Exome sequencing of extreme phenotypes to identify variants predictive of response to chemotherapy in bladder cancer.

Abstract

300 Background: Little is known about germline variants predictive of response to chemotherapy in bladder cancer (BC). We investigated germline variants in patients (pts) treated with neoadjuvant gemcitabine/cisplatin (GC) under the hypothesis that responders and non-responders may differ in rare alleles predictive of treatment outcome. Methods: The Hiseq platform (≥ 20x coverage) was used to sequence the exomes of muscle-invasive (≥cT2) BC pts representing “extreme phenotypes” defined by response to neoadjuvant GC (complete responders vs. non responders). Responders were pT0N0 at cystectomy and remained disease free >1 year. Non-responders had residual disease in the bladder at cystectomy and metastatic disease either at cystectomy or within 1 year. Rare, potentially deleterious single nucleotide variants (SNVs) unique to these phenotypes were confirmed with Sequenom and validated in an independent group of BC pts treated with GC in the neoadjuvant or first line setting. One-sided Fisher’s exact test and multivariate logistic regression were used to estimate association between SNVs and response. Results: The discovery cohort had 6 responders (4 male) with a mean age of 62 and 9 non-responders (6 male) with a mean age of 63. Filtered exome sequences identified 93 rare/potentially deleterious SNVs unique to non-responders and 45 unique to responders of which 84 and 35 were confirmed by Sequenom, respectively. The independent validation cohort consisted of 173 pts, mean age 60, 72% male, and 53% responders (complete or partial). Among 119 SNVs genotyped in this cohort, only 3 responder and 9 non-responder SNVs were identified in ≥ 3 pts. None of the responder SNVs were associated with response. One non-responder SNV (rs150721903) was significantly associated with resistance to GC (OR: 9.7, 90% CI: 1.7-56.8, p=0.011), and remained significant after adjusting for risk score (p= 0.017). rs150721903 is a missense variant in an uncharacterized protein on chromosome 8. Conclusions: Exome sequencing of extreme phenotypes identified a variant that predicts resistance to GC, demonstrating the feasibility of this pharmacogenomics approach. Further evaluation of this SNV is warranted.