Journal
BRIEFINGS IN BIOINFORMATICS
Volume 22, Issue 6, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbab283
Keywords
deep learning; next-generation sequencing; forensic; breast cancer; DNA mixture
Funding
- Center of Genomic and Precision Medicine, National Taiwan University
- Ministry of Science and Technology, Taiwan [MOST-110-2634-F-002-044]
- Center for Biotechnology, National Taiwan University, Taiwan [GTZ300]
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The study proposed a deep learning model for classifying individuals from mixtures of DNA samples with high accuracy. The model was also demonstrated to be effective in classifying subtypes of breast cancer patients, showcasing its versatility across different NGS platforms.
In this study, we proposed a deep learning (DL) model for classifying individuals from mixtures of DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms obtained through massively parallel sequencing protocol. The model was trained/tested/validated with sequenced data from 6 individuals and then evaluated using mixtures from forensic DNA samples. The model successfully identified both the major and the minor contributors with 100% accuracy for 90 DNA mixtures, that were manually prepared by mixing sequence reads of 3 individuals at different ratios. Furthermore, the model identified 100% of the major contributors and 50-80% of the minor contributors in 20 two-sample external-mixed-samples at ratios of 1:39 and 1:9, respectively. To further demonstrate the versatility and applicability of the pipeline, we tested it on whole exome sequence data to classify subtypes of 20 breast cancer patients and achieved an area under curve of 0.85. Overall, we present, for the first time, a complete pipeline, including sequencing data processing steps and DL steps, that is applicable across different NGS platforms. We also introduced a sliding window approach, to overcome the sequence length variation problem of sequencing data, and demonstrate that it improves the model performance dramatically.
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