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In silico functional pathway annotation of 86 established prostate cancer risk variants

Lenora W M Loo ; Aaron Y W Fong ; Iona Cheng ; Loïc Le Marchand

PloS one, 01 January 2015, Vol.10(2), p.e0117873 [Rivista Peer Reviewed]

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  • Titolo:
    In silico functional pathway annotation of 86 established prostate cancer risk variants
  • Autore: Lenora W M Loo ; Aaron Y W Fong ; Iona Cheng ; Loïc Le Marchand
  • Note di contenuto: Heritability is one of the strongest risk factors of prostate cancer, emphasizing the importance of the genetic contribution towards prostate cancer risk. To date, 86 established prostate cancer risk variants have been identified by genome-wide association studies (GWAS). To determine if these risk variants are located near genes that interact together in biological networks or pathways contributing to prostate cancer initiation or progression, we generated gene sets based on proximity to the 86 prostate cancer risk variants. We took two approaches to generate gene lists. The first strategy included all immediate flanking genes, up- and downstream of the risk variant, regardless of distance from the index variant, and the second strategy included genes closest to the index GWAS marker and to variants in high LD (r2 ≥0.8 in Europeans) with the index variant, within a 100 kb window up- and downstream. Pathway mapping of the two gene sets supported the importance of the androgen...
  • Fa parte di: PloS one, 01 January 2015, Vol.10(2), p.e0117873
  • Soggetti: Sciences (General)
  • Lingua: Inglese
  • Tipo: Articolo
  • Identificativo: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0117873

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