Discovery Analysis of TCGA Data Reveals Association between Germline Genotype and Survival in Ovarian Cancer Patients

<div><p>Background</p><p>Ovarian cancer remains a significant public health burden, with the highest mortality rate of all the gynecological cancers. This is attributable to the late stage at which the majority of ovarian cancers are diagnosed, coupled with the low and variable response of advanced tumors to standard chemotherapies. To date, clinically useful predictors of treatment response remain lacking. Identifying the genetic determinants of ovarian cancer survival and treatment response is crucial to the development of prognostic biomarkers and personalized therapies that may improve outcomes for the late-stage patients who comprise the majority of cases.</p> <p>Methods</p><p>To identify constitutional genetic variations contributing to ovarian cancer mortality, we systematically investigated associations between germline polymorphisms and ovarian cancer survival using data from The Cancer Genome Atlas Project (TCGA). Using stage-stratified Cox proportional hazards regression, we examined 650,000 SNP loci for association with survival. We additionally examined whether the association of significant SNPs with survival was modified by somatic alterations.</p> <p>Results</p><p>Germline polymorphisms at rs4934282 (AGAP11/C10orf116) and rs1857623 (DNAH14) were associated with stage-adjusted survival ( = 1.12e-07 and 1.80e-07, FDR  = 1.2e-04 and 2.4e-04, respectively). A third SNP, rs4869 (C10orf116), was additionally identified as significant in the exome sequencing data; it is in near-perfect LD with rs4934282. The associations with survival remained significant when somatic alterations.</p> <p>Conclusions</p><p>Discovery analysis of TCGA data reveals germline genetic variations that may play a role in ovarian cancer survival even among late-stage cases. The significant loci are located near genes previously reported as having a possible relationship to platinum and taxol response. Because the variant alleles at the significant loci are common (frequencies for rs4934282 A/C alleles = 0.54/0.46, respectively; rs1857623 A/G alleles = 0.55/0.45, respectively) and germline variants can be assayed noninvasively, our findings provide potential targets for further exploration as prognostic biomarkers and individualized therapies.</p> </div

Stage and age at diagnosis, organized by 5-year survival.

<p>Stage and age at diagnosis of samples, organized by 5-year survival. Median age is reported, with the first and third quartiles given in parentheses. values for the univariate association between stage and survival and age and survival (logrank test) are also given.</p

Survival of stage-III ovarian cancer patients by rs4934282 genotype.

<p>Kaplan-Meier survival plots for Stage III patients, stratified by germline genotype at rs4934282 (AGAP11): AA, black; AC, blue; CC, red. Confidence intervals are shown as a shaded region around each Kaplan-Meier curve. Censored observations are denoted with vertical ticks. The dashed horizontal and vertical lines mark 50% survival and five years (1825 days) respectively.</p

Stage-adjusted survival.

<p>Significant survival associations after stratification by stage; rs4934282 and rs1857623 are from SNP6 data, rs4869 is from exome/capture data (29 SNPs tested). All tests of Schoefeld residuals had , meeting the proportional hazards assumption.</p

Genomic region surrounding rs1857623.

<p>Image from <a href="http://cgwb.nci.nih.gov" target="_blank">cgwb.nci.nih.gov</a> of selected tracks for genome build NCBI36 (hg18) for the region surrounding a germline variation associated with survival in ovarian cancer upstream of DNAH14 on chromosome 1. The tracks are a custom track showing the SNP rs1857623, RefSeq gene, mRNA, spliced ESTs and mapability.</p

Genomic region containing rs4934282 and rs4869.

<p>Detailed description of the genomic region of chromosome 10 containing rs4934282 (second SNP from the right) and rs4869 (shown in green). Note the overlap between AGAP11 and C10orf116.</p

Survival of stage-III ovarian cancer patients by rs1857623 genotype.

<p>Kaplan-Meier survival plots for Stage III patients, stratified by germline genotype at rs1857623 (DNAH14): AA, black; AG, blue; GG, red. Confidence intervals are shown as a shaded region around each Kaplan-Meier curve. Censored observations are denoted with vertical ticks. The dashed horizontal and vertical lines mark 50% survival and five years (1825 days) respectively.</p

QQ plots.

<p>Quantile-quantile plot for observed values for the likelihood ratio tests of the stage-adjusted Cox models versus the expected distribution of values under independent null hypotheses. Points above the line indicate values that are more significant than expected; a large systematic deviation from this line would be indicative of population substructure driving the results. The two SNPs identified as significant, rs4934282 and rs1857623, lie well above the line and outside the small systematic deviation.</p

SIFT and logRE predictions for missense SNPs.

<p>SIFT and logRE predictions for missense SNPs. Shown are the location, gene, and RefSeq IDs for the SNPs, the nucleotide (NT) and amino acid (AA) substitutions, and the SIFT and logRE scores and predictions. SIFT scores are classified into predictions as follows: 0.00—0.05, probably damaging; 0.051—0.10, possibly damaging; 0.101—0.20, borderline; 0.201—1.00, neutral. logRE scores are classified into predictions as follows: 1—up, probably damaging; 0.7—0.99, possibly damaging; 0.5—0.69, borderline; 0.0—0.49, neutral.</p