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Development of a Large Colonoscopy-Based Longitudinal Cohort for Integrated Research of Colorectal Cancer: Partners Colonoscopy Cohort

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Abstract

Background and Aims

Conventional adenomas (CAs) and serrated polyps (SPs) are precursors to colorectal cancer (CRC). Understanding metachronous cancer risk is poor due to lack of accurate large-volume datasets. We outline the use of natural language processing (NLP) in forming the Partners Colonoscopy Cohort, an integrated longitudinal cohort of patients undergoing colonoscopies.

Methods

We identified endoscopy quality data from endoscopy reports for colonoscopies performed from 2007 to 2018 in a large integrated healthcare system, Mass General Brigham). Through modification of an established NLP pipeline, we extracted histopathological data (polyp location, histology and dysplasia) from corresponding pathology reports. Pathology and endoscopy data were merged by polyp location using a four-stage algorithm. NLP and merging procedures were validated by manual review of 500 pathology reports.

Results

305,656 colonoscopies in 213,924 patients were identified. After merging, 76,137 patients had matched polyp data for 334,750 polyps. CAs and SPs were present in 86,707 (28.5%) and 55,373 (18.2%) colonoscopies. Among patients with polyps at index screening colonoscopy, 14,931 (33.4%) had follow-up colonoscopy (median 46.4, interquartile range 33.8–62.4 months); 91 (0.2%) and 1127 (2.5%) patients developed metachronous CRC and high-risk polyps (polyps ≥ 10 mm or CAs having high-grade dysplasia/villous/tublovillous histology or SPs with dysplasia). Genetic data were available for 23,787 (31.7%) patients with polyps from the Partners Biobank. The validation study showed a positive predictive value of 100% for polyp histology and locations.

Conclusion

We created the Partners Colonoscopy Cohort providing essential infrastructure for future studies to better understand the natural history of CRC and improve screening and post-polypectomy strategies.

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Acknowledgments

We would like to thank all the gastroenterology and histopathology staff at Partner's Healthcare.

Funding

This work received on external funding.

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Authors and Affiliations

  1. Departments of Epidemiology and Nutrition, Harvard T. H. Chan School of Public Health, 667 Huntington Avenue, Kresge 906A, Boston, MA, 02115, USA

    Mathew Vithayathil, Scott Smith & Mingyang Song

  2. Research Information Science and Computing (RISC), Partners Healthcare, Boston, MA, USA

    Sergey Goryachev

  3. Division of Gastroenterology, Emerson Hospital, Concord, MA, USA

    Jennifer Nayor

  4. Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    Mingyang Song

  5. Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    Mingyang Song

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  1. Mathew Vithayathil
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  4. Jennifer Nayor
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  5. Mingyang Song
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Contributions

All authors contributed to conception and design. MV and MS undertook analysis and interpretation of the data and drafting of the article. SG, JN, MS undertook critical revision of the article.

Corresponding author

Correspondence to Mingyang Song.

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Vithayathil, M., Smith, S., Goryachev, S. et al. Development of a Large Colonoscopy-Based Longitudinal Cohort for Integrated Research of Colorectal Cancer: Partners Colonoscopy Cohort. Dig Dis Sci 67, 473–480 (2022). https://doi.org/10.1007/s10620-021-06882-x

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