1
|
Sherman MS, Challa PK, Przybyszewski EM, Wilechansky RM, Uche-Anya EN, Ott AT, McGoldrick J, Goessling W, Khalili H, Simon TG. A natural language processing algorithm accurately classifies steatotic liver disease pathology to estimate the risk of cirrhosis. Hepatol Commun 2024; 8:e0403. [PMID: 38551386 PMCID: PMC10984665 DOI: 10.1097/hc9.0000000000000403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/14/2023] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Histopathology remains the gold standard for diagnosing and staging metabolic dysfunction-associated steatotic liver disease (MASLD). The feasibility of studying MASLD progression in electronic medical records based on histological features is limited by the free-text nature of pathology reports. Here we introduce a natural language processing (NLP) algorithm to automatically score MASLD histology features. METHODS From the Mass General Brigham health care system electronic medical record, we identified all patients (1987-2021) with steatosis on index liver biopsy after excluding excess alcohol use and other etiologies of liver disease. An NLP algorithm was constructed in Python to detect steatosis, lobular inflammation, ballooning, and fibrosis stage from pathology free-text and manually validated in >1200 pathology reports. Patients were followed from the index biopsy to incident decompensated liver disease accounting for covariates. RESULTS The NLP algorithm demonstrated positive and negative predictive values from 93.5% to 100% for all histologic concepts. Among 3134 patients with biopsy-confirmed MASLD followed for 20,604 person-years, rates of the composite endpoint increased monotonically with worsening index fibrosis stage (p for linear trend <0.005). Compared to simple steatosis (incidence rate, 15.06/1000 person-years), the multivariable-adjusted HRs for cirrhosis were 1.04 (0.72-1.5) for metabolic dysfunction-associated steatohepatitis (MASH)/F0, 1.19 (0.92-1.54) for MASH/F1, 1.89 (1.41-2.52) for MASH/F2, and 4.21 (3.26-5.43) for MASH/F3. CONCLUSIONS The NLP algorithm accurately scores histological features of MASLD from pathology free-text. This algorithm enabled the construction of a large and high-quality MASLD cohort across a multihospital health care system and disclosed an accelerating risk for cirrhosis based on the index MASLD fibrosis stage.
Collapse
Affiliation(s)
- Marc S. Sherman
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Brigham Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Prasanna K. Challa
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric M. Przybyszewski
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert M. Wilechansky
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eugenia N. Uche-Anya
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ashley T. Ott
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Jessica McGoldrick
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wolfram Goessling
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Brigham Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hamed Khalili
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tracey G. Simon
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Uche-Anya EN, Gerke S, Berzin TM. Video Endoscopy as Big Data: Balancing Privacy and Progress in Gastroenterology. Am J Gastroenterol 2024; 119:600-605. [PMID: 37975601 PMCID: PMC10984632 DOI: 10.14309/ajg.0000000000002597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Eugenia N. Uche-Anya
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Gerke
- Pennsylvania State Dickinson Law, Pennsylvania State University, Carlisle, Pennsylvania, USA;
| | - Tyler M. Berzin
- Center for Advanced Endoscopy, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
3
|
Uche-Anya EN, Green PHR, Genta RM, Lebwohl B. Regional Patterns of Olmesartan Prescription and the Prevalence of Duodenal Villous Atrophy Throughout the United States. Clin Gastroenterol Hepatol 2018; 16:584-585. [PMID: 28993259 DOI: 10.1016/j.cgh.2017.09.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Eugenia N Uche-Anya
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Peter H R Green
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Robert M Genta
- Miraca Life Sciences Research Institute, Irving, Texas; Baylor College of Medicine, Houston, Texas
| | - Benjamin Lebwohl
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, New York; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York.
| |
Collapse
|
4
|
Uche-Anya EN, Packey CD, Khan AS, Sethi A. EUS-Guided Pancreatic Duct Puncture for Difficult Cannulation of Stenosed Pancreaticojejunostomy. Dig Dis Sci 2018; 63:268-269. [PMID: 29204744 DOI: 10.1007/s10620-017-4858-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/18/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Eugenia N Uche-Anya
- College of Physicians and Surgeons, Columbia University, New York City, NY, USA.
| | - Christopher D Packey
- Digestive and Liver Disease, New York Presbyterian, Columbia University Medical Center, New York City, NY, USA
| | - Ali S Khan
- Digestive and Liver Disease, New York Presbyterian, Columbia University Medical Center, New York City, NY, USA
| | - Amrita Sethi
- Digestive and Liver Disease, New York Presbyterian, Columbia University Medical Center, New York City, NY, USA
| |
Collapse
|
5
|
Uche-Anya EN, Khan AS, Packey CD, Sung D, Sethi A. Gastric pancreatic heterotopia with pancreatic intraepithelial neoplasia. Gastrointest Endosc 2017; 85:1098-1100. [PMID: 27354101 DOI: 10.1016/j.gie.2016.06.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 06/18/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Eugenia N Uche-Anya
- Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Ali S Khan
- Digestive and Liver Disease, New York Presbyterian - Columbia University Medical Center, New York, New York, USA
| | - Christopher D Packey
- Digestive and Liver Disease, New York Presbyterian - Columbia University Medical Center, New York, New York, USA
| | - Diana Sung
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Amrita Sethi
- Digestive and Liver Disease, New York Presbyterian - Columbia University Medical Center, New York, New York, USA
| |
Collapse
|