Abstract 95P
Background
Early detection of colorectal cancer (CRC) can drastically improve survival odds, reduce treatment complexity and side effects, and improve patient quality of life. In this study we develop and evaluate an assay that uses 1 mL of serum for detection of CRC using orphan noncoding RNAs (oncRNAs) across different cancer stages.
Methods
To mitigate dataset biases, we analyzed CRC and tumor-adjacent normal smRNA-seq data from The Cancer Genome Atlas (TCGA; 619 CRC tumor samples and 679 tumor-adjacent normal samples from all TCGA cancer types) and filtered against an independent, non-cancer, smRNA-seq serum dataset (31 samples) to identify 54,330 oncRNAs. By definition, oncRNAs are expressed in tumors and have negligible expression in normal tissues. To evaluate the diagnostic utility of oncRNAs in serum, we generated smRNA-seq data from an independent cohort consisting of 96 clinically-diagnosed CRC cases (average age: 53.8 years; 50% female), uniformly covering all four stages (24 each), and 95 age-matched individuals (average age: 53.1 years; 47.4% female) with no known history of cancer and independent of the data used to filter. After RNA isolation from frozen serum samples, prepared libraries were sequenced at an average depth of 18.6 million 50 bp single-end reads per sample.
Results
Of the 54,330 TCGA oncRNAs, 32,842 (60.4%) were observed in this study cohort. The sequencing depth-normalized oncRNA content was significantly higher in cancer samples (one-sided Mann-Whitney U test, P=5.8e-9) and was a good predictor of cancer status (AUC=0.83; 95% Confidence Interval [CI]: 0.77–0.89). We then trained an ensemble of 5 logistic regression models in a 5-fold cross-validation setup. In this analysis we used only oncRNAs observed in more than 5% of samples (4,527 oncRNAs), which achieved an AUC of 0.94 (0.91–0.97). At 90% specificity, the model achieved sensitivities of 0.82 (0.67–0.95) and 0.80 (0.63–0.93) for CRC stages I/II and III/IV, respectively.
Conclusions
These results indicate that oncRNAs detected in 1 mL of serum can be used for accurate, early detection of CRC. Moreover, this assay requires fewer than 20 million 50 bp single-end reads, a practical advantage for an NGS-based diagnostic assay.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
Exai Bio Inc.
Funding
Exai Bio Inc.
Disclosure
H. Goodarzi: Financial Interests, Personal, Advisory Role: Exai Bio Inc. J. Wang: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc. O.I. Afolabi: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc. L. Fish: Financial Interests, Personal, Full or part-time Employment, Full time employee: Exai Bio Inc.; Financial Interests, Personal, Stocks/Shares, Stock options from Exai Bio Inc. H. Li: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc. K. Chau: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc. P. Arensdorf: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc. F. Hormozdiari: Financial Interests, Personal, Other, Consultant: Exai Bio Inc. B. Alipanahi: Financial Interests, Personal, Full or part-time Employment: Exai Bio Inc.