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Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [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: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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2
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Man A, Di Scipio M, Grewal S, Suk Y, Trinari E, Ejaz R, Whitney R. The Genetics of Tuberous Sclerosis Complex and Related mTORopathies: Current Understanding and Future Directions. Genes (Basel) 2024; 15:332. [PMID: 38540392 PMCID: PMC10970281 DOI: 10.3390/genes15030332] [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: 02/12/2024] [Revised: 03/02/2024] [Accepted: 03/02/2024] [Indexed: 06/14/2024] Open
Abstract
The mechanistic target of rapamycin (mTOR) pathway serves as a master regulator of cell growth, proliferation, and survival. Upregulation of the mTOR pathway has been shown to cause malformations of cortical development, medically refractory epilepsies, and neurodevelopmental disorders, collectively described as mTORopathies. Tuberous sclerosis complex (TSC) serves as the prototypical mTORopathy. Characterized by the development of benign tumors in multiple organs, pathogenic variants in TSC1 or TSC2 disrupt the TSC protein complex, a negative regulator of the mTOR pathway. Variants in critical domains of the TSC complex, especially in the catalytic TSC2 subunit, correlate with increased disease severity. Variants in less crucial exons and non-coding regions, as well as those undetectable with conventional testing, may lead to milder phenotypes. Despite the assumption of complete penetrance, expressivity varies within families, and certain variants delay disease onset with milder neurological effects. Understanding these genotype-phenotype correlations is crucial for effective clinical management. Notably, 15% of patients have no mutation identified by conventional genetic testing, with the majority of cases postulated to be caused by somatic TSC1/TSC2 variants which present complex diagnostic challenges. Advancements in genetic testing, prenatal screening, and precision medicine hold promise for changing the diagnostic and treatment paradigm for TSC and related mTORopathies. Herein, we explore the genetic and molecular mechanisms of TSC and other mTORopathies, emphasizing contemporary genetic methods in understanding and diagnosing the condition.
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Affiliation(s)
- Alice Man
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Matteo Di Scipio
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shan Grewal
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Yujin Suk
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Elisabetta Trinari
- Division of Developmental Pediatrics, Department of Pediatrics, McMaster Children’s Hospital, Hamilton, ON L8N 3Z5, Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Robyn Whitney
- Division of Neurology, Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
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3
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Alrahawy M, Javed S, Atif H, Elsanhoury K, Mekhaeil K, Eskander G. Microbiome and Colorectal Cancer Management. Cureus 2022; 14:e30720. [DOI: 10.7759/cureus.30720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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Ottestad AL, Emdal EF, Grønberg BH, Halvorsen TO, Dai HY. Fragmentation assessment of FFPE DNA helps in evaluating NGS library complexity and interpretation of NGS results. Exp Mol Pathol 2022; 126:104771. [DOI: 10.1016/j.yexmp.2022.104771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/13/2022] [Accepted: 04/09/2022] [Indexed: 11/04/2022]
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Redhu N, Thakur Z. Network biology and applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Novel target capture DNA library preparation method using CircLigase-mediated hook ligation. N Biotechnol 2020; 59:44-50. [PMID: 32688061 DOI: 10.1016/j.nbt.2020.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/22/2022]
Abstract
Target capture DNA library preparation methods primarily use the biotin-streptavidin interaction to enrich target DNA, requiring complex operations and a time-consuming workflow with a series of wash steps at regulated temperatures. Here, a new method is presented termed 'hook ligation' for target DNA library preparation, using CircLigase to capture target DNA. The concept was validated by library preparation, sequencing, and acquisition of target DNA fragment information through bioinformatics analysis. An efficient reference point for single-strand DNA ligation to a hook sequence using CircLigase is also provided and it is shown that the efficiency can be influenced by the length and the position of the complementary area on the target DNA.
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Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:E521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
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Syeda MM, Wiggins JM, Corless B, Spittle C, Karlin-Neumann G, Polsky D. Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma. Methods Mol Biol 2020; 2055:155-180. [PMID: 31502151 DOI: 10.1007/978-1-4939-9773-2_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detection of cell-free, circulating tumor DNA (ctDNA) in the blood of patients with solid tumors is often referred to as "liquid biopsy." ctDNA is particularly attractive as a candidate biomarker in the blood. It is relatively stable after blood collection, can be easily purified, and can be quantitatively measured with high sensitivity and specificity using advanced technologies. Current liquid biopsy research has focused on detecting and quantifying ctDNA to (1) diagnose and characterize mutations in a patient's cancer to help select the appropriate treatment; (2) predict clinical outcomes associated with different treatments; and (3) monitor the response and/or progression of a patient's disease. The diagnostic use of liquid biopsies is probably greatest in tumors where the difficulty and/or risk of obtaining a tissue specimen for molecular diagnostics is high (e.g., lung, colon). In metastatic melanoma, however, obtaining a tissue sample for molecular diagnostics is not typically a major obstacle to patient care plans; rather predicting treatment outcomes and monitoring a patient's disease course during therapy are considered the current priorities for this cancer type. In this chapter we describe an approach to the validation of ctDNA detection assays for melanoma, focusing primarily on analytical validation, and provide methods to guide the use of droplet digital PCR assays for measuring ctDNA levels in plasma samples.
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Affiliation(s)
- Mahrukh M Syeda
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Jennifer M Wiggins
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Broderick Corless
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | | | | | - David Polsky
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA.
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Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 2019; 22:178-193. [PMID: 31848574 PMCID: PMC7820839 DOI: 10.1093/bib/bbz155] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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Affiliation(s)
- Richa Bharti
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
| | - Dominik G Grimm
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
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