Improving Breast Cancer Diagnosis and Precision Treatment with Multi-Omics Integration and Artificial Intelligence

Main Article Content

Shruti Sharma

Abstract

The most common malignancy in women is breast cancer (BC), which frequently poses a number of several challenges in molecular subtypes identification and early diagnosis. Additionally, approximately one-third of cases are detected at an advanced stage, owing to the fact that early-stage cancer is frequently asymptomatic, and there are presently no efficient early detection tools or particular biomarkers. This directly causes patients to miss the optimal treatment window. Unfortunately, breast cancer is highly heterogeneous and characterized by substantial heterogeneity and its various molecular typing have a direct impact on the effectiveness of treatments such as chemotherapy and immunotherapy as well as having a strong correlation with patients' rates of five-year survival rates. The aim of this review is to show how these skills help to identify novel medications and build individualized therapeutics. By creating early diagnostic models utilizing multi-omics data, identifying molecular subtypes of breast cancer, measuring the tumor immune microenvironment, and forecasting immunotherapy responses, it illustrates the successful use of AI technology in breast cancer diagnosis. These breakthroughs rely heavily on the discovery of new medications and the creation of specialized treatment regimens. The study also looks into the development of novel therapeutic agents and the mechanisms of drug resistance in breast cancer. This review examines recent developments in multimodal AI, which combines many imaging modalities such digital pathology, digital breast tomography (DBT), MRI, ultrasound, mammography, and multi-omics. Accurately identifying cancer subtypes, evaluating the tumor immune milieu, predicting immunotherapy responses, and assessing possible treatment resistance are all made possible by this integration. Artificial intelligence (AI) has progressed rapidly from experimental research to therapeutic applications. It can now achieve diagnosis accuracy equivalent to that of radiologists, improve specificity, and reduce workloads by 44% to 68%, all while maintaining cancer detection rates. Some research indicates that artificial intelligence might help radiologists identify more cancer patients. These advantages result in more effective screening procedures, less needless recalls, and quicker diagnosis. In the future, artificial intelligence technology is likely to give more accurate and individualized diagnostic and therapy alternatives for patients with BC. However, analyzing multi-omics data in cancer involves a number of problems, including complexity, sparsity, transparency, and ethical concerns.


 


 

Article Details

How to Cite
Shruti Sharma. (2023). Improving Breast Cancer Diagnosis and Precision Treatment with Multi-Omics Integration and Artificial Intelligence. Journal for ReAttach Therapy and Developmental Diversities, 6(7s), 1435–1447. https://doi.org/10.69980/jrtdd.v6i7s.3915
Section
Articles
Author Biography

Shruti Sharma

Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India, 

References

Abidalkareem A, Ibrahim AK, Abd M, Rehman O, Zhuang H. Identification of Gene Expression in Different Stages of Breast Cancer with Machine Learning. Cancers (Basel). 2024;16(10):1864. Published 2024 May 14. doi:10.3390/cancers16101864

Baciu C, Xu C, Alim M, Prayitno K, Bhat M. Artificial intelligence applied to omics data in liver diseases: Enhancing clinical predictions. Front Artif Intell. 2022;5:1050439. Published 2022 Nov 15. doi:10.3389/frai.2022.1050439

Blanksby SJ, Mitchell TW. Advances in mass spectrometry for lipidomics. Annu Rev Anal Chem (Palo Alto Calif). 2010;3:433-465. doi:10.1146/annurev.anchem.111808.073705

Blixt L, Bogdanovic G, Buggert M, et al. Covid-19 in patients with chronic lymphocytic leukemia: clinical outcome and B- and T-cell immunity during 13 months in consecutive patients. Leukemia. 2022;36(2):476-481. doi:10.1038/s41375-021-01424-w

Budczies J, Brockmöller SF, Müller BM, et al. Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast cancer: alterations in glutamine and beta-alanine metabolism. J Proteomics. 2013;94:279-288. doi:10.1016/j.jprot.2013.10.002

Castiglioni I, Rundo L, Codari M, et al. AI applications to medical images: From machine learning to deep learning. Phys Med. 2021;83:9-24. doi:10.1016/j.ejmp.2021.02.006

Castiglioni I, Ippolito D, Interlenghi M, et al. Machine learning applied on chest x-ray can aid in the diagnosis of COVID-19: a first experience from Lombardy, Italy. Eur Radiol Exp. 2021;5(1):7. Published 2021 Feb 2. doi:10.1186/s41747-020-00203-z

Chaudhary A, Gustafson D, Mathys A. Multi-indicator sustainability assessment of global food systems. Nat Commun. 2018;9(1):848. Published 2018 Feb 27. doi:10.1038/s41467-018-03308-7

Cheng, L., & Yeap, Q. F. (2025). The 2025 Youth Transition Report: Outcomes for youth and young adults with disabilities. Institute for Educational Leadership. https://iel.org/iel-youth-transition-reports-outcomes-for-youth-and-young-adults-with-disabilities-2025.

