title: Identification of genetic markers with synergistic survival effect in cancer.
abstract: BACKGROUND
  Cancers are complex diseases arising from accumulated genetic mutations that disrupt intracellular signaling networks. While several predisposing genetic mutations have been found, these individual mutations account only for a small fraction of cancer incidence and mortality. With large-scale measurement technologies, such as single nucleotide polymorphism (SNP) microarrays, it is now possible to identify combinatorial effects that have significant impact on cancer patient survival.
  
  
  RESULTS
  The identification of synergetic functioning SNPs on genome-scale is a computationally daunting task and requires advanced algorithms. We introduce a novel algorithm, Geninter, to identify SNPs that have synergetic effect on survival of cancer patients. Using a large breast cancer cohort we generate a simulator that allows assessing reliability and accuracy of Geninter and logrank test, which is a standard statistical method to integrate genetic and survival data.
  
  
  CONCLUSIONS
  Our results show that Geninter outperforms the logrank test and is able to identify SNP-pairs with synergetic impact on survival.
authors.forename: Riku
authors.initials: R
authors.lastname: Louhimo
authors.forename: Marko
authors.initials: M
authors.lastname: Laakso
authors.forename: Tuomas
authors.initials: T
authors.lastname: Heikkinen
authors.forename: Susanna
authors.initials: S
authors.lastname: Laitinen
authors.forename: Pekka
authors.initials: P
authors.lastname: Manninen
authors.forename: Vladimir
authors.initials: V
authors.lastname: Rogojin
authors.forename: Minna
authors.initials: M
authors.lastname: Miettinen
authors.forename: Carl
authors.initials: C
authors.lastname: Blomqvist
authors.forename: Jianjun
authors.initials: J
authors.lastname: Liu
authors.forename: Heli
authors.initials: H
authors.lastname: Nevanlinna
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000401:mortality; D003198:Computer Simulation; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers