Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants

Katie M. O'Brien, Irene Orlow, Cristina R. Antonescu, Karla Ballman, Linda McCall, Ronald DeMatteo, Lawrence S. Engel

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Gastrointestinal stromal tumors (GISTs) are rare but treatable soft tissue sarcomas. Nearly all GISTs have somatic mutations in either the KIT or PDGFRA gene, but there are no known inherited genetic risk factors. We assessed the relationship between KIT/PDGFRA mutations and select deletions or single nucleotide polymorphisms (SNPs) in 279 participants from a clinical trial of adjuvant imatinib mesylate. Given previous evidence that certain susceptibility loci and carcinogens are associated with characteristic mutations, or "signatures" in other cancers, we hypothesized that the characteristic somatic mutations in the KIT and PDGFRA genes in GIST tumors may similarly be mutational signatures that are causally linked to specific mutagens or susceptibility loci. As previous epidemiologic studies suggest environmental risk factors such as dioxin and radiation exposure may be linked to sarcomas, we chose 208 variants in 39 candidate genes related to DNA repair and dioxin metabolism or response. We calculated adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the association between each variant and 7 categories of tumor mutation using logistic regression. We also evaluated gene-level effects using the sequence kernel association test (SKAT). Although none of the association p-values were statistically significant after adjustment for multiple comparisons, SNPs in CYP1B1 were strongly associated with KIT exon 11 codon 557-8 deletions (OR = 1.9, 95% CI: 1.3-2.9 for rs2855658 and OR = 1.8, 95% CI: 1.2-2.7 for rs1056836) and wild type GISTs (OR = 2.7, 95% CI: 1.5-4.8 for rs1800440 and OR = 0.5, 95% CI: 0.3-0.9 for rs1056836). CYP1B1 was also associated with these mutations categories in the SKAT analysis (p = 0.002 and p = 0.003, respectively). Other potential risk variants included GSTM1, RAD23B and ERCC2. This preliminary analysis of inherited genetic risk factors for GIST offers some clues about the disease's genetic origins and provides a starting point for future candidate gene or gene-environment research.

Original languageEnglish (US)
Article numbere62119
JournalPLoS One
Volume8
Issue number4
DOIs
StatePublished - Apr 18 2013

Fingerprint

somatic mutation
Gastrointestinal Stromal Tumors
Tumors
Genes
Odds Ratio
Mutation
neoplasms
odds ratio
Confidence Intervals
confidence interval
Dioxins
mutation
Sarcoma
dioxins
Single Nucleotide Polymorphism
risk factors
genes
Polymorphism
sarcoma
single nucleotide polymorphism

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

O'Brien, K. M., Orlow, I., Antonescu, C. R., Ballman, K., McCall, L., DeMatteo, R., & Engel, L. S. (2013). Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants. PLoS One, 8(4), [e62119]. https://doi.org/10.1371/journal.pone.0062119

Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants. / O'Brien, Katie M.; Orlow, Irene; Antonescu, Cristina R.; Ballman, Karla; McCall, Linda; DeMatteo, Ronald; Engel, Lawrence S.

In: PLoS One, Vol. 8, No. 4, e62119, 18.04.2013.

Research output: Contribution to journalArticle

O'Brien, KM, Orlow, I, Antonescu, CR, Ballman, K, McCall, L, DeMatteo, R & Engel, LS 2013, 'Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants', PLoS One, vol. 8, no. 4, e62119. https://doi.org/10.1371/journal.pone.0062119
O'Brien KM, Orlow I, Antonescu CR, Ballman K, McCall L, DeMatteo R et al. Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants. PLoS One. 2013 Apr 18;8(4). e62119. https://doi.org/10.1371/journal.pone.0062119
O'Brien, Katie M. ; Orlow, Irene ; Antonescu, Cristina R. ; Ballman, Karla ; McCall, Linda ; DeMatteo, Ronald ; Engel, Lawrence S. / Gastrointestinal Stromal Tumors, Somatic Mutations and Candidate Genetic Risk Variants. In: PLoS One. 2013 ; Vol. 8, No. 4.
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