Integrating Genomics and Proteomics Technologies in Biological Research: Advantages, Challenges, and Prospects
DOI:
https://doi.org/10.63950/gshh.2025.1.1.2Keywords:
Genomics, Proteomics, Proteogenomics, Multi-omics Integration, Research, TechnologiesAbstract
Introduction: The integration of genomics and proteomics, two cornerstone omics technologies, has transformed our understanding of biological systems, enabling deeper insights into disease mechanisms, biomarker discovery, and the development of personalised medicine. While genomics uncovers genetic blueprints, proteomics reveals functional protein expressions, making their combined use essential for a holistic view of biological processes. This narrative review explores the current state, advantages, challenges, and prospects of integrating genomics and proteomics in biological research, particularly in the context of translational medicine and global health applications.
Methods: A systematic literature search was conducted across four databases—PubMed, Scopus, Web of Science, and Google Scholar, for English-language peer-reviewed articles published between January 2015 and May 2025. A PRISMA-based approach guided article screening and selection. Inclusion criteria focused on studies addressing multi-omics integration, relevant technologies, clinical applications, and associated ethical concerns. The findings were synthesised using thematic analysis.
Synthesis: The review highlights the growing synergy between genomics and proteomics in enhancing disease diagnosis, drug discovery, and precision medicine. Advances in next-generation sequencing and mass spectrometry, coupled with computational tools such as MOFA+ and AlphaFold, have improved data integration. However, challenges persist, including high data complexity, computational demands, ethical/legal concerns, and limited access in low-resource settings.
Conclusion: Integrated omics approaches hold immense potential to revolutionise healthcare and biological discovery. Addressing current barriers and fostering global collaboration, particularly in underrepresented regions, are critical to realising the full benefits of genomics and proteomics integration.
Downloads
References
1. Kang MG, Byun K, Kim JH, Park NH, Heinsen H, Ravid R, Steinbusch HW, Lee B, Park YM. Proteogenomics of the human hippocampus: The road ahead Biochim Biophys Acta. 2015 Jul;1854(7):788-97. https://doi.org/10.1016/j.bbapap.2015.02.010
2. Shukla HD, Mahmood J, Vujaskovic Z. Integrated proteo-genomic approach for early diagnosis and prognosis of cancer Cancer Lett. 2015 Dec 1;369(1):28-36. https://doi.org/10.1016/j.canlet.2015.08.003
3. Gangfuß A, Schara-Schmidt U, Roos A. [Genomics and proteomics in the research of neuromuscular diseases] Nervenarzt. 2022 Feb;93(2):114-121. https://doi.org/10.1007/s00115-021-01201-1
4. Fu S, Liu X, Luo M, Xie K, Nice EC, Zhang H, Huang C. Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification Expert Rev Proteomics. 2017 Apr;14(4):351-362. https://doi.org/10.1080/14789450.2017.1299006.
5. Rodriguez H, Zenklusen JC, Staudt LM, Doroshow JH, Lowy DR. The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment Cell. 2021 Apr 1;184(7):1661-1670. https://doi.org/10.1016/j.cell.2021.02.055
6. Bischoff R, Permentier H, Guryev V, Horvatovich P. Genomic variability and protein species - Improving sequence coverage for proteogenomics J Proteomics. 2016 Feb 16;134:25-36. https://doi.org/10.1016/j.jprot.2015.09.021
7. Heo YJ, Hwa C, Lee GH, Park JM, An JY. Integrative Multi-Omics Approaches in Cancer Research: From Biological Networks to Clinical Subtypes Mol Cells. 2021 Jul 31;44(7):433-443. https://doi.org/10.14348/molcells.2021.0042
8. Menschaert G, Fenyö D. Proteogenomics from a bioinformatics angle: A growing field Mass Spectrom Rev. 2017 Sep;36(5):584-599. https://doi.org/10.1002/mas.21483
9. Husain H, Ahmad R, Khan A, Inamuddin, Asiri AM. Proteomic-genomic adjustments and their confluence for elucidation of pathways and networks during liver fibrosis Int J Biol Macromol. 2018 May;111:379-392. https://doi.org/10.1016/j.ijbiomac.2017.12.168
10. Dimitrakopoulos L, Prassas I, Diamandis EP, Charames GS. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction Crit Rev Clin Lab Sci. 2017 Sep;54(6):414-432. https://doi.org/10.1080/10408363.2017.1384446.
