the pathogenicity of IRF6 gene variants through phenotype rescue experiments in irf6-/- zebrafish. We compared results from over 30 pathogenicity prediction tools on 37 IRF6 missense variants. IRF6 lacks an experimentally derived structure, so we used predicted structures to explore associations between mutational clustering and pathogenicity. We found that among these variants, 19 of 37 were unanimously predicted as deleterious by computational tools. Comparing in silico predictions with experimental findings, 12 variants predicted as pathogenic were experimentally determined as benign. Even with the recently published AlphaMissense model, 15/18 (83%) of the predicted pathogenic variants were experimentally determined as benign. In comparison, mapping variants to the protein revealed deleterious mutation clusters around the protein binding domain, whereas N-terminal variants tend to be benign, suggesting the importance of structural information in determining pathogenicity of mutations in this gene. In conclusion, incorporating gene-specific structural features of known pathogenic/benign mutations may provide meaningful insights into pathogenicity predictions in a gene-specific manner and facilitate the interpretation of variant pathogenicity.
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Affiliation(s)
- Hemma Murali
- Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Peng Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Master of Biotechnology Program, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eric C. Liao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Center for Craniofacial Innovation, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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2
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Lee JH, Park YM, Kim J, Kwon GC, Kim SY. Assessing the performance and utility of targeted next-generation sequencing for screening and genotyping of human papillomaviruses. Diagn Microbiol Infect Dis 2024; 109:116216. [PMID: 38479093 DOI: 10.1016/j.diagmicrobio.2024.116216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/24/2024] [Accepted: 02/15/2024] [Indexed: 04/30/2024]
Abstract
A next-generation sequencing (NGS)-based Ezplex HPV NGS kit (SML Genetree, Seoul, Korea) was used for human papillomavirus (HPV) screening. Of 885 cervical swab samples, HPV was detected in 162 samples. High-risk HPVs were detected in 82 samples, and other types of HPV were detected in 13 samples (HPV86, 71, 102, 91, and 114). At the read depth ≥ 500, NGS results exhibited 100 % agreement among repeated tests. HPV NGS results were compared with those of real-time PCR assays, Anyplex HPV28 (Seegene, Seoul, Korea) (n = 383) and Cobas HPV (Roche, Mannheim, Germany) (n = 64); concordances were 92.4 % and 95.0 %, respectively. Sanger sequencing of discordant results (n = 13) produced compatible results with those of HPV NGS. Pap smear abnormalities were detected in 31 patients (3.5 %), and 19 patients had high-risk HPV. Using HPV NGS for screening, rare HPV subtypes were detected, and quantitative values were obtained as read depth.
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Affiliation(s)
- Jung Hoon Lee
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Yun Mi Park
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Jimyung Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Gye Cheol Kwon
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Chungnam National University Hospital, Daejeon, South Korea
| | - Seon Young Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, South Korea.
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3
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Kim N, Hahn S, Choi YJ, Cho H, Chung H, Jang JE, Lyu CJ, Lee ST, Choi JR, Cheong JW, Shin S. Comprehensive insights into AML relapse: genetic mutations, clonal evolution, and clinical outcomes. Cancer Cell Int 2024; 24:174. [PMID: 38764048 PMCID: PMC11103850 DOI: 10.1186/s12935-024-03368-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
INTRODUCTION Acute myeloid leukemia (AML) is a complex hematologic malignancy characterized by uncontrolled proliferation of myeloid precursor cells within bone marrow. Despite advances in understanding of its molecular underpinnings, AML remains a therapeutic challenge due to its high relapse rate and clonal evolution. METHODS In this retrospective study, we analyzed data from 24 AML patients diagnosed at a single institution between January 2017 and August 2023. Comprehensive genetic analyses, including chromosomal karyotyping, next-generation sequencing, and gene fusion assays, were performed on bone marrow samples obtained at initial diagnosis and relapse. Clinical data, treatment regimens, and patient outcomes were also documented. RESULTS Mutations in core genes of FLT3, NPM1, DNMT3A, and IDH2 were frequently discovered in diagnostic sample and remained in relapse sample. FLT3-ITD, TP53, KIT, RUNX1, and WT1 mutation were acquired at relapse in one patient each. Gene fusion assays revealed stable patterns, while chromosomal karyotype analyses indicated a greater diversity of mutations in relapsed patients. Clonal evolution patterns varied, with some cases showing linear or branching evolution and others exhibiting no substantial change in core mutations between diagnosis and relapse. CONCLUSIONS Our study integrates karyotype, gene rearrangements, and gene mutation results to provide a further understanding of AML heterogeneity and evolution. We demonstrate the clinical relevance of specific mutations and clonal evolution patterns, emphasizing the need for personalized therapies and measurable residual disease monitoring in AML management. By bridging the gap between genetics and clinical outcome, we move closer to tailored AML therapies and improved patient prognoses.
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Affiliation(s)
- Namsoo Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Seungmin Hahn
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Chuhl Joo Lyu
- Department of Pediatric Hematology-Oncology, Severance Hospital, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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Szakállas N, Barták BK, Valcz G, Nagy ZB, Takács I, Molnár B. Can long-read sequencing tackle the barriers, which the next-generation could not? A review. Pathol Oncol Res 2024; 30:1611676. [PMID: 38818014 PMCID: PMC11137202 DOI: 10.3389/pore.2024.1611676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.
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Affiliation(s)
- Nikolett Szakállas
- Department of Biological Physics, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
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5
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Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
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Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
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Philipp M, Moth CW, Ristic N, Tiemann JKS, Seufert F, Panfilova A, Meiler J, Hildebrand PW, Stein A, Wiegreffe D, Staritzbichler R. MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts. Nucleic Acids Res 2024:gkae301. [PMID: 38647044 DOI: 10.1093/nar/gkae301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format. Structures are flexibly colorable, not only by energetic differences, but also by hydrophobicity, sequence conservation, or other biochemical profiling. Coloring by interface score reveals mutation impacts on binding surfaces. MutationExplorer strives for efficiency in user experience. For example, we have prepared 45 000 PDB depositions for instant retrieval and initial display. All modeling steps are performed by Rosetta. Visualizations leverage MDsrv/Mol*. MutationExplorer is available at: http://proteinformatics.org/mutation_explorer/.
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Affiliation(s)
- Michelle Philipp
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany
| | - Christopher W Moth
- Vanderbilt University, Center for Structural Biology, 465 21st Ave South, Nashville, TN 37232, USA
| | - Nikola Ristic
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Johanna K S Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark
- Novozymes A/S, 2800 Kgs. Lyngby, Denmark
| | - Florian Seufert
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Aleksandra Panfilova
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark
| | - Jens Meiler
- Vanderbilt University, Center for Structural Biology, 465 21st Ave South, Nashville, TN 37232, USA
- Leipzig University Medical School, Institute for Drug Discovery, Brüderstraße 34, 04103 Leipzig, Germany
| | - Peter W Hildebrand
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N., Denmark
| | - Daniel Wiegreffe
- Image and Signal Processing Group, Department of Computer Science, Leipzig University, Augustusplatz 10, 04109 Leipzig, Germany
| | - René Staritzbichler
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
- University Institute for Laboratory Medicine, Microbiology and Clinical Pathobiochemistry, University Hospital of Bielefeld University, Germany
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7
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Han H, Lee HJ, Kim KS, Chung J, Na HS. Comparison of the performance of MiSeq and NovaSeq in oral microbiome study. J Oral Microbiol 2024; 16:2344293. [PMID: 38645704 PMCID: PMC11028001 DOI: 10.1080/20002297.2024.2344293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 04/23/2024] Open
Abstract
Objective Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study. Methods Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens. Results NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades. Conclusion Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.
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Affiliation(s)
- Hyejung Han
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam-si, South Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, South Korea
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8
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Chen Y, Han X, Hua R, Li N, Zhang L, Hu W, Wang Y, Qian Z, Li S. Copy number variation sequencing for the products of conception: What is the optimal testing strategy. Clin Chim Acta 2024; 557:117884. [PMID: 38522821 DOI: 10.1016/j.cca.2024.117884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. METHODS CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. RESULTS Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. CONCLUSIONS We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjing Hu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhida Qian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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9
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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] [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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10
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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] [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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Ha C, Kim D, Bak M, Park JH, Kim YG, Jang JH, Kim JW, Choi JO, Jang MA. CRYAB stop-loss variant causes rare syndromic dilated cardiomyopathy with congenital cataract: expanding the phenotypic and mutational spectrum of alpha-B crystallinopathy. J Hum Genet 2024; 69:159-162. [PMID: 38212463 DOI: 10.1038/s10038-023-01218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/01/2023] [Accepted: 12/25/2023] [Indexed: 01/13/2024]
Abstract
Missense mutations in the alpha-B crystallin gene (CRYAB) have been reported in desmin-related myopathies with or without cardiomyopathy and have also been reported in families with only a cataract phenotype. Dilated cardiomyopathy (DCM) is a disorder with a highly heterogeneous genetic etiology involving more than 60 causative genes, hindering genetic diagnosis. In this study, we performed whole genome sequencing on 159 unrelated patients with DCM and identified an unusual stop-loss pathogenic variant in NM_001289808.2:c.527A>G of CRYAB in one patient. The mutant alpha-B crystallin protein is predicted to have an extended strand with addition of 19 amino acid residues, p.(Ter176TrpextTer19), which may contribute to aggregation and increased hydrophobicity of alpha-B crystallin. The proband, diagnosed with DCM at age 32, had a history of bilateral congenital cataracts but had no evidence of myopathy or associated symptoms. He also has a 10-year-old child diagnosed with bilateral congenital cataracts with the same CRYAB variant. This study expands the mutational spectrum of CRYAB and deepens our understanding of the complex phenotypes of alpha-B crystallinopathies.
