25 years after the completion of The Human Genome Project – advances, challenges and prospects of genomics

Keywords: human genome, post-genomic era, genetic variability, epigenetics, precision medicine, pharmacogenomics

Abstract

Aim. Analysis of the human genome has opened a new era of biomedical research, where the integration of molecular and technological approaches determines the development of healthcare. The aim of this study is to summarize modern advances in genomics 25 years after the completion of the Human Genome Project and to identify key scientific and clinical directions of the postgenomic era. Methods. An analytical review of literature sources, results of genomic, epigenomic and bioinformatic studies, as well as data on their clinical implementation was performed. Results. A transition from descriptive genome research to functional and applied genomics after initial sequencing was demonstrated. The important role of non-coding genomic regions in gene expression regulation, chromatin organization and genetic variability formation was established. The significance of single nucleotide polymorphisms, structural variations and polygenic risk scores in the development of monogenic and multifactorial diseases was characterized. The contribution of pharmacogenomics, tumor genomic profiling, epigenetic mechanisms and genome editing technologies to the development of personalized medicine was highlighted. Special attention was paid to ethical aspects of genetic information use, including privacy and accessibility of genomic technologies. Conclusions. Genomics has transformed from a fundamental discipline into a practical tool of clinical medicine, forming the basis for precision, preventive and predictive medicine.

References

Barker D. J. The fetal and infant origins of adult disease. BMJ. 1990. Vol. 17, 301 (6761). P. 1111. https://doi.org/10.1136/bmj.301.6761.1111.

Doroshow D. B., Doroshow J. H. Genomics and the History of Precision Oncology. Surgical Oncology Clinics. 2020. Vol. 29, No 1. P. 35–49. https://doi.org/10.1016/j.soc.2019.08.003.

Doudna J. A., Charpentier E. The new frontier of genome editing. Science. 2014. Vol. 367 (6483). Р. 1077. https://doi.org/10.1126/science.1258096.

Esteller M. Non-coding RNAs in human disease. Nature Reviews Genetics. 2011. Vol. 12. P. 861–874. https://doi.org/10.1038/nrg3074.

Greely H. T. CRISPR'd babies: human germline genome editing in the 'He Jiankui affair'. Journal Of Law And The Biosciences. 2019. Vol. 6 (1). P. 111–183. https://doi.org/10.1093/jlb/lsz010.

Horvath S. DNA methylation age of human tissues and cell types. Genome Biology. 2013. Vol. 14 (10). P. 115. https://doi.org/10.1186/gb-2013-14-10-r115.

Isakova D. N., Kolomeichuk S. N., Petrova Yu. A., Lyapina M. V., Troshina I. A., Voronin K. A., Petrov I. M. Association of polymorphic variants of TCF7L2 and PPARG genes with metabolic markers in patients with early disorders of carbohydrate metabolism. Bulletin of Experimental Biology and Medicine. 2017. Vol. 163 (6). Р. 759–763. https://doi.org/10.1007/s10517-017-3868-y.

Johnson K. B., Wei W. Q., Weeraratne D., Frisse M. E., Misulis K., Rhee K., Zhao J., Snowdon J. L. Precision Medicine, AI, and the Future of Personalized Health Care. Clinical and Translational Science. 2021. Vol. 14 (1). P. 86–93. https://doi.org/10.1111/cts.12884.

Jones K. M., Cook-Deegan R., Rotimi C. N., Callier S. L., Bentley A. R. The human genome at 20. Science. 2021. Vol. 5, 371 (6529). P. 564–569. https://doi.org/10.1126/science.abg5266.

Jones P. A., Baylin S. B. The fundamental role of epigenetic events in cancer. Nature Reviews Genetics. 2002. Vol. 3 (6). P. 415–428. https://doi.org/10.1038/nrg816.

Lee C. R., Luzum J. A., Sangkuhl K., Gammal R. S., Sabatine M. S., Stein C. M., Kisor D. F., Limdi N. A., Lee Y. M., Scott S. A., Hulot J.-S., Roden D. M., Gaedigk A., Caudle K. E., Klein T. E., Johnson J. A., Shuldiner A. R. Clinical pharmacogenetics implementation consortium guideline for CYP2C19 genotype and clopidogrel therapy. Clinical Pharmacology and Therapeutics. 2022. Vol. 112 (5). P. 959–967. https://doi.org/10.1002/cpt.2526.

Mahajan A., Taliun D., Thurner M., Robertson N. R., Torres J. M., Rayner N. W., Payne A. J., Steinthorsdottir V., Scott R. A., Grarup N., Cook J. P., Schmidt E. M., Wuttke M., Sarnowski C., Mägi R., Nano J., Gieger C., Trompet S., Lecoeur C., Preuss M. H., Prins B. P., Guo X., Bielak L. F., Below J. E., McCarthy M. I. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nature Genetics. 2018. Vol. 50 (11). Р. 1505–1513. https://doi.org/10.1038/s41588-018-0241-6.

