Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

Nguyen, Van Thien Chi; Nguyễn, Trọng Nghĩa; Doan, Nhu Nhat Tan; Pham, Thi Mong Quynh; Nguyen, Giang; Nguyen, Thanh-Binh; Tran, Thuy Thi Thu; Vo, Duy Long; Phan, Thanh Hai; Jasmine, Thanh Xuan; Nguyen, Van Chu; Nguyen, Hung; Nguyen, Trieu Vu; Nguyen, Thi Hue Hanh; Huynh, Le Anh Khoa; Tran, Trung Hieu; Dang, Quang Thong; Doan, Thuy Nguyen; Tran, Anh Tu; Nguyen, Viet Hai; Nguyen, Tuan Anh; Tran, Quang Dat; Pham, Thi Thu Thuy; Ho, Tan Dat; Nguyen, Bao Toan; Nguyen, Thanh Nhan Vo; Nguyen, Thanh Dang; Phu, Dung Thai Bieu; Phan, Boi Hoan Huu; Vo, Thi Loan; Nai, Thi Huong Thoang; Tran, Thuy Trang; Truong, My Hoang; Tran, Ngan Chau; Le, Trung Kien; Tran, Thanh Huong; Duong, Minh Long; Bach, Hoai Phuong Thi; Kim, Van Vu; Pham, Thang; Tran, Duc Huy; Le, Trinh Ngoc An; Pham, Truong-Vinh Ngoc; Le, Minh-Triet; Vo, Dac Ho; Tran, Thi Minh Thu; Nguyen, Minh Nguyen; Van, Thi Tuong Vi; Nguyen, Anh Nhu; Tran, Trang Thi; Tran, Vu Uyen; Le, Minh-Tri; Thanh, Thi; Phan, Thi Van; Nguyen, Luu Hong Dang; Nguyen, Duy; Cao, Van Thinh; Do, Thanh-Thuy Thi; Truong, Dinh-Kiet; Tang, Hung Sang; Phan, Minh-Duy; Giang, Hoa; Nguyen, Hoa; Tran, Le Son

doi:10.1101/2023.04.12.23288460

Cited by 3 publications

(4 citation statements)

References 65 publications

(84 reference statements)

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“…QUADAS-2 assessments for each study of MCED tests currently available for use are summarised in Table 3. One study of each of Galleri, 31 CancerSEEK, 33 and SPOT-MAS 64 were case-control studies, which are considered to have a high risk of bias in the ‘patient selection’ domain of the QUADAS-2 checklist. 24 There was a high concern regarding the applicability of the index test for the studies evaluating CancerSEEK, as this test has been modified (now called Cancerguard™) and is undergoing further assessment.…”

Section: Resultsmentioning

confidence: 99%

“…First CSO was correct for 83.3% (five out of six) of the cancers; the types of cancer detected by the SPOT-MAS test in the K-DETEK 8 study are presented in Appendix 7, Table 17. A case-control study 64 recruited 239 patients diagnosed with Stage I-IIIA cancers (see Appendix 7, Table 17 for the cancer types among recruited patients) and 474 healthy controls as a validation cohort for the SPOT-MAS test. Specificity of the SPOT-MAS test was high (97.0, 95% CI 95.1% to 98.4%) with only 14 out of the 474 healthy controls with FP results.…”

Section: Resultsmentioning

confidence: 99%

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Multi-cancer early detection tests for general population screening: a systematic literature review

Wade,

Nevitt,

Liu

et al. 2024

Preprint

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Background: General population cancer screening in the UK is limited to selected cancers. Blood-based multi-cancer early detection (MCED) tests aim to detect potential cancer signals from multiple cancers in the blood. The use of an MCED test for population screening requires a high specificity and a reasonable sensitivity to detect early-stage disease, so that the benefits of earlier diagnosis and treatment can be realised. Objective: To undertake a systematic literature review of the clinical effectiveness evidence on blood-based MCED tests for screening. Methods: Comprehensive searches of electronic databases (including MEDLINE and Embase) and trial registers were undertaken in September 2023 to identify published and unpublished studies of MCED tests. Test manufacturer websites and reference lists of included studies and pertinent reviews were checked for additional studies. The target population was individuals aged 50 to 79 years without clinical suspicion of cancer. Outcomes of interest included test accuracy, number and proportion of cancers detected (by site and stage), time to diagnostic resolution, mortality, potential harms, health-related quality of life (HRQoL), acceptability and satisfaction. Risk of bias was assessed using the QUADAS-2 checklist. Results were summarised using narrative synthesis. Stakeholders contributed to protocol development, report drafting, and interpretation of review findings. Results: Over 8000 records were identified. Thirty-six studies met the inclusion criteria: one ongoing randomised controlled trial (RCT), 13 completed cohort studies, 17 completed case-control studies and five ongoing cohort or case-control studies. Individual tests claimed to detect from three to over 50 different types of cancer. Diagnostic accuracy of currently available MCED tests varied substantially: Galleri ® (GRAIL) sensitivity 20.8% to 66.3%, specificity 98.4% to 99.5% (3 studies); CancerSEEK (Exact Sciences) sensitivity 27.1% to 62.3%, specificity 98.9% to 99.1% (2 studies); SPOT-MAS ™ (Gene Solutions) sensitivity 72.4% to 100%, specificity 97.0% to 99.9% (2 studies); TruCheck ™ (Datar Cancer Genetics) sensitivity 90.0%, specificity 96.4% (1 study); CDA (AnPac Bio) sensitivity 40.0%, specificity 97.6% (1 study). AICS ® (Ajinomoto) screens for individual cancers separately, so no overall test performance statistics are available. Where reported, sensitivity was lower for detecting earlier stage cancers (Stage I-II) compared with later stage cancers (Stage III-IV). Studies of seven other MCED tests at an unclear stage of development were also summarised. Limitations: Study selection was complex; it was often difficult to determine the stage of development of MCED tests. The evidence was limited; there were no completed RCTs and most included studies had a high overall risk of bias, primarily owing to limited follow-up of participants with negative test results. Only one study of Galleri recruited asymptomatic individuals aged over 50 in the USA, however, study results may not be representative of the UK general screening population. No meaningful results were reported relating to patient relevant outcomes, such as mortality, potential harms, HRQoL, acceptability or satisfaction. Conclusions: All currently available MCED tests reported high specificity (>96%). Sensitivity was highly variable and influenced by study design, population, reference standard test used and length of follow-up. Future work: Further research should report patient relevant outcome and consider patient and service impacts.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Multi-cancer early detection tests for general population screening: a systematic literature review