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Affiliation(s)
- Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Darae Kim
- Division of Cardiology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Minjung Bak
- Division of Cardiology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jong-Ho Park
- Clinical Genome Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
- Clinical Genome Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jin-Oh Choi
- Division of Cardiology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
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12
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Couto RDS, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Genomoviruses in Liver Samples of Molossus molossus Bats. Microorganisms 2024; 12:688. [PMID: 38674632 PMCID: PMC11052389 DOI: 10.3390/microorganisms12040688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences & Technology, UPES University, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
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13
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Ermini L, Driguez P. The Application of Long-Read Sequencing to Cancer. Cancers (Basel) 2024; 16:1275. [PMID: 38610953 PMCID: PMC11011098 DOI: 10.3390/cancers16071275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment.
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Affiliation(s)
- Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Patrick Driguez
- Bioscience Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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14
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Hwang N, Kim SM, Kim YG, Ha C, Lee J, Choi BO, Sung WJ, Kim SH, Kim YM, Lee YW, Kim J, Kim JW, Jang JH, Lee J, Park HD. Clinical feature, GALC variant spectrum, and genotype-phenotype correlation in Korean Krabbe disease patients: Multicenter experience over 13 years. Clin Genet 2024. [PMID: 38515343 DOI: 10.1111/cge.14523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/14/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Krabbe disease (KD) is an autosomal recessive neurodegenerative disorder caused by deficiency of the galactocerebrosidase (GALC) due to variants in the GALC gene. Here, we provide the first and the largest comprehensive analysis of clinical and genetic characteristics, and genotype-phenotype correlations of KD in Korean in comparison with other ethnic groups. From June 2010 to June 2023, 10 patients were diagnosed with KD through sequencing of GALC. Clinical features, and results of GALC sequencing, biochemical test, neuroimaging, and neurophysiologic test were obtained from medical records. An additional nine previously reported Korean KD patients were included for review. In Korean KD patients, the median age of onset was 2 years (3 months-34 years) and the most common phenotype was adult-onset (33%, 6/18) KD, followed by infantile KD (28%, 5/18). The most frequent variants were c.683_694delinsCTC (23%) and c.1901T>C (23%), while the 30-kb deletion was absent. Having two heterozygous pathogenic missense variants was associated with later-onset phenotype. Clinical features were similar to those of other ethnic groups. In Korean KD patients, the most common phenotype was the adult-onset type and the GALC variant spectrum was different from that of the Caucasian population. This study would further our understanding of KD.
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Affiliation(s)
- Narae Hwang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sang-Mi Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won Jae Sung
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Pusan, Republic of Korea
| | - Yong-Wha Lee
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyung-Doo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Medical Device Management and Research, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
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15
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Zhang P, Zhao X, Li Q, Xu Y, Cheng Z, Yang L, Wang H, Tao Y, Huang G, Wu R, Zhou H, Zhao S. Proband-independent haplotyping based on NGS-based long-read sequencing for detecting pathogenic variant carrier status in preimplantation genetic testing for monogenic diseases. Front Mol Biosci 2024; 11:1329580. [PMID: 38516188 PMCID: PMC10955336 DOI: 10.3389/fmolb.2024.1329580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Preimplantation genetic testing for monogenic diseases (PGT-M) can be used to select embryos that do not develop disease phenotypes or carry disease-causing genes for implantation into the mother's uterus, to block disease transmission to the offspring, and to increase the birth rate of healthy newborns. However, the traditional PGT-M technique has some limitations, such as its time consumption, experimental procedural complexity, and the need for a complete family or reference embryo to construct the haplotype. In this study, proband-independent haplotyping based on NGS-based long-read sequencing (Phbol-seq) was used to effectively construct haplotypes. By targeting the mutation sites of single gene disease point mutations and small fragment deletion carriers, embryos carrying parental disease-causing mutations were successfully identified by linkage analysis. The efficiency of embryo resolution was then verified by classical Sanger sequencing, and it was confirmed that the construction of haplotype and SNP linkage analysis by Phbol-seq could accurately and effectively detect whether embryos carried parental pathogenic mutations. After the embryos confirmed to be nonpathogenic by Phbol-seq-based PGT-M and confirmed to have normal copy number variation by Phbol-seq-based PGT-A were transplanted into the uterus, gene detection in amniotic fluid of the implanted embryos was performed, and the results confirmed that Phbol-seq technology could accurately distinguish normal genotype embryos from genetically modified carrier embryos. Our results suggest that Phbol-seq is an effective strategy for accurately locating mutation sites and accurately distinguishing between embryos that inherit disease-causing genes and normal embryos that do not. This is critical for Phbol-seq-based PGT-M and could help more single-gene disease carriers with incomplete families, de novo mutations or suspected germline mosaicism to have healthy babies with normal phenotypes. It also helps to reduce the transmission of monogenic genetic diseases in the population.
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Affiliation(s)
- Peiyu Zhang
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Xiaomei Zhao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qinshan Li
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yaqiong Xu
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Zengmei Cheng
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Lu Yang
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Houmei Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yang Tao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of The First People’s Hospital of Bijie, Bijie, China
| | - Guanyou Huang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Rui Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Hua Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shuyun Zhao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
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16
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Jang MA. Next-Generation Sequencing-Based Molecular Profiling Using Cell-Free DNA: A Valuable Tool for the Diagnostic and Prognostic Evaluation of Patients With Gastric Cancer. Ann Lab Med 2024; 44:119-121. [PMID: 37880993 PMCID: PMC10628754 DOI: 10.3343/alm.2023.0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Affiliation(s)
- Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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17
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Philipp M, Moth CW, Ristic N, Tiemann JK, Seufert F, Panfilova A, Meiler J, Hildebrand PW, Stein A, Wiegreffe D, Staritzbichler R. MUTATIONEXPLORER- A WEBSERVER FOR MUTATION OF PROTEINS AND 3D VISUALIZATION OF ENERGETIC IMPACTS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.23.533926. [PMID: 38464310 PMCID: PMC10925206 DOI: 10.1101/2023.03.23.533926] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted. In addition to a basic per-residue input format, MutationExplorer can also upload an entire replacement sequence. Previously the purview of desktop applications, such an upload can back-mutate PDB structures to wildtype sequence in a single step. Another supported variation source is human single nucelotide polymorphisms (SNPs), genomic coordinates input in VCF format.
