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JCO Clinical Cancer Informatics
Article . 2019 . Peer-reviewed
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Validation of a Semiautomated Natural Language Processing–Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance

Authors: Zhengyi, Deng; Kanhua, Yin; Yujia, Bao; Victor Diego, Armengol; Cathy, Wang; Ankur, Tiwari; Regina, Barzilay; +3 Authors

Validation of a Semiautomated Natural Language Processing–Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance

Abstract

PURPOSE Quantifying the risk of cancer associated with pathogenic mutations in germline cancer susceptibility genes—that is, penetrance—enables the personalization of preventive management strategies. Conducting a meta-analysis is the best way to obtain robust risk estimates. We have previously developed a natural language processing (NLP) –based abstract classifier which classifies abstracts as relevant to penetrance, prevalence of mutations, both, or neither. In this work, we evaluate the performance of this NLP-based procedure. MATERIALS AND METHODS We compared the semiautomated NLP-based procedure, which involves automated abstract classification and text mining, followed by human review of identified studies, with the traditional procedure that requires human review of all studies. Ten high-quality gene–cancer penetrance meta-analyses spanning 16 gene–cancer associations were used as the gold standard by which to evaluate the performance of our procedure. For each meta-analysis, we evaluated the number of abstracts that required human review (workload) and the ability to identify the studies that were included by the authors in their quantitative analysis (coverage). RESULTS Compared with the traditional procedure, the semiautomated NLP-based procedure led to a lower workload across all 10 meta-analyses, with an overall 84% reduction (2,774 abstracts v 16,941 abstracts) in the amount of human review required. Overall coverage was 93%—we are able to identify 132 of 142 studies—before reviewing references of identified studies. Reasons for the 10 missed studies included blank and poorly written abstracts. After reviewing references, nine of the previously missed studies were identified and coverage improved to 99% (141 of 142 studies). CONCLUSION We demonstrated that an NLP-based procedure can significantly reduce the review workload without compromising the ability to identify relevant studies. NLP algorithms have promising potential for reducing human efforts in the literature review process.

Keywords

Neoplasms, Biomarkers, Tumor, Computational Biology, Humans, Reproducibility of Results, Genetic Predisposition to Disease, Penetrance, Algorithms, Natural Language Processing, Workflow

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
24
Top 10%
Top 10%
Top 10%
bronze