Ching T, Zhu X, Garmire LX. Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data. PLoS Comput Biol. 2018;14(4):e1006076. Published 2018 Apr 10. doi:10.1371/journal.pcbi.1006076

Coudray N, Ocampo PS, Sakellaropoulos T, et al. Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning. Nat Med. 2018;24(10):1559-1567. doi:10.1038/s41591-018-0177-5

Demircioglu T, Karakus M, Ucar S. Developing Students' Critical Thinking Skills and Argumentation Abilities Through Augmented Reality-Based Argumentation Activities in Science Classes. Sci Educ (Dordr). Published online August 22, 2022. doi:10.1007/s11191-022-00369-5

Duan GL, Zhou Y, Tong YP, Mukhopadhyay R, Rosen BP, Zhu YG. A CDC25 homologue from rice functions as an arsenate reductase. New Phytol. 2007;174(2):311-321. doi:10.1111/j.1469-8137.2007.02009.x

Geyer PE, Arend FM, Doll S, et al. High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion. EMBO Mol Med. 2021;13(8):e14167. doi:10.15252/emmm.202114167

Hagiwara S, Shiohama T, Takahashi S, et al. Comprehensive High-Depth Proteomic Analysis of Plasma Extracellular Vesicles Containing Preparations in Rett Syndrome. Biomedicines. 2024;12(10):2172. Published 2024 Sep 24. doi:10.3390/biomedicines12102172

Han, J., Kamber, M., & Pei, J. (2012). Data mining: Concepts and techniques (3rd ed.). Waltham, MA: Morgan Kaufmann Publishers. DOI: 10.1016/C2009-0-61819-5

Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome Biol. 2017;18(1):83. Published 2017 May 5. doi:10.1186/s13059-017-1215-1

I. H., et al. (2021). Artificial intelligence in cancer diagnosis and therapy: A comprehensive review. Journal of AI in Medicine, 12(4), 102–115.

Disis MLN, Guthrie KA, Liu Y, et al. Safety and Outcomes of a Plasmid DNA Vaccine Encoding the ERBB2 Intracellular Domain in Patients With Advanced-Stage ERBB2-Positive Breast Cancer: A Phase 1 Nonrandomized Clinical Trial. JAMA Oncol. 2023;9(1):71-78. doi:10.1001/jamaoncol.2022.5143

Jiang Y, Sun C, Xu J, et al. Synthesis-on-substrate of quantum dot solids. Nature. 2022;612(7941):679-684. doi:10.1038/s41586-022-05486-3

Jinthanasatian, P., Auephanwiriyakul, S., & Theera-Umpon, N. (2017). Microarray data classification using neuro-fuzzy classifier with firefly algorithm. In 2017 IEEE Symposium Series on Computational Intelligence (SSCI) (pp. 1–6). Honolulu, HI, USA: IEEE. DOI: 10.1109/SSCI.2017.8285324

Johansson, R. (2019). Numerical Python: Scientific computing and data science applications with NumPy, SciPy and Matplotlib (2nd ed.). Apress. https://doi.org/10.1007/978-1-4842-4246-9

Jung KW, Kang MJ, Park EH, et al. Prediction of Cancer Incidence and Mortality in Korea, 2023. Cancer Res Treat. 2023;55(2):400-407. doi:10.4143/crt.2023.448

Kather JN, Heij LR, Grabsch HI, et al. Pan-cancer image-based detection of clinically actionable genetic alterations. Nat Cancer. 2020;1(8):789-799. doi:10.1038/s43018-020-0087-6

Kato TA, Sartorius N, Shinfuku N. Forced social isolation due to COVID-19 and consequent mental health problems: Lessons from hikikomori. Psychiatry Clin Neurosci. 2020;74(9):506-507. doi:10.1111/pcn.13112

Kim S, Chen J, Cheng T, et al. PubChem 2023 update. Nucleic Acids Res. 2023;51(D1):D1373-D1380. doi:10.1093/nar/gkac956

Kong J, Shin Y, Röhr JA, et al. CO2 doping of organic interlayers for perovskite solar cells. Nature. 2021;594(7861):51-56. doi:10.1038/s41586-021-03518-y

Kristensen VN, Lingjærde OC, Russnes HG, Vollan HK, Frigessi A, Børresen-Dale AL. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer. 2014;14(5):299-313. doi:10.1038/nrc3721

Li YH, Yu CY, Li XX, et al. Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res. 2018;46(D1):D1121-D1127. doi:10.1093/nar/gkx1076

Li Z, Li S, Luo M, et al. dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res. 2022;50(D1):D471-D479. doi:10.1093/nar/gkab1017

Lu MY, Williamson DFK, Chen TY, Chen RJ, Barbieri M, Mahmood F. Data-efficient and weakly supervised computational pathology on whole-slide images. Nat Biomed Eng. 2021;5(6):555-570. doi:10.1038/s41551-020-00682-w

Massard C, Michiels S, Ferté C, et al. High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial. Cancer Discov. 2017;7(6):586-595. doi:10.1158/2159-8290.CD-16-1396

Mertins P, Mani DR, Ruggles KV, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature.2016;534(7605):55-62. doi:10.1038/nature18003

Rahaman, M. M., Islam, M. R., Bhuiyan, M. M. R., Noman, I. R., Aziz, M. M., & Das, K. (2025, March). Harnessing big data in biotechnology: A machine learning approach to multi-omics. In 2025 International Conference on Machine Learning and Autonomous Systems (ICMLAS) (pp. 1391-1401). IEEE.

Subramanian I, Farahnik J, Mischley LK. Synergy of pandemics-social isolation is associated with worsened Parkinson severity and quality of life. NPJ Parkinsons Dis. 2020;6:28. Published 2020 Oct 8. doi:10.1038/s41531-020-00128-9

Topol EJ. High-performance medicine: the convergence of human and artificial intelligence. Nat Med. 2019;25(1):44-56. doi:10.1038/s41591-018-0300-7