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Affiliation(s)
- Michelle Philipp
- Leipzig University, Image and Signal Processing Group, Leipzig, Germany
| | - Christopher W. Moth
- Vanderbilt University, Center for Structural Biology, Nashville, Tennessee, USA
| | - Nikola Ristic
- Leipzig University, Institute for Medical Physics and Biophysics, Leipzig, Germany
| | - Johanna K.S. Tiemann
- University of Copenhagen, Linderstrøm-Lang Centre for Protein Science, Copenhagen N., Denmark, and Novozymes A/S, Lyngby, Denmark
| | - Florian Seufert
- Leipzig University, Institute for Medical Physics and Biophysics, Leipzig, Germany
| | - Aleksandra Panfilova
- University of Copenhagen, Linderstrøm-Lang Centre for Protein Science, Copenhagen N., Denmark
| | - Jens Meiler
- Vanderbilt University, Center for Structural Biology, Nashville, Tennessee, USA, and Leipzig University Medical School, Institute for Drug Discovery, Leipzig, Germany
| | - Peter W. Hildebrand
- Leipzig University, Institute for Medical Physics and Biophysics, Leipzig, Germany, and Charité Universitätsmedizin Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany, and Berlin Institute of Health, Berlin, Germany
| | - Amelie Stein
- University of Copenhagen, Linderstrøm-Lang Centre for Protein Science, Copenhagen N., Denmark
| | - Daniel Wiegreffe
- Leipzig University, Image and Signal Processing Group, Leipzig, Germany
| | - René Staritzbichler
- Leipzig University, Institute for Medical Physics and Biophysics, Leipzig, Germany
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18
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Tasopoulou KM, Karakasiliotis I, Argyriou C, Bampali M, Tsaroucha AK, Dovrolis N, Christaina E, Georgiadis GS. Next-Generation Sequencing of microRNAs in Small Abdominal Aortic Aneurysms: MiR-24 as a Biomarker. Ann Vasc Surg 2024; 99:366-379. [PMID: 37922957 DOI: 10.1016/j.avsg.2023.09.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/28/2023] [Accepted: 09/02/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Small abdominal aortic aneurysms (AAAs) are asymptomatic but can potentially lead to rupture if left undetected. To date, there is a lack of simple nonradiologic routine tests available for diagnosing AAAs. MicroRNAs (miRNAs) have been proven to be good-quality biomarkers in several diseases, including AAA. METHODS An attempt to identify a panel of circulating miRNAs with differential expression in AAAs via next-generation sequencing (NGS) was performed in serum samples: small AAAs (n = 3), large AAAs (n = 3), and controls (n = 3). For miR-24, validation with real-time polymerase chain reaction (PCR) was undertaken in a larger group (n = 80). RESULTS In the NGS study, 23 miRNAs were identified as differentially expressed (with statistical significance) in small AAAs in comparison with controls. Among them, miR-24 showed the largest upregulation with 23-fold change (log2FC 4.5, P = 0.024). For large AAAs compared with controls, and small AAAs compared with large AAAs, a panel of 33 and 131 miRNAs showed statistically significant differential expression, respectively. Based on the results of the NGS stage, a literature search was performed, and information regarding AAA pathogenesis, coronary artery disease, and peripheral arterial disease was documented where applicable: miR-24, miR-103, miR-193a, miR-486, miR-582, and miR-3663. Of these 6 miRNAs, miR-24 was chosen for further validation with real-time PCR. Additionally, in the NGS study analysis, 17 miRNAs were common between the small-large AAAs, small AAAs-controls, and large AAAs-controls comparisons: miR-7846, miR-3195, miR-486-2, miR-3194, miR-5589, miR-1538, miR-3178, miR-4771-1, miR-5695, miR-6504, miR-1908, miR-6823, miR-3159, miR-23a, miR-7853, miR-496, and miR-193a. Interestingly, in the validation stage with real-time PCR, miR-24 was found downregulated in small and large AAAs compared with controls (fold-changes: 0.27, P = 0.015 and 0.15, P = 0.005, respectively). No correlation was found between average Ct values, aneurysm diameter, and patients' age. CONCLUSIONS Our findings further highlight the importance of miR-24 as a potential biomarker as well as a therapeutic target for abdominal aneurysmal disease. Future research and validation of a panel of miRNAs for AAA would aid in diagnosis and discrimination between diseases with overlapping pathogeneses.
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Affiliation(s)
- Kalliopi-Maria Tasopoulou
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Argyriou
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Bampali
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alexandra K Tsaroucha
- Department of Experimental Surgery, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eleni Christaina
- Department of Biostatistics, Democritus University of Thrace, Alexandroupolis, Greece
| | - George S Georgiadis
- Department of Vascular Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
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19
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Hu T, Li K, He L, Huang F, Yang F, Chen S, Wang H, Ma D, Huang X, Wu P. Testing for viral DNA integration among HPV-positive women to detect cervical precancer: An observational cohort study. BJOG 2024; 131:309-318. [PMID: 37408516 DOI: 10.1111/1471-0528.17597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
OBJECTIVE Human papillomavirus (HPV) integration is a crucial genetic step in cervical carcinogenesis. This study aimed to evaluate the performance of an HPV integration test for the triage of HPV-positive women. DESIGN An observational cohort study. SETTING A cervical cancer screening programme in China. POPULATION 1393 HPV-positive women aged 25-65 years undergoing routine cervical cancer screening and HPV integration testing with 1-year follow-up. METHODS The sensitivity, specificity, positive predictive value and negative predictive value between HPV integration and cytology were compared. MAIN OUTCOME MEASURES Cervical intraepithelial neoplasia grade 3 or more severe (CIN3+). RESULTS Among 1393 HPV-positive patients, 138 (9.9% [8.3-11.5%]) were HPV integration test positive compared with 537 who had abnormal cervical cytology (38.5% [36.0-41.1%]). Compared with cytology, HPV integration exhibited higher specificity (94.5% [93.3-95.8%] versus 63.8% [61.2-66.4%]) and equivalent sensitivity (70.5% [61.4-79.7%] versus 70.5% [61.4-79.7%]) for detection of CIN3+. HPV integration-negative women accounted for 90.1% (1255/1393) of the total population and had a low immediate CIN3+ risk (2.2%). At 1-year follow-up, the progression rate in the HPV integration-positive women was higher than in the HPV integration-negative women (12.0% versus 2.1%, odds ratio 5.6, 95% CI, 2.6-11.9). In 10 conservatively managed integration-negative CIN2 patients, all showed spontaneous regression and seven showed HPV clearance after 1-year follow-up. CONCLUSION The HPV integration test may be a precise risk stratification tool for HPV-positive women and could avoid excessive use of invasive biopsies.
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Affiliation(s)
- Ting Hu
- Department of Gynaecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kexin Li
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang He
- Department of Gynaecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fanwei Huang
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Yang
- Wuhan KDWS Biological Technology Co., Ltd, New Technology Platform, Wuhan, China
| | - Shimin Chen
- Wuhan KDWS Biological Technology Co., Ltd, New Technology Platform, Wuhan, China
| | - Hui Wang
- Department of Gynaecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Ding Ma
- Department of Gynaecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyuan Huang
- Department of Gynaecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Wu
- National Clinical Research Centre for Obstetrics and Gynaecology, Cancer Biology Research Centre (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Gynaecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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20
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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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Kouniaki DI, Fotopoulos KV, Tarassi K, Tsirogianni A. Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing. Genes (Basel) 2024; 15:150. [PMID: 38397140 PMCID: PMC10888046 DOI: 10.3390/genes15020150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/13/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.
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Affiliation(s)
- Diamanto I. Kouniaki
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
| | - Konstantinos V. Fotopoulos
- School of Electrical and Computer Engineering, National Technical University of Athens (ECE-NTUA), 15772 Zografou, Greece;
| | - Katerina Tarassi
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
| | - Alexandra Tsirogianni
- Immunology and Histocompatibility Department, Evangelismos General Hospital, 10676 Athens, Greece; (D.I.K.); (K.T.)
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22
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Park JW, Bae SJ, Yun JH, Kim S, Park M. Assessment of Genetic Stability in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Using Droplet Digital PCR. Int J Mol Sci 2024; 25:1101. [PMID: 38256178 PMCID: PMC10815998 DOI: 10.3390/ijms25021101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Unintended genetic modifications that occur during the differentiation and proliferation of human induced pluripotent stem cells (hiPSCs) can lead to tumorigenicity. This is a crucial concern in the development of stem cell-based therapies to ensure the safety and efficacy of the final product. Moreover, conventional genetic stability testing methods are limited by low sensitivity, which is an issue that remains unsolved. In this study, we assessed the genetic stability of hiPSCs and hiPSC-derived cardiomyocytes using various testing methods, including karyotyping, CytoScanHD chip analysis, whole-exome sequencing, and targeted sequencing. Two specific genetic mutations in KMT2C and BCOR were selected from the 17 gene variants identified by whole-exome and targeted sequencing methods, which were validated using droplet digital PCR. The applicability of this approach to stem cell-based therapeutic products was further demonstrated with associated validation according to the International Council for Harmonisation (ICH) guidelines, including specificity, precision, robustness, and limit of detection. Our droplet digital PCR results showed high sensitivity and accuracy for quantitatively detecting gene mutations, whereas conventional qPCR could not avoid false positives. In conclusion, droplet digital PCR is a highly sensitive and precise method for assessing the expression of mutations with tumorigenic potential for the development of stem cell-based therapeutics.
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Affiliation(s)
| | | | | | | | - Misun Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (J.W.P.); (S.J.B.); (J.H.Y.); (S.K.)
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23
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Nuñez-Borque E, Palacio-Garcia L, Fernández-Bravo S, Esteban V. Study of MicroRNAs Expression in Food Allergy. Methods Mol Biol 2024; 2717:337-350. [PMID: 37737996 DOI: 10.1007/978-1-0716-3453-0_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Food allergy is a current worldwide problem. Consequently, it is necessary to identify the different molecules that modulate these reactions and that can be used as potential biomarkers. In recent years there has been increasing interest in the field of allergy on microRNAs (miRNAs). These molecules regulate a wide variety of physiological processes and have been proposed as promising candidate biomarkers.Currently, next-generation sequencing (NGS) has allowed to determine the profile of all miRNAs from different samples. In addition, there are several methods to extract RNA and miRNAs, from different sources such as serum, extracellular vesicles (EVs), and/or cell extracts. Following extraction, a retrotranscription step must be carried out before miRNA levels can be quantified by quantitative polymerase chain reaction (qPCR).This chapter aimed to describe the discovery techniques used to determine the differential profile of miRNAs from different types of samples, as well as the diverse methods employed to extract these molecules and quantify specific changes in their levels by qPCR.