11. Kumar D, Dash D. Proteogenomic Tools and Approaches to Explore Protein Coding Landscapes of Eukaryotic Genomes Adv Exp Med Biol. 2016;926:1-10. https://doi.org/10.1007/978-3-319-42316-6_1
12. Eicher T, Patt A, Kautto E, Machiraju R, Mathé E, Zhang Y. Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge BMC Bioinformatics. 2019 Dec 20;20(Suppl 24):669. https://doi.org/10.1186/s12859-019-3253-z
13. Staal JA, Pei Y, Rood BR. A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors Int J Mol Sci. 2016 Oct 19;17(10):1744. https://doi.org/10.3390/ijms17101744
14. Vaudel M, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies Adv Exp Med Biol. 2016;926:65-75. https://doi.org/10.1007/978-3-319-42316-6_5
15. Kumar D, Bansal G, Narang A, Basak T, Abbas T, Dash D. Integrating transcriptome and proteome profiling: Strategies and applications Proteomics. 2016 Oct;16(19):2533-2544. https://doi.org/10.1002/pmic.201600140
16. Barbieri R, Guryev V, Brandsma CA, Suits F, Bischoff R, Horvatovich P. Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine Adv Exp Med Biol. 2016;926:21-47. https://doi.org/10.1007/978-3-319-42316-6_3
17. Ansari D, Torén W, Zhou Q, Hu D, Andersson R. Proteomic and genomic profiling of pancreatic cancer Cell Biol Toxicol. 2019 Aug;35(4):333-343. https://doi.org/10.1007/s10565-019-09465-9
18. Verma A, Halder A, Marathe S, Purwar R, Srivastava S. A proteogenomic approach to target neoantigens in solid tumors Expert Rev Proteomics. 2020 Nov-Dec;17(11-12):797-812. https://doi.org/10.1080/14789450.2020.1881889
19. Das T, Andrieux G, Ahmed M, Chakraborty S. Integration of Online Omics-Data Resources for Cancer Research Front Genet. 2020 Oct 23;11:578345. https://doi.org/10.3389/fgene.2020.578345
20. Chiou SH, Lee KT. Proteomic analysis and translational perspective of hepatocellular carcinoma: Identification of diagnostic protein biomarkers by an onco-proteogenomics approach Kaohsiung J Med Sci. 2016 Nov;32(11):535-544. https://doi.org/10.1016/j.kjms.2016.09.002
21. Fernández-Lázaro D, Garrosa E, Seco-Calvo J, Garrosa M. Potential Satellite Cell-Linked Biomarkers in Aging Skeletal Muscle Tissue: Proteomics and Proteogenomics to Monitor Sarcopenia Proteomes. 2022 Aug 19;10(3):29. https://doi.org/10.3390/proteomes10030029
22. Verstappe B, Scott CL. Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations Clin Exp Immunol. 2024 Oct 16;218(2):151-162. https://doi.org/10.1093/cei/uxae077
23. Shi L, Ng JK, Xiong Q, Ao KF, Shin SK, Law CT, Mu W, Liu GM, Rao S, Tsui SK. Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps. BMC Genomics. 2025 May 26;26(1):529. https://doi.org/10.1186/s12864-025-11719-2
24. Lin MR, Tsai CL, Liao CS, Wei CY, Chou WH, Hsiao TH, Chang WC. Exploring the genomic and transcriptomic profiles of glycemic traits and drug repurposing J Biomed Sci. 2025 May 21;32(1):50. https://doi.org/10.1186/s12929-025-01137-7
25. Lee Y, Lee M, Shin Y, Kim K, Kim T. Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications Int J Mol Sci. 2025 Apr 22;26(9):3949. https://doi.org/10.3390/ijms26093949
26. Sun H, Chen S, Kong J. Cerebrospinal Fluid Metabolomics and Proteomics Integration in Neurological Syndromes Methods Mol Biol. 2025;2914:303-321. https://doi.org/10.1007/978-1-0716-4462-1_21
27. Wang Z, Zhang T, Tang M. Navigating nanotoxicity: Unraveling nanomaterial-induced effects via multi-omics integration NanoImpact. 2025 May 16;38:100565. https://doi.org/10.1016/j.impact.2025.100565
28. Morabito A, De Simone G, Pastorelli R, Brunelli L, Ferrario M. Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review J Transl Med. 2025 Apr 10;23(1):425. https://doi.org/10.1186/s12967-025-06446-x
