A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer

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van den Driest, Lisa and Kelly, Patricia and Marshall, Alan and Johnson, Caroline H. and Lasky-Su, Jessica and Lannigan, Alison and Rattray, Zahra and Rattray, Nicholas J.W. (2024) A gap analysis of UK biobank publications reveals SNPs associated with intrinsic subtypes of breast cancer. Computational and Structural Biotechnology Journal, 23. pp. 2200-2210. ISSN 2001-0370 (https://doi.org/10.1016/j.csbj.2024.05.001)

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Abstract

Breast cancer is a multifaceted disease and a leading cause of cancer morbidity and mortality in females across the globe. In 2020 alone, 2.3 million women were diagnosed and 685,000 died of breast cancer worldwide. With the number of diagnoses projected to increase to 3 million per year by 2040 it is essential that new methods of detection and disease stratification are sought to decrease this global cancer burden. Although significant improvements have been made in breast cancer diagnosis and treatment, the prognosis of breast cancer remains poor in some patient groups (i.e. triple negative breast cancer), necessitating research into better patient stratification, diagnosis and drug discovery. The UK Biobank, a comprehensive biomedical and epidemiological database with a wide variety of multiomics data (genomics, proteomics, metabolomics) offers huge potential to uncover groundbreaking discoveries in breast cancer research leading to improved patient stratification. Combining genomic, proteomic, and metabolic profiles of breast cancer in combination with histological classification, can aid treatment decisions through accurate diagnosis and prognosis prediction of tumor behaviour. Here, we systematically reviewed PubMed publications reporting the analysis of UK Biobank data in breast cancer research. Our analysis of UK Biobank studies in the past five years identified 125 publications, of which 76 focussed on genomic data analysis. Interestingly, only two studies reported the analysis of metabolomics and proteomics data, with none performing multiomics analysis of breast cancer. A meta-analysis of the 76 publications identified 2,870 genetic variants associated with breast cancer across 445 genes. Subtype analysis revealed differential genetic alteration in 13 of the 445 genes and the identification of 59 well-established breast cancer genes. in differential pathways. Pathway interaction analyses illuminated their involvement in general cancer biomolecular pathways (e.g. DNA damage repair, Gene expression). While our meta-analysis only measured genetic differences in breast cancer due to current usage of UK Biobank data, minimal multi-omics analyses have been performed and the potential for harnessing multi-omics strategies within the UK Biobank cohort holds promise for unravelling the biological signatures of distinct breast cancer subtypes further in the future.

ORCID iDs

van den Driest, Lisa ORCID logoORCID: https://orcid.org/0000-0002-6687-5032, Kelly, Patricia, Marshall, Alan, Johnson, Caroline H., Lasky-Su, Jessica, Lannigan, Alison, Rattray, Zahra ORCID logoORCID: https://orcid.org/0000-0002-8371-8549 and Rattray, Nicholas J.W. ORCID logoORCID: https://orcid.org/0000-0002-3528-6905;
CORE (COnnecting REpositories)