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Affiliation(s)
- Emilio Nuñez-Borque
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Lucía Palacio-Garcia
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sergio Fernández-Bravo
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain.
- Faculty of Medicine and Biomedicine, Alfonso X El Sabio University, Madrid, Spain.
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24
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Kim JA, Jang M, Jang SY, Kim D, Kim Y, Kim J, Park TK, Jang J. Overcoming challenges associated with identifying FBN1 deep intronic variants through whole-genome sequencing. J Clin Lab Anal 2024; 38:e25009. [PMID: 38234087 PMCID: PMC10829686 DOI: 10.1002/jcla.25009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Marfan syndrome (MFS), caused by pathogenic variants of FBN1 (fibrillin-1), is a systemic connective tissue disorder with variable phenotypes and treatment responsiveness depending on the variant. However, a significant number of individuals with MFS remain genetically unexplained. In this study, we report novel pathogenic intronic variants in FBN1 in two unrelated families with MFS. METHODS We evaluated subjects with suspected MFS from two unrelated families using Sanger sequencing or multiplex ligation-dependent probe amplification of FBN1 and/or panel-based next-generation sequencing. As no pathogenic variants were identified, whole-genome sequencing was performed. Identified variants were analyzed by reverse transcription-PCR and targeted sequencing of FBN1 mRNA harvested from peripheral blood or skin fibroblasts obtained from affected probands. RESULTS We found causative deep intronic variants, c.6163+1484A>T and c.5788+36C>A, in FBN1. The splicing analysis revealed an insertion of in-frame or out-of-frame intronic sequences of the FBN1 transcript predicted to alter function of calcium-binding epidermal growth factor protein domain. Family members carrying c.6163+1484A>T had high systemic scores including prominent skeletal features and aortic dissection with lesser aortic dilatation. Family members carrying c.5788+36C>A had more severe aortic root dilatation without aortic dissection. Both families had ectopia lentis. CONCLUSION Variable penetrance of the phenotype and negative genetic testing in MFS families should raise the possibility of deep intronic FBN1 variants and the need for additional molecular studies. This study expands the mutation spectrum of FBN1 and points out the importance of intronic sequence analysis and the need for integrative functional studies in MFS diagnosis.
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Affiliation(s)
- Jee Ah Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Mi‐Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Shin Yi Jang
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Duk‐Kyung Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
- Division of Cardiology, Department of Medicine, Samsung Changwon HospitalSungkyunkwan University School of MedicineChangwon‐siKorea
| | - Young‐gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Jong‐Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Taek Kyu Park
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
| | - Ja‐Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical CenterSungkyunkwan University School of MedicineSeoulKorea
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25
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Li C, Fan S, Zhao H, Liu X. CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data. J Bioinform Comput Biol 2023; 21:2350026. [PMID: 38212874 DOI: 10.1142/s0219720023500269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Copy number variation (CNV), as a type of genomic structural variation, accounts for a large proportion of structural variation and is related to the pathogenesis and susceptibility to some human diseases, playing an important role in the development and change of human diseases. The development of next-generation sequencing technology (NGS) provides strong support for the design of CNV detection algorithms. Although a large number of methods have been developed to detect CNVs using NGS data, it is still considered a difficult problem to detect CNVs with low purity and coverage. In this paper, a new calculation method CNV-FB is proposed to detect CNVs from NGS data. The core idea of CNV-FB is to randomly sample the read depth values of the genome fragment, and then each sample is individually detected for outliers, and finally combined into a final outlier score. The CNV-FB method was applied to simulation data and real data experiments and compared with the other five methods of the same type. The results show that the CNV-FB method has a better detection effect than other methods. Therefore, the CNV-FB method may be an effective algorithm for detecting genomic mutations.
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Affiliation(s)
- Chengyou Li
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Shiqiang Fan
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Haiyong Zhao
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Xiaotong Liu
- School of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, P. R. China
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26
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Wang X, Li R, Qian S, Yu D. Multilevel omics for the discovery of biomarkers in pediatric sepsis. Pediatr Investig 2023; 7:277-289. [PMID: 38050541 PMCID: PMC10693667 DOI: 10.1002/ped4.12405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/27/2023] [Indexed: 12/06/2023] Open
Abstract
Severe sepsis causes organ dysfunction and continues to be the leading reason for pediatric death worldwide. Early recognition of sepsis could substantially promote precision treatment and reduce the risk of pediatric death. The host cellular response to infection during sepsis between adults and pediatrics could be significantly different. A growing body of studies focused on finding markers in pediatric sepsis in recent years using multi-omics approaches. This narrative review summarized the progress in studying pediatric sepsis biomarkers from genome, transcript, protein, and metabolite levels according to the omics technique that has been applied for biomarker screening. It is most likely not a single biomarker could work for precision diagnosis of sepsis, but a panel of markers and probably a combination of markers detected at multi-levels. Importantly, we emphasize the importance of group distinction of infectious agents in sepsis patients for biomarker identification, because the host response to infection of bacteria, virus, or fungus could be substantially different and thus the results of biomarker screening. Further studies on the investigation of sepsis biomarkers that were caused by a specific group of infectious agents should be encouraged in the future, which will better improve the clinical execution of personalized medicine for pediatric sepsis.
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Affiliation(s)
- Xinyu Wang
- Laboratory of DermatologyBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityKey Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's HealthBeijingChina
| | - Rubo Li
- Department of Pediatric Intensive Care UnitBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Suyun Qian
- Department of Pediatric Intensive Care UnitBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Dan Yu
- Laboratory of DermatologyBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityKey Laboratory of Major Diseases in Children, Ministry of Education, National Center for Children's HealthBeijingChina
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27
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Yang T, Li W, Huang T, Zhou J. Genetic Testing Enhances the Precision Diagnosis and Treatment of Breast Cancer. Int J Mol Sci 2023; 24:16607. [PMID: 38068930 PMCID: PMC10706486 DOI: 10.3390/ijms242316607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The contemporary comprehension of breast cancer has progressed to the molecular level. As a heterogeneous malignancy, conventional pathological diagnosis and histological classification could no longer meet the needs of precisely managing breast cancer. Genetic testing based on gene expression profiles and gene mutations has emerged and substantially contributed to the precise diagnosis and treatment of breast cancer. Multigene assays (MGAs) are explored for early-stage breast cancer patients, aiding the selection of adjuvant therapy and predicting prognosis. For metastatic breast cancer patients, testing specific genes indicates potentially effective antitumor agents. In this review, genetic testing in early-stage and metastatic breast cancer is summarized, as well as the advantages and challenges of genetic testing in breast cancer.
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Affiliation(s)
| | | | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China (W.L.)
| | - Jun Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China (W.L.)
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Ding W, Huang L, Wu Y, Su J, He L, Tang Z, Zhang M. The role of pyroptosis-related genes in the diagnosis and subclassification of sepsis. PLoS One 2023; 18:e0293537. [PMID: 37939116 PMCID: PMC10631697 DOI: 10.1371/journal.pone.0293537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
Pyroptosis is a new form of programmed cell death recognized as crucial in developing sepsis. However, there is limited research on the mechanism of pyroptosis-related genes in sepsis-related from the Gene Expression Omnibus (GEO) database and standardized. The expression levels of pyroptosis-related genes were extracted, and differential expression analysis was conducted. A prediction model was constructed using random forest (RF), support vector machine (SVM), weighted gene co-expression new analysis (WGCNA), and nomogram techniques to assess the risk of sepsis. The relationship between pyroptosis-related subgroups and the immune microenvironment and inflammatory factors was studied using consistent clustering algorithms, principal component analysis (PCA), single-sample genomic enrichment analysis (ssGSEA), and immune infiltration. A risk prediction model based on 3 PRGs has been constructed and can effectively predict the risk of sepsis. Patients with sepsis can be divided into two completely different subtypes of pyroptosis-related clusters. Cluster B is highly correlated with the lower proportion of Th17 celld and has lower levels of expression of inflammatory factors. This study utilizes mechanical learning methods to further investigate the pathogenesis of sepsis, explore potential biomarkers, provide effective molecular targets for its diagnosis and treatment of sepsis.
