Abstract LB-196: Sequencing symptom control: Results from the Alliance N08C1 and N08CA genetics of chemotherapy neuropathy trials.
Authors: Beutler Andreas S. , Kulkarni Amit , Kanwar Rahul , Qin Rui , Cunningham Julie M. , Therneau Terry M. , Loprinzi Charles L. 
Published: August 2014

Abstract
Introduction: Symptom control is an important objective in the care of patients with cancer and a critical goal for long-term survivors of antineoplastic treatments. Commonly used chemotherapies, including paclitaxel, are associated with a toxic effect on the peripheral nervous system in a substantial fraction of patients, termed chemotherapy induced peripheral neuropathy (CIPN), that is often debilitating. CIPN cannot be predicted from clinical parameters in neurologically normal subjects, suggesting a genetic basis as the root cause. Patients with hereditary neuropathy (HN) due to one of ~50 recognized genes are prone to developing severe CIPN even if the hereditary predisposition is clinically silent.
Assessment of CIPN has usually been an afterthought of cancer treatment studies using crude symptom measurement instruments. N08C1 and N08CA are recent clinical trials_the latter analyzed only in early 2013_focusing on extensive phenotyping by patient reported outcomes (PRO) to support genetic investigations of paclitaxel-related CIPN. Massively parallel (“nextgen”) DNA sequencing is the genetic technology of choice and represents an as-yet unrealized potential to study cancer symptom control.
Methods: Exome sequencing_analysis of 20,794 genes at nucleotide resolution_was performed on blood of CIPN cases (n=73) and controls (n=46) from N08C1. The primary endpoint was the association of HN genes with CIPN. Bioinformatic analysis determined SNV and other genetic variations across 6.2x107 nucleotides. The association of genes with CIPN was statistically examined by the over-dispersion test C-alpha. The role of singleton SNV was assessed by a burden test. N08CA served as validation.
Results: 386,644 SNV were detected with an estimated sensitivity of 90% and specificity of 99.9%; the orthogonal validation rate (PCR of &gt;1000 genotypes) was 99.7%. The association of the minor allele (C&gt;T) at rs7349683 in the gene EPHA5, previously reported by Baldwin et al. (2012) for CALGB40101, was confirmed in N08C1.
Two hereditary neuropathy genes were identified as new CIPN candidate genes:
Firstly, ARHGEF10 was highly significant with p=5x10-4 based on single gene testing and p&lt;0.02 after Bonferroni correction for multiple testing of 41 hereditary neuropathy genes with non-synonymous SNV. Three SNV were predictive, rs17683288, rs2294039 and rs9657362, the latter with an odds ratio (OR)=3.62. Validation in an independent patient group (n=75) from another paclitaxel CIPN trial, N08CA, confirmed the impact of ARHGEF10 on CIPN (p&lt;0.025; rs9657362 OR=2.51).
Secondly, peraxin (PRX) was disrupted by non-synonymous singleton SNV in n=8 cases and n=0 controls (OR=6.4; unadjusted p=0.04). 7 of the 8 mutations were also scored as deleterious by both Polyphen 2 and SIFT. Because PRX SNV were non-recurrent validation was performed in N08C1 by Sanger sequencing. Several neuro-genes across the exome were noted as additional CIPN gene candidates.
Conclusions: ARHGEF10 and PRX associations with CIPN suggest that CIPN and HN might share genetic roots in a subset of patients. Construct validity of N08C1 is supported by confirmation of a published result from CALGB40101 relating EPHA5 to CIPN. Germline exome sequencing in cancer patients is highly informative for understanding complex pharmacogenomic traits including outcomes in symptom control research.
Citation Format: Andreas S. Beutler, Amit Kulkarni, Rahul Kanwar, Rui Qin, Julie M. Cunningham, Terry M. Therneau, Charles L. Loprinzi. Sequencing symptom control: Results from the Alliance N08C1 and N08CA genetics of chemotherapy neuropathy trials. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-196. doi:10.1158/1538-7445.AM2013-LB-196