A community effort to identify and correct mislabeled samples in proteogenomic studies

Patterns (N Y). 2021 May 7;2(5):100245. doi: 10.1016/j.patter.2021.100245. eCollection 2021 May 14.


Sample mislabeling or misannotation has been a long-standing problem in scientific research, particularly prevalent in large-scale, multi-omic studies due to the complexity of multi-omic workflows. There exists an urgent need for implementing quality controls to automatically screen for and correct sample mislabels or misannotations in multi-omic studies. Here, we describe a crowdsourced precisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge, which provides a framework for systematic benchmarking and evaluation of mislabel identification and correction methods for integrative proteogenomic studies. The challenge received a large number of submissions from domestic and international data scientists, with highly variable performance observed across the submitted methods. Post-challenge collaboration between the top-performing teams and the challenge organizers has created an open-source software, COSMO, with demonstrated high accuracy and robustness in mislabeling identification and correction in simulated and real multi-omic datasets.

Keywords: DSML 3: Development/Pre-production: Data science output has been rolled out/validated across multiple domains/problems.