Wade,

Nevitt,

Liu

et al. 2024

Preprint

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“…Large language models have recently made impressive strides in capturing patterns of social cognition [25,26,134–137], and various neural architectures have been able to capture some patterns of human Theory of Mind in gridworld tasks [138–140]. However, these models have yet to approach the logical and causal reasoning capacity that humans develop by childhood [139,141,142].…”

Section: Discussionmentioning

confidence: 99%

Emotion prediction as computation over a generative theory of mind

Houlihan

Kleiman-Weiner

Hewitt

et al. 2023

Phil. Trans. R. Soc. A.

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From sparse descriptions of events, observers can make systematic and nuanced predictions of what emotions the people involved will experience. We propose a formal model of emotion prediction in the context of a public high-stakes social dilemma. This model uses inverse planning to infer a person’s beliefs and preferences, including social preferences for equity and for maintaining a good reputation. The model then combines these inferred mental contents with the event to compute ‘appraisals’: whether the situation conformed to the expectations and fulfilled the preferences. We learn functions mapping computed appraisals to emotion labels, allowing the model to match human observers’ quantitative predictions of 20 emotions, including joy, relief, guilt and envy. Model comparison indicates that inferred monetary preferences are not sufficient to explain observers’ emotion predictions; inferred social preferences are factored into predictions for nearly every emotion. Human observers and the model both use minimal individualizing information to adjust predictions of how different people will respond to the same event. Thus, our framework integrates inverse planning, event appraisals and emotion concepts in a single computational model to reverse-engineer people’s intuitive theory of emotions. This article is part of a discussion meeting issue ‘Cognitive artificial intelligence’.

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“…evaluation of large-scale multi-view 3D reconstruction with RANCOM technique [87], CRITIC technique [88][89][90][91][92], COMET technique [93][94][95][96][97][98], MAIRCA technique [99][100][101] and QUALIFLEX technique [102][103][104][105][106].…”

mentioning

confidence: 99%

Enhanced Combined Techniques for Interval-Valued Intuitionistic Fuzzy Multiple-Attribute Group Decision-Making and Applications to Quality Evaluation of Large-Scale Multi-View 3D Reconstruction

Bian,

Che

2023

IEEE Access

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With the widespread application of computer vision in many fields, quickly and accurately obtaining the three-dimensional information covered by the target object has become a concern in the field of vision research. Large scale multi view Iterative reconstruction refers to obtaining multiple images of the target object through the camera, then obtaining the corresponding relationship between points and spatial mapping relationship between each image through the pixel information on the image, and then obtaining the 3D information of the target object through the relationship between points and space, finally completing the multi view Iterative reconstruction of the target object. Multi view Iterative reconstruction has a wide range of applications, and has very important applications in medical treatment, industrial detection, space technology, etc. Compared with binocular or multi camera stereo vision, monocular stereo vision has obvious advantages in terms of cost, structure and the way to obtain pictures. Multi view Iterative reconstruction of objects can be completed by processing multiple images to achieve the effect of multi camera stereo vision. The quality evaluation of large-scale multi-view 3D reconstruction is the MAGDM. Recently, the TODIM and EDAS technique has been employed to manage MAGDM. The interval-valued intuitionistic fuzzy sets (IVIFSs) are employed as a useful tool for portraying uncertain information during the quality evaluation of large-scale multi-view 3D reconstruction. In this paper, the interval-valued intuitionistic fuzzy TODIM-EDAS (IVIF-TODIM-EDAS) technique is built to manage the MAGDM under IVIFSs. At last, the numerical example for quality evaluation of large-scale multi-view 3D reconstruction is employed to show the IVIF-TODIM-EDAS decision technique. The main contribution of this paper is outlined: (1) the TODIM technique based on EDAS has been extended to IVIFSs based on Entropy technique; (2) the Entropy technique is employed to manage weight based on score values under IVIFSs. (3) the IVIF-TODIM-EDAS technique is founded to manage the MAGDM under IVIFSs; (4) a numerical example for quality evaluation of large-scale multi-view 3D reconstruction and some comparative analysis is supplied to verify the proposed technique. INDEX TERMS: Multiple-attribute group decision-making (MAGDM); interval-valued intuitionistic fuzzy sets (IVIFSs); TODIM technique; EDAS technique; large-scale multi-view 3D reconstruction

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Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

Cited by 3 publications

References 65 publications

Multi-cancer early detection tests for general population screening: a systematic literature review

Multi-cancer early detection tests for general population screening: a systematic literature review

Emotion prediction as computation over a generative theory of mind

Enhanced Combined Techniques for Interval-Valued Intuitionistic Fuzzy Multiple-Attribute Group Decision-Making and Applications to Quality Evaluation of Large-Scale Multi-View 3D Reconstruction

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