Identification of inherited genetic variations influencing prognosis in early-onset breast cancer

Sajjad Rafiq, William Tapper, Andrew Collins, Sofia Khan, Ioannis Politopoulos, Sue Gerty, Carl Blomqvist, Fergus J Couch, Heli Nevanlinna, Jianjun Liu, Diana Eccles

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Abstract

Genome-Wide Association Studies (GWAS) have begun to investigate associations between inherited genetic variations and breast cancer prognosis. Here, we report our findings from a GWAS conducted in 536 patients with early-onset breast cancer aged 40 or less at diagnosis and with a mean follow-up period of 4.1 years (SD = 1.96). Patients were selected from the Prospective Study of Outcomes in Sporadic versus Hereditary breast cancer. A Bonferroni correction for multiple testing determined that a P value of 1.0 × 10 -7 was a statistically significant association signal. Following quality control, we identified 487,496 single nucleotide polymorphisms (SNP) for association tests in stage 1. In stage 2, 35 SNPs with the most significant associations were genotyped in 1,516 independent cases from the same early-onset cohort. In stage 2, 11 SNPs remained associated in the same direction (P ≤ 0.05). Fixed effects meta-analysis models identified one SNP associated at close to genome wide level of significance 556 kb upstream of the ARRDC3 locus [HR=1.61; 95% confidence interval (CI), 1.33-1.96; P=9.5 × 10 -7]. Four further associations at or close to the PBX1, RORα, NTN1, and SYT6 loci also came close to genome-wide significance levels (P = 10-6). In the first ever GWAS for the identification of SNPs associated with prognosis in patients with early-onset breast cancer, we report a SNP upstream of the ARRDC3 locus as potentially associated with prognosis (median follow-up time for genotypes: CC = 4 years, CT = 3 years, and TT = 2.7 years; Wilcoxon rank-sum test CC vs. CT, P=4×10-4 and CT vs. TT, P=0.76). Four further loci may also be associated with prognosis.

Original languageEnglish (US)
Pages (from-to)1883-1891
Number of pages9
JournalCancer Research
Volume73
Issue number6
DOIs
StatePublished - Mar 15 2013

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Single Nucleotide Polymorphism
Breast Neoplasms
Genome-Wide Association Study
Nonparametric Statistics
Genome
Quality Control
Meta-Analysis
Genotype
Prospective Studies
Confidence Intervals

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Rafiq, S., Tapper, W., Collins, A., Khan, S., Politopoulos, I., Gerty, S., ... Eccles, D. (2013). Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. Cancer Research, 73(6), 1883-1891. https://doi.org/10.1158/0008-5472.CAN-12-3377

Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. / Rafiq, Sajjad; Tapper, William; Collins, Andrew; Khan, Sofia; Politopoulos, Ioannis; Gerty, Sue; Blomqvist, Carl; Couch, Fergus J; Nevanlinna, Heli; Liu, Jianjun; Eccles, Diana.

In: Cancer Research, Vol. 73, No. 6, 15.03.2013, p. 1883-1891.

Research output: Contribution to journalArticle

Rafiq, S, Tapper, W, Collins, A, Khan, S, Politopoulos, I, Gerty, S, Blomqvist, C, Couch, FJ, Nevanlinna, H, Liu, J & Eccles, D 2013, 'Identification of inherited genetic variations influencing prognosis in early-onset breast cancer', Cancer Research, vol. 73, no. 6, pp. 1883-1891. https://doi.org/10.1158/0008-5472.CAN-12-3377
Rafiq, Sajjad ; Tapper, William ; Collins, Andrew ; Khan, Sofia ; Politopoulos, Ioannis ; Gerty, Sue ; Blomqvist, Carl ; Couch, Fergus J ; Nevanlinna, Heli ; Liu, Jianjun ; Eccles, Diana. / Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. In: Cancer Research. 2013 ; Vol. 73, No. 6. pp. 1883-1891.
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