Mani S., Lalani S. R., Pammi M. Genomics and multiomics in the age of precision medicine. Pediatric Research. 2025. Vol. 97. P. 1399–1410. https://doi.org/10.1038/s41390-025-04021-0.

Mattick S. J. The Functional genomics of noncoding RNA. Science. 2005. Vol. 309 (5740). P. 1527–1528. https://doi.org/10.1126/science.1117806.

Miga K. H., Koren S., Rhie A., Vollger M. R., Gershman A., Bzikadze A., Brooks S., Howe E., Porubsky D., Logsdon G. A., Schneider V. A., Potapova T., Wood J., Chow W., Armstrong J., Fredrickson J., Pak E., Tigyi K., Kremitzki M., Markovic C., Maduro V., Dutra A., Bouffard G. G., Chang A. M., Hansen N. F., Wilfert A. B., Thibaud-Nissen F., Schmitt A. D., Belton J.-M., Selvaraj S., Dennis M. Y., Soto D. C., Sahasrabudhe R., Kaya G., Quick J., Loman N. J., Holmes N., Loose M., Surti U., Risques R. A., Graves Lindsay T. A., Fulton R., Hall I., Paten B., Howe K., Timp W., Young A., Mullikin J. C., Pevzner P. A., Gerton J. L., Sullivan B. A., Eichler E. E., Phillippy A. M. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020. Vol. 585. P. 79–84. https://doi.org/10.1038/s41586-020-2547-7.

O’Connor O., McVeigh T. P. Increasing use of artificial intelligence in genomic medicine for cancer care- the promise and potential pitfalls. BJC Reports. 2025. Vol. 3. P. 20. https://doi.org/10.1038/s44276-025-00135-4.

Pegoraro G., Misteli T. The central role of chromatin maintenance in aging. Aging. Albany NY. 2009. Vol. 1 (12). P. 1017–1022. https://doi.org/10.18632/aging.100106.

Portillo-Ledesma S., Chung S., Hoffman J., Schlick T. Regulation of chromatin architecture by transcription factor binding. bio-Rxiv. 2024. https://doi.org/10.7554/eLife.91320.

Privacy and Progress in Whole Genome Sequencing. Presidential Commission for the Study of Bioethical Issues. Washington, DC, 2012. 160 p.

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014. Vol. 24, 511 (7510). P. 421–427. https://doi.org/10.1038/nature13595.

Showpnil I. A., Hernandez Gonzalez M. E., Ramadesikan S., Marhabaie M., Daley A., Dublin-Ryan L., Pastore M. T., Gu-rusamy U., Hunter J. M., Stone B. S., Bartholomew D. W., Manickam K., Miller A. R., Wilson R. K., Stottmann R. W., Koboldt D. C. Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes. NPJ Genomic Medicine. 2024. Vol. 9. P. 66. https://doi.org/10.1038/s41525-024-00454-4.

The ENCODE Project Consortium, Moore J. E., Purcaro M. J., Pratt H. E., Epstein C. B., Shoresh N., Adrian J., Kawli T., Davis C. A., Dobin A., Kaul R., Halow J., Van Nostrand E. L., Freese P., Gorkin D. U., Shen Y., He Y., Mackiewicz M., Pauli-Behn F., Williams B. A., Mortazavi A., Keller C. A., Zhang X.-O., Elhajjajy S. I., Huey J., Dickel D. E., Snetkova V., Wei X., Wang X., Rivera-Mulia J. C., Rozowsky J., Zhang J., Chhetri S. B., Zhang J., Victorsen A., White K. P., Visel A., Yeo G. W., Burge C. B., Lécuyer E., Gilbert D. M., Dekker J., Rinn J., Mendenhall E. M., Ecker J. R., Kellis M., Klein R. J., Noble W. S., Kundaje A., Guigó R., Farnham P. J., Cherry J. M., Myers R. M., Ren B., Graveley B. R., Gerstein M. B., Pennacchio L. A., Snyder M. P., Bernstein B. E., Wold B., Hardison R. C., Gingeras T. R., Stamatoyannopoulos J. A., Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020. Vol. 583. P. 699–710. https://doi.org/10.1038/s41586-020-2493-4.

The Human Genome Project. National Human Genome Research Institute. Retrieved from: https://www.genome.gov/human-genome-project.

Tomazou E. M., Meissner A. Epigenetic regulation of pluripotency. Advances in Experimental Medicine and Biology. 2010. Vol. 695. P. 26–40. https://doi.org/10.1007/978-1-4419-7037-4_3.

Waddington C. H. The epigenotype. 1942. International Journal of Epidemiology. 2012. Vol. 41 (1). P. 10–13. https://doi.org/10.1093/ije/dyr184.