We have performed a small replication study focusing on PRCA cases from high-risk PRCA pedigrees in Utah. At a nominal significance level, our study confirms the associations previously found for rs10993994 and rs5945619 at chromosomes 10q11 and Xp11 (p=0.022 and p=0.035, respectively) (7
). For three other SNPs, rs2660753, rs6465657 and rs7931342, our MAF and risk estimates, although not significant, were also consistent with that previously suggested. Risk estimates for rs10993994 and rs5945619 remained similar when PRCA cases were restricted to only those with aggressive disease. For familial, early onset disease, a study-wide significant association was identified for rs10993994 (p<0.0001).
Due to our ability to analyze pedigree-based samples using Genie (10
), we were able to incorporate into our association study existing genotype data from two very large pedigrees. A benefit of this is the ability to follow the segregation of associated variants through the pedigrees. For rs10993994, we investigated the existence of a shared genomic segment IBD in the early-onset PRCA cases of two large pedigrees, but found no evidence of such. This is, perhaps, the expected outcome for common, moderate risk variants.
It is of note that of the seven variants identified by Eeles et al (7
), each of the two that we are able to replicate here (rs10993994 and rs5945619) were independently identified as best findings in other recent genome-wide studies (13
). Variant rs5945572, approximately 12kb p-ter and in strong linkage disequilibrium with rs5945619 (r2
of 0.91), was the most significant finding on the X chromosome in a GWA analysis of Icelanders (14
). Variant rs10993994 was the most significant finding in both the Eeles et al (7
) and the Thomas et al (13
) GWA studies, with an estimated effect size second in magnitude only to those found at 8q24 in both.
Lines of evidence, including from our study, are beginning to appear to suggest that enriching for familial disease and early age at diagnosis may increase power to detect the association for rs10993994. Our result was highly significant (p<0.0001) for familial, early onset disease (diagnosis ≤65 years), with a per allele OR=2.20 (95% CI 1.48–3.27), compared to OR=1.42 (95% CI 1.05–1.90) for familial PRCA only. This is consistent with what has previously been observed. The GWA phase of the Eeles et al (7
) study (stage 1) focused on PRCA cases with either a family history or early onset. The risk estimate for stage 1 was a per allele OR of 1.62 (95% CI 1.47–1.78). The stage 2 population-based sample estimated the same risk to be 1.25 (95% CI 1.17–1.34). Supplemental material from Eeles et al (7
) showed that when stage 2 was stratified by age at diagnosis, a linear trend was observed with the highest risk for rs10993994 exhibited in the earliest cohort 1.36 (95%CI 1.18–1.57 for diagnosis<55 years) and lowest in the oldest cohort 1.17 (95% CI 1.04–1.31, for diagnosis≥70 years), although the trend was not statistically significant. In the GWA study of Thomas et al (13
), PRCA cases were not selected for family history, and the risk estimate was a heterozygous OR=1.24 (95% CI 1.10–1.39). Our higher risk estimates for familial and early onset PRCA suggest that the higher risk estimates also observed for the phase 1 Eeles et al (7
) study are due to the PRCA characteristics that were enriched for (family history and early onset), rather than an initial over-estimate of the risk size.
While the value of this study is the strong familial nature of the cases, the clear limitation is the limited sample size and low power for several of the SNPs studied. It is of note that the two SNPs replicated with nominal evidence were those with the most power (both ≥90%). The negative results for other SNPs should be considered in light of the more limited power for analyses at those loci.
In conclusion, in a small case-control sample containing PRCA cases from Utah high-risk pedigrees, we have significantly replicated variants rs10993994 (10q11) and rs5945619 (Xp11). In particular, it appears that the susceptibility locus at 10q11 maybe involved in familial, early onset disease.