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Affiliation(s)
- Wencong Ding
- Department of Nephrology, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Laping Huang
- Intensive Care Unit, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Yifeng Wu
- Intensive Care Unit, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Junwei Su
- Intensive Care Unit, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Liu He
- Intensive Care Unit, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Zhongxiang Tang
- Intensive Care Unit, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
| | - Min Zhang
- Department of Nephrology, Affiliated Guangdong Hospital of Integrated Traditional Chinese and Western Medicine of Guangzhou University of Chinese Medicine, Foshan, 528000, Guangdong, China
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Das T, Joseph J, Simunovic MP, Grzybowski A, Chen KJ, Dave VP, Sharma S, Staropoli P, Flynn H. Consensus and controversies in the science of endophthalmitis management: Basic research and clinical perspectives. Prog Retin Eye Res 2023; 97:101218. [PMID: 37838286 DOI: 10.1016/j.preteyeres.2023.101218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
Infectious endophthalmitis is a severe intraocular infection caused by bacteria, or less commonly by fungi. It can occur after penetrating eye procedures, trauma, or the spread of infection from contiguous structures or via emboli from distant organs. Because of the time-critical nature of the treatment, endophthalmitis is treated with the clinical diagnosis and modified by the microbiological report of the intraocular contents. The current strategy for managing endophthalmitis relies on pre-clinical literature, case series, and one large multi-center randomized clinical trial on post-cataract surgery endophthalmitis. Culture-susceptibility of the microorganisms from undiluted vitreous guides the definitive treatment in non-responsive cases. Strategies to reduce the incidence of endophthalmitis after penetrating eye procedures have been developed concurrently with refined means of treatment. Despite these advances, outcomes remain poor for many patients. Although consensus articles have been published on managing endophthalmitis, treatment patterns vary, and controversies remain. These include (1) the use of newer methods for early and precise microbiological diagnosis; (2) the choice of intravitreal antibiotics; (3) the need for systemic therapy; (4) early and complete vitrectomy. Here, we review the current consensus and address controversies in diagnosing and managing endophthalmitis. This review is intended to familiarize physicians and ophthalmologists with different aspects of endophthalmitis management to make informed decisions.
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Affiliation(s)
- Taraprasad Das
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V, Prasad Eye Institute, Hyderabad, India.
| | - Joveeta Joseph
- Jhaveri Microbiology Center, L V Prasad Eye Institute, Hyderabad, India.
| | - Matthew P Simunovic
- Save Sight Institute, University of Sydney, NSW, 2006, Australia; Sydney Eye Hospital, 8 Macquarie St., Sydney, NSW, 2000, Australia.
| | - Andrzej Grzybowski
- Institute for Research in Ophthalmology, Foundation for Ophthalmology Development, Poznan, Poland.
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Vivek Pravin Dave
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V Prasad Eye Institute, Hyderabad, India.
| | - Savitri Sharma
- Jhaveri Microbiology Center, L V Prasad Eye Institute, Hyderabad, India.
| | - Patrick Staropoli
- Anant Bajaj Retina Institute, Srimati Kanuri Santhamma Centre for Vitreoretinal Disease, L V Prasad Eye Institute, Hyderabad, India.
| | - Harry Flynn
- Bascom Palmer Eye Institute, Miami, FL, USA.
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Nuñez-Borque E, Fernandez-Bravo S, Rodríguez Del Rio P, Palacio-García L, Di Giannatale A, Di Paolo V, Galardi A, Colletti M, Pascucci L, Tome-Amat J, Cuesta-Herranz J, Ibañez-Sandin MD, Laguna JJ, Benito-Martin A, Esteban V. Novel mediator in anaphylaxis: decreased levels of miR-375-3p in serum and within extracellular vesicles of patients. Front Immunol 2023; 14:1209874. [PMID: 37965316 PMCID: PMC10642912 DOI: 10.3389/fimmu.2023.1209874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction Anaphylaxis is among the most severe manifestations of allergic disorders, but its molecular basis remains largely unknown and reliable diagnostic markers are not currently available. MicroRNAs (miRNAs) regulate several pathophysiological processes and have been proposed as non-invasive biomarkers. Therefore, this study aims to evaluate their involvement in anaphylactic reaction and their value as biomarkers. Methods Acute (anaphylaxis) and baseline (control) serum samples from 67 patients with anaphylaxis were studied. Among them, 35 were adults with drug-induced anaphylaxis, 13 adults with food-induced anaphylaxis and 19 children with food-induced anaphylaxis. The circulating serum miRNAs profile was characterized by next-generation sequencing (NGS). For this purpose, acute and baseline samples from 5 adults with drug-induced anaphylaxis were used. RNA was extracted, retrotranscribed, sequenced and the readings obtained were mapped to the human database miRBase_20. In addition, a system biology analysis (SBA) was performed with its target genes and revealed pathways related to anaphylactic mediators signaling. Moreover, functional and molecular endothelial permeability assays were conducted with miR-375-3p-transfected cells in response to cAMP. Results A total of 334 miRNAs were identified, of which 21 were significant differentially expressed between both phases. Extracellular vesicles (EVs) were characterized by Western blot, electron microscopy and NanoSight. A decrease of miR-375-3p levels was determined by qPCR in both serum and EVs of patients with anaphylaxis (****p<.0001). Precisely, the decrease of miR-375-3p correlated with the increase of two inflammatory cytokines: monocyte chemoattractant protein-1 (MCP-1) and granulocyte macrophage colony-stimulating factor (GM-CSF). On the other hand, functional and molecular data obtained showed that miR-375-3p partially blocked the endothelial barrier maintenance and stabilization by disassembly of cell-cell junctions exhibiting low Rac1-Cdc42 levels. Discussion These findings demonstrate a differential serum profile of circulating miRNAs in patients with anaphylaxis and exhibit the miR-375-3p modulation in serum and EVs during drug- and food-mediated anaphylactic reactions. Furthermore, the in silico and in vitro studies show a negative role for miR-375-3p/Rac1-Cdc42 in the endothelial barrier stability.
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Affiliation(s)
- Emilio Nuñez-Borque
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Sergio Fernandez-Bravo
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Pablo Rodríguez Del Rio
- Allergy Department, Hospital Infantil Universitario Niño Jesús, Fundación Hospital Niño Jesús (HNJ), Instituto de Investigación del Hospital de La Princesa (IIS-P), Madrid, Spain
| | - Lucia Palacio-García
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Angela Di Giannatale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Virginia Di Paolo
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Angela Galardi
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Marta Colletti
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Jaime Tome-Amat
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA), Universidad Politécnica de Madrid, Madrid, Spain
| | - Javier Cuesta-Herranz
- Department of Allergy. Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Dolores Ibañez-Sandin
- Allergy Department, Hospital Infantil Universitario Niño Jesús, Fundación Hospital Niño Jesús (HNJ), Instituto de Investigación del Hospital de La Princesa (IIS-P), Madrid, Spain
| | - José Julio Laguna
- Allergy Unit, Allergo-Anaesthesia Unit, Cruz Roja Central Hospital, Villanueva de la Cañada, Madrid, Spain
- Faculty of Medicine and Biomedicine, Universidad Alfonso X el Sabio (UAX), Madrid, Spain
| | - Alberto Benito-Martin
- Faculty of Medicine and Biomedicine, Universidad Alfonso X el Sabio (UAX), Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Faculty of Medicine and Biomedicine, Universidad Alfonso X el Sabio (UAX), Madrid, Spain
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Majidian S, Agustinho DP, Chin CS, Sedlazeck FJ, Mahmoud M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol 2023; 24:221. [PMID: 37798733 PMCID: PMC10552390 DOI: 10.1186/s13059-023-03061-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.
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Affiliation(s)
- Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | | | | | - Fritz J Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, 77030, USA.
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
| | - Medhat Mahmoud
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Liu C, Li K, Sui Y, Liu H, Zhang Y, Lu Y, Lu W, Chen Y, Wang G, Xu S, Xiang T, Cai Y, Huang K. Different gene alterations in patients with non-small-cell lung cancer between the eastern and southern China. Heliyon 2023; 9:e20171. [PMID: 37767514 PMCID: PMC10520317 DOI: 10.1016/j.heliyon.2023.e20171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Geographical differences are conspicuous in lung cancer, and the distinct molecular features of lung tumor between Western patients and Asian patients have been demonstrated. However, the etiology of non-small-cell lung cancer (NSCLC) and the distribution of associated molecular aberrations in China have not been fully elucidated. The mutational profiles of 12 lung cancer-related genes were investigated in 85 patients from eastern China and 88 patients from southern China who had been histologically confirmed NSCLC. Overall, 93.6% (162/173) of tumor samples harbored at least one somatic alteration. The most frequently mutated genes were TP53 (56.1%), EGFR (50.3%), and KRAS (14.5%). We found that EGFR mutated much more frequently (60.0% vs 40.9%, P = 0.012) and TP53 mutations had significantly lower incidence (47.1% vs 64.8%, P = 0.019) in eastern cohort than that in southern cohort. Mutational signature analysis revealed a region-related mutagenesis mechanism characterized by a high prevalence of C to T transitions mainly occurring at CpG dinucleotides in southern patients. This study reveals the difference in the mutational features between NSCLC patients in eastern and southern China. The distinct patterns of gene mutation could provide clues for the mechanism of carcinogenesis of lung cancer, offering opportunities to stratify patients into optimal treatment plans based on genomic profiles.