29. Kahraman Ilıkkan Ö. Lactobacillomics as a new notion in lactic acid bacteria research through omics integration World J Microbiol Biotechnol. 2025 Feb 11;41(2):68. https://doi.org/10.1007/s11274-025-04285-y
30. Zhang F, Zhu M, Chen Y, Wang G, Yang H, Lu X, Li Y, Chang HM, Wu Y, Ma Y, Yuan S, Zhu W, Dong X, Zhao Y, Yu Y, Wang J, Mu L. Harnessing omics data for drug discovery and development in ovarian aging Hum Reprod Update. 2025 May 1;31(3):240-268. https://doi.org/10.1093/humupd/dmaf002
31. Gong X, Su L, Huang J, Liu J, Wang Q, Luo X, Yang G, Chi H. An overview of multi-omics technologies in rheumatoid arthritis: applications in biomarker and pathway discovery Front Immunol. 2024 Jul 30;15:1381272. https://doi.org/10.3389/fimmu.2024.1381272
32. Luo Y, Zhao C, Chen F. Multiomics Research: Principles and Challenges in Integrated Analysis Biodes Res. 2024 Dec 5;6:0059. https://doi.org/10.34133/bdr.0059.
33. Lin M, Xu F, Sun J, Song J, Shen Y, Lu S, Ding H, Lan L, Chen C, Ma W, Wu X, Song Z, Wang W. Integrative multi-omics analysis unravels the host response landscape and reveals a serum protein panel for early prognosis prediction for ARDS Crit Care. 2024 Jul 2;28(1):213. https://doi.org/10.1186/s13054-024-05000-3
34. Zhang H, Zhou Y, Yu B, Deng Y, Wang Y, Fang S, Song X, Fan X, Zhou H. Multi-Omics Approaches to Discover Biomarkers of Thyroid Eye Disease: A Systematic Review Int J Biol Sci. 2024 Nov 11;20(15):6038-6055. https://doi.org/10.7150/ijbs.103977
35. George NP, Kwon M, Jang YE, Kim SG, Hwang JS, Lee SS, Lee G. Integrative Analysis of Metabolome and Proteome in the Cerebrospinal Fluid of Patients with Multiple System Atrophy Cells. 2025 Feb 12;14(4):265. https://doi.org/10.3390/cells14040265
36. Cominetti O, Dayon L. Unravelling disease complexity: integrative analysis of multi-omic data in clinical research Expert Rev Proteomics. 2025 Apr;22(4):149-162. https://doi.org/10.1080/14789450.2025.2491357
37. Zhang W, Huang H, Wang L, Lehmann BD, Chen SX. An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery bioRxiv [Preprint]. 2025 Mar 6:2025.03.05.641533. https://doi.org/10.1101/2025.03.05.641533
38. Ambikan A, Akusjärvi SS, Sperk M, Neogi U. System-level integrative omics analysis to identify the virus-host immunometabolic footprint during infection Adv Immunol. 2024;164:73-100. https://doi.org/10.1016/bs.ai.2024.08.002
39. Sathyanarayanan A, Mueller TT, Ali Moni M, Schueler K; ECNP TWG Network members; Baune BT, Lio P, Mehta D, Baune BT, Dierssen M, Ebert B, Fabbri C, Fusar-Poli P, Gennarelli M, Harmer C, Howes OD, Janzing JGE, Lio P, Maron E, Mehta D, Minelli A, Nonell L, Pisanu C, Potier MC, Rybakowski F, Serretti A, Squassina A, Stacey D, van Westrhenen R, Xicota L. Multi-omics data integration methods and their applications in psychiatric disorders Eur Neuropsychopharmacol. 2023 Apr;69:26-46. https://doi.org/10.1016/j.euroneuro.2023.01.001
40. Fang S, Chen B, Zhang Y, Sun H, Liu L, Liu S, Li Y, Xu X. Computational Approaches and Challenges in Spatial Transcriptomics Genomics Proteomics Bioinformatics. 2023 Feb;21(1):24-47. https://doi.org/10.1016/j.gpb.2022.10.001
41. Pokhriyall M, Shukla N, Singh TR, Suravajhala P. Proteogenomic Approaches for Diseasome Studies Methods Mol Biol. 2025;2859:253-264. https://doi.org/10.1007/978-1-0716-4152-1_14
42. Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics. 2021 Mar;18(3):221-232. https://doi.org/10.1080/14789450.2021.1914594
