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Phenotype Submission - Endometriosis

Cohort Definition Name: Endometriosis

Contributor Names: Molle McKillop / Noémie Elhadad

Clinical Description: (Taken from McKillop’s dissertation)

Condition: Endometriosis

Overview

Endometriosis is a complex, enigmatic, chronic disease in which endometrial-like cells grow outside the uterus [Vercellini et al., 2014]. These cells are usually found in the pelvic region, but can become established in more distant tissue like the lungs, diaphragm, and intestines. During the menstrual cycle, the ectopic endometrial-like tissue bleeds into places from which the menstrual fluid cannot escape, causing the formation of adhesions and cysts [Hao et al., 2009]. The disease is estimated to impact approximately 10% of women in reproductive age, with estimates between 5% and 15% [Wheeler 1989, Cramer and Missmer 2002, Damewood et al., 1997]. The prevalence of endometriosis is hard to estimate given a lack of biomarkers for the disease and the need for laparoscopic surgery for diagnosis [Ahn et al., 2017].

Synonyms

Adenomyosis [essentially endometriosis of the uterine muscle]

Presentation

Diagnostic guidelines describe symptoms of endometriosis as pelvic pain and infertility [Armstrong 2011, Riazi et al., 2015]. However the literature documents other prevalent symptoms which include but are not limited to severe menstrual pain, pain with sexual intercourse, chronic pain, constipation, and bloating [Khazali 2016]. Because of the symptomatic variation and non-specific symptoms, diagnosing endometriosis is challenging and often incidental [Dunselman et al., 2014].

Diagnostic Evaluation

Doctors will ask to ascertain the location of the pain and when it occurs, and will likely perform a pelvic exam to palpitate and source pain. Additional diagnostic measurements may involve an ultrasound to identify cysts associated with endometriosis, employ magnetic resonance imaging to find endometrial implants, or include laparoscopic surgery to identify and biopsy tissue.

Differential Diagnoses

Differential diagnoses include appendicitis, chlamydia, a urinary tract infection and cystitis, diverticulitis, an ectopic pregnancy, gonorrhea, ovarian cysts, ovarian torsion, or pelvic inflammatory disease. [MedScape, Endometrial Differential Diagnoses]

Treatment Plan

  • Pain medication (NSAIDs, ibuprofen, naproxen sodium) to ease painful menstrual cramps
  • Hormone therapy, which may slow endometrial tissue growth and prevent new implants
  • Surgery (laparoscopic to remove endometrial tissue, or hysterectomy)

Prognosis

Because endometriosis is idiopathic (i.e. no known cause) and not entirely preventable, the short-term prognosis for endometriosis is mainly for the patient and clinical team to identify ways to alleviate painful symptoms and reduce additional risks. Over the long-term, endometriosis is one of the most common conditions linked to female infertility (e.g. the American Society for Reproductive Medicine found that 24-50% of infertile women have endometriosis), although doctors don’t know exactly how endometriosis might affect fertility. Endometrial tissue may grow back, and symptoms may return even after surgery. Schedule regular check-ups with a doctor to look for signs of endometrial tissue growth or recurrence. [Edited from the Hopkins Medicine description of endometriosis]

Exclusions

Other suspected conditions that should be considered when evaluating a patient with suspected endometriosis include dysmenorrhea, pelvic adhesions, serositis, functional or neoplastic ovarian cyst, uterine malformation, adenomyosis, colon cancer, or ovarian cancer. In particular, endometriosis should be considered in women with chronic pelvic pain who do not respond to standard NSAIDs or oral contraceptive therapy (in contrast to primary dysmenorrhea). [MedScape, Endometriosis Differential Diagnoses]

Ambiguity

Endometrial cancer or neoplasm, endometrial hyperplasia

Subtypes

Doctors classify endometriosis into four stages, corresponding to where endometrial tissue occurs in the body, how far it has spread, and how much tissue is in those areas. [Edited from the Hopkins Medicine description of endometriosis]

