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Yu H, Yau SST. Automated recognition of chromosome fusion using an alignment-free natural vector method. Front Genet 2024; 15:1364951. [PMID: 38572414 PMCID: PMC10987741 DOI: 10.3389/fgene.2024.1364951] [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: 01/03/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Chromosomal fusion is a significant form of structural variation, but research into algorithms for its identification has been limited. Most existing methods rely on synteny analysis, which necessitates manual annotations and always involves inefficient sequence alignments. In this paper, we present a novel alignment-free algorithm for chromosomal fusion recognition. Our method transforms the problem into a series of assignment problems using natural vectors and efficiently solves them with the Kuhn-Munkres algorithm. When applied to the human/gorilla and swamp buffalo/river buffalo datasets, our algorithm successfully and efficiently identifies chromosomal fusion events. Notably, our approach offers several advantages, including higher processing speeds by eliminating time-consuming alignments and removing the need for manual annotations. By an alignment-free perspective, our algorithm initially considers entire chromosomes instead of fragments to identify chromosomal structural variations, offering substantial potential to advance research in this field.
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Affiliation(s)
- Hongyu Yu
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
| | - Stephen S.-T. Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China
- Yanqi Lake Beijing Institute of Mathematical Science and Applications (BIMSA), Beijing, China
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Webster J, Dang HX, Chauhan PS, Feng W, Shiang A, Harris PK, Pachynski RK, Chaudhuri AA, Maher CA. PACT: a pipeline for analysis of circulating tumor DNA. Bioinformatics 2023; 39:btad489. [PMID: 37549060 PMCID: PMC10415172 DOI: 10.1093/bioinformatics/btad489] [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: 01/18/2023] [Revised: 06/26/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
MOTIVATION Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants. RESULTS We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments. AVAILABILITY AND IMPLEMENTATION PACT is freely available at https://github.com/ChrisMaherLab/PACT.
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Affiliation(s)
- Jace Webster
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Wenjia Feng
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Alex Shiang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | | | - Russell K Pachynski
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Aadel A Chaudhuri
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Biomedical Engineering, Washington University in St. Louis, MO 63130, United States
- Department of Computer Science and Engineering, Washington University in St. Louis, MO 63130, United States
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States
- Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Biomedical Engineering, Washington University in St. Louis, MO 63130, United States
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Legason ID, Ogwang MD, Chamba C, Mkwizu E, El Mouden C, Mwinula H, Chirande L, Schuh A, Chiwanga F. A protocol to clinically evaluate liquid biopsies as a tool to speed up diagnosis of children and young adults with aggressive infection-related lymphoma in East Africa "(AI-REAL)". BMC Cancer 2022; 22:484. [PMID: 35501771 PMCID: PMC9059110 DOI: 10.1186/s12885-022-09553-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Background The capacity for invasive tissue biopsies followed by histopathology diagnosis in sub-Saharan Africa is severely limited. Consequently, many cancer patients are diagnosed late and outcomes are poor. Here, we propose to evaluate circulating tumour (ct) DNA analysis (“liquid biopsy”), a less invasive and faster approach to diagnose endemic EBV-driven lymphomas (EBVL) in East Africa. Methods We will evaluate the clinical utility of an already validated ctDNA test prospectively in a head-to-head comparison against histopathology. The primary endpoint is the time from presentation to the specialist centre to a final diagnosis of EBV- Lymphoma. Secondary endpoints include the sensitivity and specificity of liquid biopsy and health economic benefits over histopathology. One hundred forty-six patients will be recruited over 18 months. Patients will be eligible if they are 3–30 years of age and have provided written consent or assent as per IRB guidelines. Tissue and venous blood samples will be processed as per established protocols. Clinical data will be captured securely and in real-time into a REDCap database. The time from presentation to diagnosis will be documented. The sensitivity and specificity of the methods can be estimated within 5% error margin with 95% confidence level using 73 cases and 73 controls. Health-economic assessment will include micro-costing of ctDNA test and histopathology. All results will be reviewed in a multidisciplinary tumour board. Discussion The study evaluates the clinical utility of ctDNA in improving the speed of diagnostic pathways for EBVL in sub-Saharan Africa. Our results would provide proof-of-principle that ctDNA can be used as a diagnostic tool in areas without access to regular pathology, that transfer of the tool is feasible, and that it leads to an earlier and faster diagnosis. The potential clinical and economic impact of this proposal is thus significant. If successful, this study will provide appropriate, and cost-effective diagnostic tools that will promote earlier diagnosis of EBVL and potentially other cancers in countries with restricted healthcare resources. Trial registration Pan African Clinical Trials Registry: PACTR202204822312651, registered on 14th-April-2022.
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Affiliation(s)
- Ismail D Legason
- AI-REAL Study, St Mary's Hospital Lacor, Gulu& African Field Epidemiology Network, 180, Gulu-Uganda. African Field Epidemiology Network, 12874, Kampala, Uganda.
| | - Martin D Ogwang
- AI-REAL Study, St Mary's Hospital Lacor, Gulu& African Field Epidemiology Network, 180, Gulu-Uganda. African Field Epidemiology Network, 12874, Kampala, Uganda
| | - Clara Chamba
- AI-REAL Study, Muhimbili University of Health and Allied Sciences, Dar es Salam, Tanzania
| | - Elifuraha Mkwizu
- AI-REAL Study, Kilimanjaro Christian Medical Center, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Claire El Mouden
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Hadija Mwinula
- Molecular Diagnostic Center, Department of Oncology, University of Oxford, Oxford, UK
| | - Lulu Chirande
- AI-REAL Study, Muhimbili University of Health and Allied Sciences, Dar es Salam, Tanzania
| | - Anna Schuh
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Faraja Chiwanga
- AI-REAL Study, Muhimbili National Hospital, Dar es Salaam, Tanzania
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