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Affiliation(s)
- Chengdong Liu
- Department of thoracic surgery, Naval Medical Center of PLA, 338 Huaihai Road, Changning District, Shanghai 200052, China
| | - Kangbao Li
- Department of Geriatrics, Gastroenterology Ward, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Yi Sui
- Singlera Genomics Inc., Shanghai 201318, China
| | - Hongmei Liu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yuan Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Wei Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Yongfeng Chen
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Gehui Wang
- Singlera Genomics Inc., Shanghai 201318, China
| | - Suqian Xu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yongguang Cai
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Kenan Huang
- Department of Thoracic Surgery, Shanghai Changzheng Hospital, Navy Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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Kim YG, Park J, Park EY, Kim SM, Lee SY. Analysis of MicroRNA Signature Differentially Expressed in Pancreatic Islet Cells Treated with Pancreatic Cancer-Derived Exosomes. Int J Mol Sci 2023; 24:14301. [PMID: 37762604 PMCID: PMC10532014 DOI: 10.3390/ijms241814301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Since the majority of patients with pancreatic cancer (PC) develop insulin resistance and/or diabetes mellitus (DM) prior to PC diagnosis, PC-induced diabetes mellitus (PC-DM) has been a focus for a potential platform for PC detection. In previous studies, the PC-derived exosomes were shown to contain the mediators of PC-DM. In the present study, the response of normal pancreatic islet cells to the PC-derived exosomes was investigated to determine the potential biomarkers for PC-DM, and consequently, for PC. Specifically, changes in microRNA (miRNA) expression were evaluated. The miRNA specimens were prepared from the untreated islet cells as well as the islet cells treated with the PC-derived exosomes (from 50 patients) and the healthy-derived exosomes (from 50 individuals). The specimens were subjected to next-generation sequencing and bioinformatic analysis to determine the differentially expressed miRNAs (DEmiRNAs) only in the specimens treated with the PC-derived exosomes. Consequently, 24 candidate miRNA markers, including IRS1-modulating miRNAs such as hsa-miR-144-5p, hsa-miR-3148, and hsa-miR-3133, were proposed. The proposed miRNAs showed relevance to DM and/or insulin resistance in a literature review and pathway analysis, indicating a potential association with PC-DM. Due to the novel approach used in this study, additional evidence from future studies could corroborate the value of the miRNA markers discovered.
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Affiliation(s)
- Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (Y.-g.K.); (S.-M.K.)
| | - Jisook Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; (J.P.); (E.Y.P.)
| | - Eun Young Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul 06351, Republic of Korea; (J.P.); (E.Y.P.)
| | - Sang-Mi Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (Y.-g.K.); (S.-M.K.)
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea; (Y.-g.K.); (S.-M.K.)
- Department of Clinical Pharmacology and Therapeutics, Samsung Medical Center, Seoul 06351, Republic of Korea
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Bukłaho PA, Kiśluk J, Nikliński J. Diagnostics and treatment of ovarian cancer in the era of precision medicine - opportunities and challenges. Front Oncol 2023; 13:1227657. [PMID: 37746296 PMCID: PMC10516548 DOI: 10.3389/fonc.2023.1227657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Due to predictions of increasing incidences and deaths from ovarian cancer, this neoplasm is a challenge for modern health care. The advent of NGS technology has made it possible to understand the molecular characteristics of many cancers, including ovarian cancer. The data obtained in research became the basis for the development of molecularly targeted therapies thus leading to the entry of NGS analysis into the diagnostic process of oncological patients. This review presents targeted therapies currently in preclinical or clinical trials, whose promising results offer hope for their use in clinical practice in the future. As more therapeutic options emerge, it will be necessary to modify molecular diagnostic regimens to select the best treatment for a given patient. New biomarkers are needed to predict the success of planned therapy. An important aspect of public health is molecular testing in women with a familial predisposition to ovarian cancer enabling patients to be included in prevention programs. NGS technology, despite its high throughput, poses many challenges, from the quality of the diagnostic material used for testing to the interpretation of results and classification of sequence variants. The article highlights the role of molecular testing in ongoing research and also its role in the diagnostic and therapeutic process in the era of personalized medicine. The spread of genetic testing in high-risk groups, the introduction of more targeted therapies and also the possibility of agnostic therapies could significantly improve the health situation for many women worldwide.
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Affiliation(s)
- Patrycja Aleksandra Bukłaho
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
- Doctoral School, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Zhang Y, Jiang X, Ye W, Sun J. Clinical features and outcome of eight patients with Chlamydia psittaci pneumonia diagnosed by targeted next generation sequencing. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:915-930. [PMID: 37552996 PMCID: PMC10500319 DOI: 10.1111/crj.13681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/29/2023] [Accepted: 07/23/2023] [Indexed: 08/10/2023]
Abstract
INTRODUCTION The clinical symptoms of Chlamydia psittaci pneumonia are still poorly understood. This study was designed to summarize the clinical features and outcome of eight C. psittaci pneumonia patients diagnosed by targeted next generation sequencing (tNGS). METHODS We included eight C. psittaci pneumonia patients admitted to our hospital from January 2021 to July 2022. The tNGS was performed to the samples collected from bronchoalveolar lavage fluid of each patient. Their clinical data were analysed, including baseline features, clinical symptoms, chest radiographic findings and laboratory examinations. RESULTS The tNGS sequence number for C. psittaci was in a range of 10 to 1722. The radiographic characteristics were mainly featured by patchy consolidation shadows, ground-glass density shadows, air bronchogram and slight pleural effusion. Within 1-3 days after hospitalization, most patients showed increased neutrophil ratio, C-reactive protein and erythrocyte sedimentation rate, and decreased lymphocyte count, total protein, albumin and prealbumin. Some patients showed increased glutamic-pyruvic transaminase, glutamic-oxaloacetic transaminase and lactate dehydrogenase levels. Three critically ill patients showed increased creatine kinase, creatine kinase isoenzyme and high-sensitivity troponin T (hs-TnT) levels. CONCLUSIONS A poultry or bird contact history, typical flu-like symptoms, patchy consolidation, ground-glass density shadow and air bronchogram may contribute to the diagnosis and treatment of C. psittaci pneumonia. Increase in creatine kinase, creatine kinase isoenzyme and hs-TnT may indicate a severe condition. Moxifloxacin and minocycline were effective in the management of C. psittaci pneumonia.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory MedicineShandong Provincial Third HospitalJinanP.R. China
| | - Xiangsen Jiang
- Imaging CenterShandong Provincial Third HospitalJinanP.R. China
| | - Wei Ye
- Department of Respiratory MedicineShandong Provincial Third HospitalJinanP.R. China
| | - Jinlin Sun
- Department of Respiratory MedicineShandong Provincial Third HospitalJinanP.R. China
- Department of Respiratory MedicineHui Ya Hospital of The First Affiliated Hospital, Sun Yat‐Sen UniversityHuizhouP.R. China
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Cooper RM, Wright JA, Ng JQ, Goyne JM, Suzuki N, Lee YK, Ichinose M, Radford G, Ryan FJ, Kumar S, Thomas EM, Vrbanac L, Knight R, Woods SL, Worthley DL, Hasty J. Engineered bacteria detect tumor DNA. Science 2023; 381:682-686. [PMID: 37561843 PMCID: PMC10852993 DOI: 10.1126/science.adf3974] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Synthetic biology has developed sophisticated cellular biosensors to detect and respond to human disease. However, biosensors have not yet been engineered to detect specific extracellular DNA sequences and mutations. Here, we engineered naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids, and tumors. We characterized the functionality of the biosensors in vitro with coculture assays and then validated them in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observed horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. This cellular assay for targeted, CRISPR-discriminated horizontal gene transfer (CATCH) enables the biodetection of specific cell-free DNA.
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Affiliation(s)
- Robert M. Cooper
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA, 92093
| | - Josephine A. Wright
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
| | - Jia Q. Ng
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Jarrad M. Goyne
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
| | - Nobumi Suzuki
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Young K. Lee
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Mari Ichinose
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Georgette Radford
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Feargal J. Ryan
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia, 5042
| | - Shalni Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093
| | - Elaine M. Thomas
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Laura Vrbanac
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Rob Knight
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA, 92093
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, 92093
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093
| | - Susan L. Woods
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia, 5000
| | - Daniel L. Worthley
- Precision Cancer Medicine Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia, 5000
- Colonoscopy Clinic, Brisbane, QLD, Australia, 4000
| | - Jeff Hasty
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA, 92093
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA, 92093
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92093
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Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
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Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
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Lubin IM, Astles JR, Bunn JD, Cornish NE, Lazaro G, Marshall AA, Stang HL, De Jesús VR. The Clinical Laboratory Is an Integral Component to Health Care Delivery : An Expanded Representation of the Total Testing Process. Am J Clin Pathol 2023; 160:124-129. [PMID: 37105541 DOI: 10.1093/ajcp/aqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVES Developing an expanded representation of the total testing process that includes contemporary elements of laboratory practice can be useful to understanding and optimizing testing workflows across clinical laboratory and patient care settings. METHODS Published literature and meeting reports were used by the coauthors to inform the development of the expanded representation of the total testing process and relevant examples describing its uses. RESULTS A visual representation of the total testing process was developed and contextualized to patient care scenarios using a number of examples covering the detection of blood culture contamination, use of next-generation sequencing, and pharmacogenetic testing. CONCLUSIONS The expanded representation of the total testing process can serve as a model and framework to document and improve the use of clinical testing within the broader context of health care delivery. This representation recognizes increased engagement among clinical laboratory professionals with patients and other health care providers as essential to making informed decisions. The increasing use of data is highlighted as important to ensuring quality, appropriate test utilization, and sustaining an efficient workflow across clinical laboratory and patient care settings. Maintaining a properly resourced and competent workforce is also featured as an essential component to the testing process.
