Genomic signature of prognosis for Stage II colorectal cancer from FFPE tissue

A39 We have developed a microarray with specific content that is focused around colorectal cancer, the Colorectal Cancer DSA TM Research Tool. The DSA™ range of tools (patent pending) are the first microarrays based on the transcriptome of an individual disease delivering reliable and relevant information not available on other arrays. Designed to maximise the expression data obtained from the chosen disease setting, these arrays enable Almac Diagnostics to generate significantly more information relevant to the disease of interest than that obtained with generic arrays. These arrays are powered by the Affymetrix Genechip™ system. Using this tool we have developed an accurate prognostic signature using formalin-fixed paraffin-embedded (FFPE) tissues capable of predicting disease recurrence in patients with stage II CRC as the basis for an in vitro diagnostic (IVD) test.
 Primary tumours (FFPE) from 143 patients with stage II CRC were collected from 7 different hospitals, in 3 countries (USA, UK, Ireland). Tumours were from patients treated with surgery alone. Within the study group we defined 2 prognostic cohorts: a “poor prognostic cohort” (n=56) that relapsed within 5 years post surgery and a “good prognostic cohort” (n=87) that were disease free with a minimum of 5 years follow up. Patient samples were randomly divided to generate a training set of 93 and an independent test set of 50 samples. RNA processing and microarray hybridisations were performed using standardised in-house protocols. RNA expression data was analysed using Partial Least Squares (PLS) discriminant analysis to identify transcripts that best discriminate between patients at high risk of relapse versus patients likely to remain disease free, post surgery . Expression profiling based on the 93 FFPE samples in the training set, identified a 91-transcript signature capable of identifying the recurrent population. The ability of the signature to predict recurrence was then evaluated in the independent test set of 50 samples. The overall accuracy was 80%, with a sensitivity of 79%, specificity of 81% and associated positive predictive value (PPV) of 62% and relative risk of 6.7.
 Using our Colorectal Cancer DSA TM research tool we have derived and validated a prognostic signature that accurately stratifies stage II CRC patients according to their risk of recurrence post surgery. Using a 91-transcript signature, we were able to stratify an independent set of stage II colorectal cancer patients to identify a sub-population with an approximately 7-fold higher risk of developing recurrent disease within five years of surgery. This signature will now form the basis for the development of an IVD test using FFPE tissues in stage II CRC.