rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations
| العنوان: | rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations |
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| المؤلفون: | Zhenhua Yu, Furui Liu, Fangyuan Shi, Fang Du |
| المصدر: | Briefings in Bioinformatics. 24 |
| بيانات النشر: | Oxford University Press (OUP), 2023. |
| سنة النشر: | 2023 |
| مصطلحات موضوعية: | Molecular Biology, Information Systems |
| الوصف: | Intra-tumor heterogeneity (ITH) is one of the major confounding factors that result in cancer relapse, and deciphering ITH is essential for personalized therapy. Single-cell DNA sequencing (scDNA-seq) now enables profiling of single-cell copy number alterations (CNAs) and thus aids in high-resolution inference of ITH. Here, we introduce an integrated framework called rcCAE to accurately infer cell subpopulations and single-cell CNAs from scDNA-seq data. A convolutional autoencoder (CAE) is employed in rcCAE to learn latent representation of the cells as well as distill copy number information from noisy read counts data. This unsupervised representation learning via the CAE model makes it convenient to accurately cluster cells over the low-dimensional latent space, and detect single-cell CNAs from enhanced read counts data. Extensive performance evaluations on simulated datasets show that rcCAE outperforms the existing CNA calling methods, and is highly effective in inferring clonal architecture. Furthermore, evaluations of rcCAE on two real datasets demonstrate that it is able to provide a more refined clonal structure, of which some details are lost in clonal inference based on integer copy numbers. |
| تدمد: | 1477-4054 1467-5463 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8ff5433d11a062610def5fe561308269 https://doi.org/10.1093/bib/bbad108 |
| حقوق: | EMBARGO |
| رقم الأكسشن: | edsair.doi.dedup.....8ff5433d11a062610def5fe561308269 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14774054 14675463 |
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