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Affiliation(s)
- Ira M Lubin
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - J Rex Astles
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Jake D Bunn
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Nancy E Cornish
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Gerardo Lazaro
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Ashley A Marshall
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Heather L Stang
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
| | - Victor R De Jesús
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, US
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Murugesan S, Al Khodor S. Salivary microbiome and hypertension in the Qatari population. J Transl Med 2023; 21:454. [PMID: 37422685 PMCID: PMC10329805 DOI: 10.1186/s12967-023-04247-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND The prevalence of hypertension in Qatar is 33 percent of the adult population. It is postulated that the salivary microbiome can regulate blood pressure (BP). However, limited investigations exist to prove this hypothesis. Therefore, we examined the difference in the salivary microbiome composition between hypertensive and normotensive Qatari subjects. METHODS A total of 1190 Qatar Genome Project (QGP) participants (Mean age = 43 years) were included in this study. BP for all participants was classified into Normal (n = 357), Stage1 (n = 336), and Stage2: (n = 161) according to the American Heart Association guidelines. 16S-rRNA libraries were sequenced and analyzed using QIIME-pipeline, and PICRUST was used to predict functional metabolic routes. Machine Learning (ML) strategies were applied to identify salivary microbiome-based predictors of hypertension. RESULTS Differential abundant analysis (DAA) revealed that Bacteroides and Atopobium were the significant members of the hypertensive groups. Alpha and beta diversity indices indicated dysbiosis between the normotensive and hypertensive groups. ML-based prediction models revealed that these markers could predict hypertension with an AUC (Area under the curve) of 0.89. Functional predictive analysis disclosed that Cysteine and Methionine metabolism and the sulphur metabolic pathways involving the renin-angiotensin system were significantly higher in the normotensive group. Therefore, members of Bacteroides and Atopobium can serve as predictors of hypertension. Likewise, Prevotella, Neisseria, and Haemophilus can be the protectors that regulate BP via nitric acid synthesis and regulation of the renin-angiotensin system. CONCLUSION It is one of the first studies to assess salivary microbiome and hypertension as disease models in a large cohort of the Qatari population. Further research is needed to confirm these findings and validate the mechanisms involved.
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Affiliation(s)
- Selvasankar Murugesan
- Maternal and Child Health Division, Research Department, Sidra Medicine, 26999, Doha, Qatar
| | - Souhaila Al Khodor
- Maternal and Child Health Division, Research Department, Sidra Medicine, 26999, Doha, Qatar.
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Kim SY, Huh HJ. Measurable Residual Disease Testing Using Next-Generation Sequencing in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:323-324. [PMID: 36843399 PMCID: PMC9989539 DOI: 10.3343/alm.2023.43.4.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Affiliation(s)
- Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Hee Jin Huh
- Department of Laboratory Medicine, Dongguk University Ilsan Hospital, Goyang, Korea
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Kerkhof J, Rastin C, Schenkel L, Lin H, Sadikovic B. Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants. Expert Rev Mol Diagn 2023; 23:827-841. [PMID: 37542410 DOI: 10.1080/14737159.2023.2245747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants. METHODS A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues. RESULTS High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system. CONCLUSION Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.
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Affiliation(s)
- Jennifer Kerkhof
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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42
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Kim JJ, Jang JE, Lee HA, Park MR, Kook HW, Lee ST, Choi JR, Min YH, Shin S, Cheong JW. Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:328-336. [PMID: 36843401 PMCID: PMC9989530 DOI: 10.3343/alm.2023.43.4.328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/04/2022] [Accepted: 01/27/2023] [Indexed: 02/28/2023] Open
Abstract
Background AML is a heterogeneous disease, and despite intensive therapy, recurrence is still high in AML patients who achieve the criterion for cytomorphologic remission (residual tumor burden [measurable residual disease, MRD]<5%). This study aimed to develop a targeted next-generation sequencing (NGS) panel to detect MRD in AML patients and validate its performance. Methods We designed an error-corrected, targeted MRD-NGS panel without using physical molecular barcodes, including 24 genes. Fifty-four bone marrow and peripheral blood samples from 23 AML patients were sequenced using the panel. The panel design was validated using reference material, and accuracy was assessed using droplet digital PCR. Results Dilution tests showed excellent linearity and a strong correlation between expected and observed clonal frequencies (R>0.99). The test reproducibly detected MRD in three dilution series samples, with a sensitivity of 0.25% for single-nucleotide variants. More than half of samples from patients with morphologic remission after one month of chemotherapy had detectable mutations. NGS-MRD positivity for samples collected after one month of chemotherapy tended to be associated with poor overall survival and progression-free survival. Conclusions Our highly sensitive and accurate NGS-MRD panel can be readily used to monitor most AML patients in clinical practice, including patients without gene rearrangement. In addition, this NGS-MRD panel may allow the detection of newly emerging clones during clinical relapse, leading to more reliable prognoses of AML.
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Affiliation(s)
- Jin Ju Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hyeon Ah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hye Won Kook
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Yoo Hong Min
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
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Jang MA. Rapid Targeted Genomic Testing: A Powerful Tool for Diagnostic Evaluation of Critically Ill Neonates and Infants With Suspected Genetic Diseases. Ann Lab Med 2023; 43:223-224. [PMID: 36544333 PMCID: PMC9791018 DOI: 10.3343/alm.2023.43.3.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea,Corresponding author: Mi-Ae Jang, M.D., Ph.D. Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, 170 Jomaru-ro, Wonmi-gu, Bucheon 14584, Korea Tel: +82-32-621-6725, Fax: +82-32-621-5944 E-mail:
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Wu H, Xiong X, CUI X, Xiong J, Zhang Y, Xiang L, Xu TAO. Analysis of the influence of pyroptosis-related genes on molecular characteristics in patients with acute myocardial infarction. Medicine (Baltimore) 2023; 102:e33620. [PMID: 37083810 PMCID: PMC10118340 DOI: 10.1097/md.0000000000033620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/04/2023] [Indexed: 04/22/2023] Open
Abstract
Pyroptosis is a newly identified mode of programmed cell death, but the potential role in patients with acute myocardial infarction (AMI) remains unclear. In this study, bioinformatics methods were used to identify differentially expressed genes from peripheral blood transcriptome data between normal subjects and patients with AMI which were downloaded by the Gene Expression Omnibus database. Comparing Random Forest (RF) and Support Vector Machine (SVM) training algorithms were used to identify pyroptosis-related genes, predicting patients with AMI by nomogram based on informative genes. Moreover, clustering was used to amplify the feature of pyroptosis, in order to facilitate analysis distinct biological differences. Diversity analysis indicated that a majority of pyroptosis-related genes are expressed at higher levels in patients with AMI. The receiver operating characteristic curves show that the RF model is more responsive than the SVM machine learning model to the pyroptosis characteristics of these patients in vivo. We obtained a column line graph diagnostic model which was developed based on 19 genes established by the RF model. After the consensus clustering algorithm of single sample Gene Set Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis, the results for them found that pyroptosis-related genes mediate the activation of multiple immune cells and many inflammatory pathways in the body. We used RF and SVM algorithms to determine 19 pyroptosis-related genes and evaluate their immunological effects in patients with AMI. We also constructed a series of by nomogram related to pyroptosis-related genes to predict the risk of developing AMI.
