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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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Povedano E, Ruiz-Valdepeñas Montiel V, Gamella M, Pedrero M, Barderas R, Peláez-García A, Mendiola M, Hardisson D, Feliú J, Yáñez-Sedeño P, Campuzano S, Pingarrón JM. Amperometric Bioplatforms To Detect Regional DNA Methylation with Single-Base Sensitivity. Anal Chem 2020; 92:5604-5612. [PMID: 32073832 DOI: 10.1021/acs.analchem.0c00628] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This work reports the first bioplatform able to determine electrochemically 5-hydroxymethylcytosine (5-hmC) methylation events at localized sites and single-base sensitivity. The described bioplatform relies on a specific antibody (anti-5-hmC), further conjugated with commercial bioreagents loaded with multiple horseradish peroxidase (HRP) molecules, recognizing the epimark in a target DNA, captured through hybridization onto streptavidin-magnetic microbeads (Strep-MBs) modified with a complementary DNA capture probe. The electrochemical detection is performed by amperometry (-0.20 V vs Ag pseudoreference electrode) at disposable screen-printed carbon electrodes (SPCEs) in the presence of H2O2/hydroquinone (HQ) upon magnetic capture of the modified MBs onto the SPCE. The use of the commercial bioreagents ProtA-polyHRP80 and Histostar, very scarcely explored so far in electrochemical biosensors, provides high sensitivities for a synthetic target DNA sequence with a unique 5-hmC in the promoter region of MGMT tumor suppressor gene. Amplification factors of 43.6 and 55.2 were achieved using ProtA-polyHRP80 or Histostar, respectively, compared to the conventional secondary antibody labeling. This amplification was crucial to detect methylation events at single-nucleotide resolution achieving limits of detection (LODs) of 23.0 and 13.2 pM, respectively, without any target DNA amplification. The ProtA-polyHRP80-based bioplatform, selected as a compromise between sensitivity and cost per determination, exhibited full discrimination toward the target 5-hmC against the closely related 5-mC. In addition, the bioplatform detected 5-hmC at the regional level (MGMT promoter region) in just 10 ng of genomic DNA (gDNA, ∼2700 genomes) extracted from cancer cells and tissues from colorectal cancer (CRC) patients within 60 min.
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Affiliation(s)
- Eloy Povedano
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Maria Gamella
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - María Pedrero
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain.,Translational Oncology Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Jaime Feliú
- Center for Biomedical Research in the Cancer Network, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Paloma Yáñez-Sedeño
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Susana Campuzano
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - José M Pingarrón
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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