43. Binetti M, Lauro A, Vaccari S, Cervellera M, Tonini V. Proteogenomic biomarkers in colorectal cancers: clinical applications Expert Rev Proteomics. 2020 May;17(5):355-363. https://doi.org/10.1080/14789450.2020.1782202
44. Philips TJ, Erickson BK, Thomas SN. Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer. Front. Oncol. 2025 Jan 7;14:1503107. https://doi.org/10.3389/fonc.2024.1503107
45. Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics Mol Cell Proteomics. 2017 Jun;16(6):959-981. https://doi.org/10.1074/mcp.MR117.000024
46. Song YC, Das D, Zhang Y, Chen MX, Fernie AR, Zhu FY, Han J. Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants. Trends Biotechnol. 2023 Dec;41(12):1532-1548. https://doi.org/10.1016/j.tibtech.2023.05.010
47. Nishimura T, Nakamura H, Végvári Á, Marko-Varga G, Furuya N, Saji H. Current status of clinical proteogenomics in lung cancer. Expert Rev Proteomics. 2019 Sep;16(9):761-772. https://doi.org/10.1080/14789450.2019.1654861
48. Rao R, Gulfishan M, Kim MS, Kashyap MK. Deciphering Cancer Complexity: Integrative Proteogenomics and Proteomics Approaches for Biomarker Discovery Methods Mol Biol. 2025;2859:211-237. https://doi.org/10.1007/978-1-0716-4152-1_12
49. Ruggles KV, Fenyö D. Next Generation Sequencing Data and Proteogenomics Adv Exp Med Biol. 2016;926:11-19. https://doi.org/10.1007/978-3-319-42316-6_2
50. Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses Genes (Basel). 2023 Jun 16;14(6):1281. https://doi.org/10.3390/genes14061281
51. Díez P, Fuentes M. Proteogenomics for the Comprehensive Analysis of Human Cellular and Serum Antibody Repertoires Adv Exp Med Biol. 2016;926:153-162. https://doi.org/10.1007/978-3-319-42316-6_10
52. Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):521-45. https://doi.org/10.1146/annurev-anchem-071015-041722
53. Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R. Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine Clin Chim Acta. 2019 Nov;498:38-46. https://doi.org/10.1016/j.cca.2019.08.010
54. Choi S, An JY. Multiomics in cancer biomarker discovery and cancer subtyping. Adv Clin Chem. 2025;124:161-195. https://doi.org/10.1016/bs.acc.2024.10.004
55. Roos A, Thompson R, Horvath R, Lochmüller H, Sickmann A. Intersection of Proteomics and Genomics to "Solve the Unsolved" in Rare Disorders such as Neurodegenerative and Neuromuscular Diseases Proteomics Clin Appl. 2018 Mar;12(2). https://doi.org/10.1002/prca.201700073
56. Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Rev Proteomics. 2019 May;16(5):375-390. https://doi.org/10.1080/14789450.2019.1609944
57. Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteomics. 2017 Aug;14(8):649-663. https://doi.org/10.1080/14789450.2017.1352474
58. Fels U, Gevaert K, Van Damme P. Proteogenomics in Aid of Host-Pathogen Interaction Studies: A Bacterial Perspective Proteomes. 2017 Oct 11;5(4):26. https://doi.org/10.3390/proteomes5040026
59. Subbannayya Y, Pinto SM, Gowda H, Prasad TS. Proteogenomics for understanding oncology: recent advances and future prospects. Expert Rev Proteomics. 2016;13(3):297-308. https://doi.org/10.1586/14789450.2016.1136217
60. Paraskar G, Bhattacharya S, Kuttiappan A. The Role of Proteomics and Genomics in the Development of Colorectal Cancer Diagnostic Tools and Potential New Treatments ACS Pharmacol Transl Sci. 2025 Apr 10;8(5):1227-1250. https://doi.org/10.1021/acsptsci.4c00686
Downloads
Published
Data Availability Statement
All data used for this review are publicly available.
Issue
Section
License
Copyright (c) 2025 Enitan SS, Adejumo EN, Osakue OE, Eke SS, Akele RY, Edafetanure-Ibeh OM, Enitan CB (Author)
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
