Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study.
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2022-01
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Abstract
We present a methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center observational study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545 women. Heterogeneity in these multidimensional data required thorough and non-trivial preprocessing, including scaling by controls and weighting to mitigate data redundancy, while the various data types (continuous and categorical) required novel methodology using a weighted Tanimoto indices approach. Data domains only available on a subset of the cohort were integrated using a semi-supervised clustering approach. Novel contrast criterion for determination of the optimal number of clusters in consensus clustering was introduced and compared with existing criteria. Distinctiveness of the clusters was confirmed by using multiple criteria for cluster quality, and by testing for significantly different variables in pairwise comparisons of the clusters. Cluster dynamics were explored by analyzing longitudinal data at 3- and 12-month follow-up. Five clusters of women with LUTS were identified using the developed methodology. None of the clusters could be characterized by a single symptom, but rather by a distinct combination of symptoms with various levels of severity. Targeted proteomics of serum samples demonstrated that differentially abundant proteins and affected pathways are different across the clusters. The clinical relevance of the identified clusters is discussed and compared with the current conventional approaches to the evaluation of LUTS patients. The rationale and thought process are described for the selection of procedures for data preprocessing, clustering, and cluster evaluation. Suggestions are provided for minimum reporting requirements in publications utilizing clustering methodology with multiple heterogeneous data domains.
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Andreev, Victor P, Margaret E Helmuth, Gang Liu, Abigail R Smith, Robert M Merion, Claire C Yang, Anne P Cameron, J Eric Jelovsek, et al. (2022). Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study. PloS one, 17(6). p. e0268547. 10.1371/journal.pone.0268547 Retrieved from https://hdl.handle.net/10161/27464.
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John E Jelovsek
Dr. Jelovsek is the F. Bayard Carter Distinguished Professor of OBGYN at Duke University and serves as Director of Data Science for Women’s Health. He is Board Certified in OBGYN by the American Board of OBGYN and in Female Pelvic Medicine & Reconstructive Surgery by the American Board of OBGYN and American Board of Urology. He has an active surgical practice in urogynecology based out of Duke Raleigh. He has expertise as a clinician-scientist in developing and evaluating clinical prediction models using traditional biostatistics and machine learning approaches. These “individualized” patient-centered prediction tools aim to improve decision-making regarding the prevention of lower urinary tract symptoms (LUTS) and other pelvic floor disorders after childbirth (PMID:29056536), de novo stress urinary incontinence and other patient-perceived outcomes after pelvic organ prolapse surgery, risk of transfusion during gynecologic surgery, and urinary outcomes after mid-urethral sling surgery (PMID: 26942362). He also has significant expertise in leading trans-disciplinary teams through NIH-funded multi-center research networks and international settings. As alternate-PI for the Cleveland Clinic site in the NICHD Pelvic Floor Disorders Network, he was principal investigator on the CAPABLe trial (PMID: 31320277), one of the largest multi-center trials for fecal incontinence studying anal exercises with biofeedback and loperamide for the treatment of fecal incontinence. He was the principal investigator of the E-OPTIMAL study (PMID: 29677302), describing the long-term follow up sacrospinous ligament fixation compared to uterosacral ligament suspension for apical vaginal prolapse. He was also primary author on research establishing the minimum important clinical difference for commonly used measures of fecal incontinence. Currently, he serves as co-PI in the NIDDK Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) (U01DK097780-05) where he has been involved in studies in the development of Symptoms of Lower Urinary Tract Dysfunction Research Network Symptom Index-29 (LURN SI-29) and LURN SI-10 questionnaires for men and women with LUTS. He is also the site-PI for the PREMIER trial (1R01HD105892): Patient-Centered Outcomes of Sacrocolpopexy versus Uterosacral Ligament Suspension for the Treatment of Uterovaginal Prolapse.
Cindy Louise Amundsen
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- Evaluation of the urinary microbiome as it relates to recurrent urinary tract infections and lower urinary tract symptoms
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