Machine learning to detect the SINEs of cancer.
Douville, C
Lahouel, K
Kuo, A
Grant, H
Avigdor, BE
Curtis, SD
Summers, M
Cohen, JD
Wang, Y
Mattox, A
Dudley, J
Dobbyn, L
Popoli, M
Ptak, J
Nehme, N
Silliman, N
Blair, C
Romans, K
Thoburn, C
Gizzi, J
Schoen, RE
Tie, J
Gibbs, P
Ho-Pham, LT
Tran, BNH
Tran, TS
Nguyen, TV
Goggins, M
Wolfgang, CL
Wang, T-L
Shih, I-M
Lennon, AM
Hruban, RH
Bettegowda, C
Kinzler, KW
Papadopoulos, N
Vogelstein, B
Tomasetti, C
- Publisher:
- American Association for the Advancement of Science (AAAS)
- Publication Type:
- Journal Article
- Citation:
- Sci Transl Med, 2024, 16, (731), pp. eadi3883
- Issue Date:
- 2024-01-24
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Full metadata record
Field | Value | Language |
---|---|---|
dc.contributor.author | Douville, C | |
dc.contributor.author | Lahouel, K | |
dc.contributor.author | Kuo, A | |
dc.contributor.author | Grant, H | |
dc.contributor.author | Avigdor, BE | |
dc.contributor.author | Curtis, SD | |
dc.contributor.author | Summers, M | |
dc.contributor.author | Cohen, JD | |
dc.contributor.author | Wang, Y | |
dc.contributor.author | Mattox, A | |
dc.contributor.author | Dudley, J | |
dc.contributor.author | Dobbyn, L | |
dc.contributor.author | Popoli, M | |
dc.contributor.author | Ptak, J | |
dc.contributor.author | Nehme, N | |
dc.contributor.author | Silliman, N | |
dc.contributor.author | Blair, C | |
dc.contributor.author | Romans, K | |
dc.contributor.author | Thoburn, C | |
dc.contributor.author | Gizzi, J | |
dc.contributor.author | Schoen, RE | |
dc.contributor.author | Tie, J | |
dc.contributor.author | Gibbs, P | |
dc.contributor.author | Ho-Pham, LT | |
dc.contributor.author | Tran, BNH | |
dc.contributor.author | Tran, TS | |
dc.contributor.author | Nguyen, TV | |
dc.contributor.author | Goggins, M | |
dc.contributor.author | Wolfgang, CL | |
dc.contributor.author | Wang, T-L | |
dc.contributor.author | Shih, I-M | |
dc.contributor.author | Lennon, AM | |
dc.contributor.author | Hruban, RH | |
dc.contributor.author | Bettegowda, C | |
dc.contributor.author | Kinzler, KW | |
dc.contributor.author | Papadopoulos, N | |
dc.contributor.author | Vogelstein, B | |
dc.contributor.author | Tomasetti, C | |
dc.date.accessioned | 2024-02-27T06:40:25Z | |
dc.date.available | 2024-02-27T06:40:25Z | |
dc.date.issued | 2024-01-24 | |
dc.identifier.citation | Sci Transl Med, 2024, 16, (731), pp. eadi3883 | |
dc.identifier.issn | 1946-6234 | |
dc.identifier.issn | 1946-6242 | |
dc.identifier.uri | http://hdl.handle.net/10453/175902 | |
dc.description.abstract | We previously described an approach called RealSeqS to evaluate aneuploidy in plasma cell-free DNA through the amplification of ~350,000 repeated elements with a single primer. We hypothesized that an unbiased evaluation of the large amount of sequencing data obtained with RealSeqS might reveal other differences between plasma samples from patients with and without cancer. This hypothesis was tested through the development of a machine learning approach called Alu Profile Learning Using Sequencing (A-PLUS) and its application to 7615 samples from 5178 individuals, 2073 with solid cancer and the remainder without cancer. Samples from patients with cancer and controls were prespecified into four cohorts used for model training, analyte integration, and threshold determination, validation, and reproducibility. A-PLUS alone provided a sensitivity of 40.5% across 11 different cancer types in the validation cohort, at a specificity of 98.5%. Combining A-PLUS with aneuploidy and eight common protein biomarkers detected 51% of the cancers at 98.9% specificity. We found that part of the power of A-PLUS could be ascribed to a single feature-the global reduction of AluS subfamily elements in the circulating DNA of patients with solid cancer. We confirmed this reduction through the analysis of another independent dataset obtained with a different approach (whole-genome sequencing). The evaluation of Alu elements may therefore have the potential to enhance the performance of several methods designed for the earlier detection of cancer. | |
