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Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer by Héctor Climente-González; Christine Lonjou; Fabienne Lesueur; Dominique Stoppa-Lyonnet; Nadine Andrieu; Chloé-Agathe Azencott; GENESIS study group is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer about?
Genome-wide association studies (GWAS) explore the genetic causes of complex diseases. However, classical approaches ignore the biological context of the genetic variants and genes under study. To address this shortcoming, one can use biological networks, which model functional relationships, to search for functionally related susceptibility loci. Many such network methods exist, each arising from different mathematical frameworks, pre-processing steps, and assumptions about the network properties of the susceptibility mechanism. Unsurprisingly, this results in disparate solutions. To explore how to exploit these heterogeneous approaches, we selected six network methods and applied them to GENESIS, a nationwide French study on familial breast cancer. First, we verified that network methods recovered more interpretable results than a standard GWAS. We addressed the heterogeneity of their solutions by studying their overlap, computing what we called the __consensus__. The key gene in this consensus solution was __COPS5__, a gene related to multiple cancer hallmarks. Another issue we observed was that network methods were unstable, selecting very different genes on different subsample
Who reads Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Héctor Climente-González; Christine Lonjou; Fabienne Lesueur; Dominique Stoppa-Lyonnet; Nadine Andrieu; Chloé-Agathe Azencott; GENESIS study group
- Publisher
- Public Library of Science (PLoS)
- Published
- 2021
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)