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

Seungyeul Yoo; Zhiao Shi; Bo Wen; SoonJye Kho; Renke Pan; Hanying Feng; Hong Chen; Anders Carlsson; Patrik Edén; Weiping Ma; Michael Raymer; Ezekiel J Maier; Zivana Tezak; Elaine Johanson; Denise Hinton; Henry Rodriguez; Jun Zhu; Emily Boja; Pei Wang; Bing Zhang

doi:10.1016/j.patter.2021.100245

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.

Authors

Seungyeul Yoo^{1

2

3}, Zhiao Shi^{4

5}, Bo Wen^{4

5}, SoonJye Kho⁶, Renke Pan⁷, Hanying Feng⁷, Hong Chen⁷, Anders Carlsson^{8

9}, Patrik Edén⁸, Weiping Ma^{1

2}, Michael Raymer⁶, Ezekiel J Maier¹⁰, Zivana Tezak¹¹, Elaine Johanson¹², Denise Hinton¹³, Henry Rodriguez¹⁴, Jun Zhu^{1

2

3}, Emily Boja¹⁴, Pei Wang^{1

2}, Bing Zhang^{4

5}

Affiliations

¹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
² Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
³ Sema4, a Mount Sinai Venture, Stamford, CT 06902, USA.
⁴ Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.
⁵ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁶ Wright State University, Dayton, OH 45453, USA.
⁷ Sentieon Inc., San Jose, CA 95134, USA.
⁸ Computational Biology & Biological Physics, Lund University, Lund 221-00, Sweden.
⁹ Bionamic AB, Lund 221-00, Sweden.
¹⁰ Booz Allen Hamilton, McLean, VA 22102, USA.
¹¹ Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD 20993, USA.
¹² Office of Health Informatics, Office of the Chief Scientist, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA.
¹³ Office of the Chief Scientist, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD 20993, USA.
¹⁴ Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Abstract

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.