dc.format | Print-Electronic | |
dc.language | eng | |
dc.publisher | American Association for the Advancement of Science (AAAS) | |
dc.relation.ispartof | Sci Transl Med | |
dc.relation.isbasedon | 10.1126/scitranslmed.adi3883 | |
dc.rights | info:eu-repo/semantics/openAccess | |
dc.subject | 06 Biological Sciences, 11 Medical and Health Sciences | |
dc.subject.classification | 3206 Medical biotechnology | |
dc.subject.classification | 4003 Biomedical engineering | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Reproducibility of Results | |
dc.subject.mesh | Neoplasms | |
dc.subject.mesh | Short Interspersed Nucleotide Elements | |
dc.subject.mesh | Machine Learning | |
dc.subject.mesh | Aneuploidy | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Neoplasms | |
dc.subject.mesh | Aneuploidy | |
dc.subject.mesh | Reproducibility of Results | |
dc.subject.mesh | Short Interspersed Nucleotide Elements | |
dc.subject.mesh | Machine Learning | |
dc.subject.mesh | Humans | |
dc.subject.mesh | Reproducibility of Results | |
dc.subject.mesh | Neoplasms | |
dc.subject.mesh | Short Interspersed Nucleotide Elements | |
dc.subject.mesh | Machine Learning | |
dc.subject.mesh | Aneuploidy | |
dc.title | Machine learning to detect the SINEs of cancer. | |
dc.type | Journal Article | |
utslib.citation.volume | 16 | |
utslib.location.activity | United States | |
utslib.for | 06 Biological Sciences | |
utslib.for | 11 Medical and Health Sciences | |
pubs.organisational-group | University of Technology Sydney | |
pubs.organisational-group | University of Technology Sydney/Faculty of Engineering and Information Technology | |
pubs.organisational-group | University of Technology Sydney/Strength - CHT - Health Technologies | |
pubs.organisational-group | University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering | |
pubs.organisational-group | University of Technology Sydney/Centre for Health Technologies (CHT) | |
utslib.copyright.status | open_access | * |
dc.date.updated | 2024-02-27T06:40:24Z | |
pubs.issue | 731 | |
pubs.publication-status | Published | |
pubs.volume | 16 | |
utslib.citation.issue | 731 |
Abstract:
We previously described an approach called RealSeqS to evaluate aneuploidy in plasma cell-free DNA through the amplification of ~350,000 repeated elements with a single primer. We hypothesized that an unbiased evaluation of the large amount of sequencing data obtained with RealSeqS might reveal other differences between plasma samples from patients with and without cancer. This hypothesis was tested through the development of a machine learning approach called Alu Profile Learning Using Sequencing (A-PLUS) and its application to 7615 samples from 5178 individuals, 2073 with solid cancer and the remainder without cancer. Samples from patients with cancer and controls were prespecified into four cohorts used for model training, analyte integration, and threshold determination, validation, and reproducibility. A-PLUS alone provided a sensitivity of 40.5% across 11 different cancer types in the validation cohort, at a specificity of 98.5%. Combining A-PLUS with aneuploidy and eight common protein biomarkers detected 51% of the cancers at 98.9% specificity. We found that part of the power of A-PLUS could be ascribed to a single feature-the global reduction of AluS subfamily elements in the circulating DNA of patients with solid cancer. We confirmed this reduction through the analysis of another independent dataset obtained with a different approach (whole-genome sequencing). The evaluation of Alu elements may therefore have the potential to enhance the performance of several methods designed for the earlier detection of cancer.
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