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Affiliation(s)
- Huan Wu
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xiaoman Xiong
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xueying CUI
- Qingyun County People’s Hospital, Qingyun, Shandong, China
| | - Jianlong Xiong
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yan Zhang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Liubo Xiang
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - TAO Xu
- School of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
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Filis P, Kyrochristos I, Korakaki E, Baltagiannis EG, Thanos D, Roukos DH. Longitudinal ctDNA profiling in precision oncology and immunο-oncology. Drug Discov Today 2023; 28:103540. [PMID: 36822363 DOI: 10.1016/j.drudis.2023.103540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Serial analysis of circulating tumor DNA (ctDNA) over the disease course is emerging as a prognostic, predictive and patient-monitoring biomarker. In the metastatic setting, several multigene ctDNA assays have been approved or recommended by regulatory organizations for personalized targeted therapy, especially for lung cancer. By contrast, in nonmetastatic disease, detection of ctDNA resulting from minimal residual disease (MRD) following multimodal treatment with curative intent presents major technical challenges. Several studies using tumor genotyping-informed serial ctDNA profiling have provided promising findings on the sensitivity and specificity of ctDNA in predicting the risk of recurrence. We discuss progress, limitations and future perspectives relating to the use of ctDNA as a biomarker to guide targeted therapy in metastatic disease, as well as the use of ctDNA MRD detection to guide adjuvant treatment in the nonmetastatic setting.
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Affiliation(s)
- Panagiotis Filis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Medical Oncology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
| | - Efterpi Korakaki
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Physiology, Medical School, University of Ioannina, Ioannina 45110, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Surgery, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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Dacic S. State of the Art of Pathologic and Molecular Testing. Hematol Oncol Clin North Am 2023; 37:463-473. [PMID: 36964109 DOI: 10.1016/j.hoc.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Advances in the treatment of non-small cell lung carcinoma have resulted in improved histologic classification and the implementation of molecular testing for predictive biomarkers into the routine diagnostic workflow. Over the past decade, molecular testing has evolved from single-gene assays to high-thoroughput comprehensive next-generation sequencing. Economic barriers, suboptimal turnaround time to obtain the results, and limited tissue available for molecular assays resulted in adoption of liquid biopsies (ctDNA) into clinical practice. Multiplex immunohistochemical/immunofluorescence assays evaluating tumor microenvironment together with the AI approaches are anticipated to translate from research into clinical care.
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Affiliation(s)
- Sanja Dacic
- Department of Pathology, Yale School of Medicine, 200 South Frontage Road, EP2-631, New Haven, CT 06510, USA.
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Moon I, Kong MG, Ji YS, Kim SH, Park SK, Suh J, Jang MA. Clinical, Mutational, and Transcriptomic Characteristics in Elderly Korean Individuals With Clonal Hematopoiesis Driver Mutations. Ann Lab Med 2023; 43:145-152. [PMID: 36281508 PMCID: PMC9618905 DOI: 10.3343/alm.2023.43.2.145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Background Clonal hematopoiesis of indeterminate potential (CHIP), which is defined as the presence of blood cells originating from somatically mutated hematopoietic stem cells, is common among the elderly and is associated with an increased risk of hematologic malignancies. We investigated the clinical, mutational, and transcriptomic characteristics in elderly Korean individuals with CHIP mutations. Methods We investigated CHIP in 90 elderly individuals aged ≥60 years with normal complete blood counts at a tertiary-care hospital in Korea between June 2021 and February 2022. Clinical and laboratory data were prospectively obtained. Targeted next-generation sequencing of 49 myeloid malignancy driver genes and massively parallel RNA sequencing were performed to explore the molecular spectrum and transcriptomic characteristics of CHIP mutations. Results We detected 51 mutations in 10 genes in 37 (41%) of the study individuals. CHIP prevalence increased with age. CHIP mutations were observed with high prevalence in DNMT3A (26 individuals) and TET2 (eight individuals) and were also found in various other genes, including KDM6A, SMC3, TP53, BRAF, PPM1D, SRSF2, STAG1, and ZRSR2. Baseline characteristics, including age, confounding diseases, and blood cell parameters, showed no significant differences. Using mRNA sequencing, we characterized the altered gene expression profile, implicating neutrophil degranulation and innate immune system dysregulation. Conclusions Somatic CHIP driver mutations are common among the elderly in Korea and are detected in various genes, including DNMT3A and TET2. Our study highlights that chronic dysregulation of innate immune signaling is associated with the pathogenesis of various diseases, including hematologic malignancies.
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Affiliation(s)
- Inki Moon
- Division of Cardiology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Min Gyu Kong
- Division of Cardiology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Young Sok Ji
- Division of Hematooncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Se Hyung Kim
- Division of Hematooncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Seong Kyu Park
- Division of Hematooncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Jon Suh
- Division of Cardiology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
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Advances in the Microbiological Diagnosis of Prosthetic Joint Infections. Diagnostics (Basel) 2023; 13:diagnostics13040809. [PMID: 36832297 PMCID: PMC9954824 DOI: 10.3390/diagnostics13040809] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
A significant number of prosthetic joint infections (PJI) are culture-negative and/or misinterpreted as aseptic failures in spite of the correct implementation of diagnostic culture techniques, such as tissue sample processing in a bead mill, prolonged incubation time, or sonication of removed implants. Misinterpretation may lead to unnecessary surgery and needless antimicrobial treatment. The diagnostic value of non-culture techniques has been investigated in synovial fluid, periprosthetic tissues, and sonication fluid. Different feasible improvements, such as real-time technology, automated systems and commercial kits are now available to support microbiologists. In this review, we describe non-culture techniques based on nucleic acid amplification and sequencing methods. Polymerase chain reaction (PCR) is a frequently used technique in most microbiology laboratories which allows the detection of a nucleic acid fragment by sequence amplification. Different PCR types can be used to diagnose PJI, each one requiring the selection of appropriate primers. Henceforward, thanks to the reduced cost of sequencing and the availability of next-generation sequencing (NGS), it will be possible to identify the whole pathogen genome sequence and, additionally, to detect all the pathogen sequences present in the joint. Although these new techniques have proved helpful, strict conditions need to be observed in order to detect fastidious microorganisms and rule out contaminants. Specialized microbiologists should assist clinicians in interpreting the result of the analyses at interdisciplinary meetings. New technologies will gradually be made available to improve the etiologic diagnoses of PJI, which will remain an important cornerstone of treatment. Strong collaboration among all specialists involved is essential for the correct diagnosis of PJI.
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Lv X, Zheng Z, Zhi X, Zhou Y, Lv J, Zhou Y, Wu B, Liu S, Shi W, Song Z, Xu J, Qu J, Xu D, Gu F. Identification of RPGR ORF15 mutation for X-linked retinitis pigmentosa in a large Chinese family and in vitro correction with prime editor. Gene Ther 2023; 30:160-166. [PMID: 35794468 DOI: 10.1038/s41434-022-00352-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/28/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
X-linked retinitis pigmentosa (XLRP) is the most severe form of Retinitis Pigmentosa (RP) and one of the leading causes of blindness in the world. Currently, there is no effective treatment for RP. In the present study, we recruited a XLRP family and identified a 4 bp deletion mutation (c. 2234_2237del) in RPGR ORF15 with Sanger sequencing, which was located in the exact same region as the missing XES (X chromosome exome sequencing) coverage. Then, we generated cell lines harboring the identified mutation and corrected it via enhanced prime editing system (ePE). Collectively, Sanger sequencing identified a pathogenic mutation in RPGR ORF15 for XLRP which was corrected with ePE. This study provides a valuable insight for genetic counseling of the afflicted family members and prenatal diagnosis, also paves a way for applying prime editing based gene therapy in those patients.
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Affiliation(s)
- Xiujuan Lv
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Zheng Zheng
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Xiao Zhi
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Yilin Zhou
- College of Engineering, Boston University, Boston, MA, USA
| | - Jineng Lv
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Yue Zhou
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Binrong Wu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Sixiu Liu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Wei Shi
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, Beijing, 100054, China
| | - Zongming Song
- Henan Eye Hospital, Henan Eye Institute, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou, Henan, China
| | - Jinling Xu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Jia Qu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China
| | - Dan Xu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China.
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, 325027, China.
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Development and clinical applications of an enclosed automated targeted NGS library preparation system. Clin Chim Acta 2023; 540:117224. [PMID: 36627008 DOI: 10.1016/j.cca.2023.117224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The rapid development of next-generation sequencing (NGS) technology has promoted its wide clinical application in precision medicine for oncology. However, laborious and time-consuming manual operations, highly skilled personnel requirements, and cross-contamination are major challenges for the clinical implementation of NGS technology-based tests. The Automated NGS Diagnostic Solutions (ANDiS) 500 system is a fully enclosed cassette-dependent automated NGS library preparation system. This platform could produce qualified targeted amplicon library in three steps with only 15 min of hands-on time. Rigorous cross-contamination test using simulated contaminant plasmids confirmed that the design of disposable cassette guarantees zero sample cross-contamination. The BRCA1 and BRCA2 mutation detection panel and gastrointestinal cancer-related gene analysis panel for the ANDiS 500 platform showed 100% accuracy and precision in detecting germ-line mutations and somatic mutations respectively. Furthermore, those panels showed 100% concordance with verified methods in a prospective cohort study enrolling 363 patients and a cohort of 45 pan-cancer samples. In conclusion, the ANDiS 500 automated platform could overcome major challenges for implementing NGS assays clinically and is eligible for routine clinical tests.
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