A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer

Rahaf M. Ahmad, Bassam R. Ali, Fatma Al-Jasmi, Richard O. Sinnott, Noura Al Dhaheri, Mohd Saberi Mohamad

Research output: Contribution to journalReview articlepeer-review

Abstract

Studies continue to uncover contributing risk factors for breast cancer (BC) development including genetic variants. Advances in machine learning and big data generated from genetic sequencing can now be used for predicting BC pathogenicity. However, it is unclear which tool developed for pathogenicity prediction is most suited for predicting the impact and pathogenicity of variant effects. A significant challenge is to determine the most suitable data source for each tool since different tools can yield different prediction results with different data inputs. To this end, this work reviews genetic variant databases and tools used specifically for the prediction of BC pathogenicity. We provide a description of existing genetic variants databases and, where appropriate, the diseases for which they have been established. Through example, we illustrate how they can be used for prediction of BC pathogenicity and discuss their associated advantages and disadvantages. We conclude that the tools that are specialized by training on multiple diverse datasets from different databases for the same disease have enhanced accuracy and specificity and are thereby more helpful to the clinicians in predicting and diagnosing BC as early as possible.

Original languageEnglish
Article numberbbad479
JournalBriefings in Bioinformatics
Volume25
Issue number1
DOIs
Publication statusPublished - Jan 1 2024

Keywords

  • artificial intelligence
  • breast cancer
  • data science
  • genetic variants database
  • machine learning
  • pathogenicity prediction

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

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