References

  1. [Vercellini et al., 2014] - Vercellini P, Viganò P, Somigliana E, Fedele L. Endometriosis: pathogenesis and treatment. Nat Rev Endocrinol. 2014 May;10(5):261-75. doi: 10.1038/nrendo.2013.255. Epub 2013 Dec 24. PMID: 24366116.
  2. [Hao et al., 2009] - Hao, Min, W. H. Zhao, and Y. H. Wang. “Correlation between pelvic adhesions and pain symptoms of endometriosis.” Zhonghua fu chan ke za zhi 44.5 (2009): 333-336.
  3. [Wheeler 1989] - Wheeler, J. M. “Epidemiology of endometriosis-associated infertility.” The Journal of reproductive medicine 34.1 (1989): 41-46.
  4. [Cramer and Missmer 2002] - Cramer, Daniel W., and Stacey A. Missmer. “The epidemiology of endometriosis.” Annals of the new york Academy of Sciences 955.1 (2002): 11-22.
    APA
  5. [Damewood et al., 1997] - Damewood, Marian, et al. “Current approaches to endometriosis.” Patient Care 31.1 (1997): 34-43.
  6. [Ahn et al., 2017] - Ahn, Soo Hyun, Vinay Singh, and Chandrakant Tayade. “Biomarkers in endometriosis: challenges and opportunities.” Fertility and sterility 107.3 (2017): 523-532.
    APA
  7. [Armstrong 2011] - Armstrong, Carrie. 2011 - ACOG updates guidelines on diagnosis and treatment of endometriosis.
  8. [Riazi et al., 2015] - Riazi, Hedyeh, et al. “Clinical diagnosis of pelvic endometriosis: a scoping review.” BMC women’s health 15 (2015): 1-12.
  9. [Khazali 2016] - Khazali, Shaheen. “Endometriosis classification-the quest for the Holy Grail?.” Journal of Reproduction and Infertility 17.2 (2016): 67-68.
    APA
  10. [Dunselman et al., 2014] - Dunselman, G. A. J., et al. “ESHRE guideline: management of women with endometriosis.” Human reproduction 29.3 (2014): 400-412.
  11. [MedScape, Endometrial Differential Diagnoses] - Endometriosis Differential Diagnoses
  12. [Edited from the Hopkins Medicine description of endometriosis] - Endometriosis | Johns Hopkins Medicine

Logical Description: [following Gowtham’s previous suggestions]

Event Entry Criteria:

  • an occurrence of procedure expected to be performed for persons with endometriosis with a diagnosis of endometriosis within 30 days of the procedure

Inclusion rule:

  • should have two more diagnosis in the future
  • should be female
  • should be between 15 to 49 years

Exit criteria:

  • A person is expected to be in the phenotype for the rest of their life (i.e. the disease never ends)

Recommended study applications: This cohort was tested and assessed using data from a tertiary-care academic medical center. The main requirements are that the OMOP database uses procedure codes for endometriosis-related examinations.

Assertion statement: This cohort was executed on the Columbia OMOP data and was validated with clinician review, and was published as a part of McKillop’s dissertation.

The cohort JSON is available for download at: ATLAS

Regarding validation [taken from McKillop’s dissertation]:

This phenotype was clinically validated and reviewed - in total, 1,406 patient records from Columbia University’s EHR were reviewed by two clinical experts. Setting expected confidence limits between 0.6 and 1, a subset of 38 records were used for calculating Cohen’s Kappa. Agreement between the two annotators was very good, and a kappa score of 0.89 (p-value <0.05) was achieved. Across all phenotype definitions, cohort B [the linked phenotype] had the highest overall performance with a precision of 85%, recall of 70%, and a negative predictive value of 84%

@Gowtham_Rao - here is an update to the previous Endometriosis submission (Phenotype Submission - Endometriosis - #3 by Gowtham_Rao) to the PhenotypeLibrary. I followed the new formatting information you mentioned on the submission page, let me know if there’s anything else you’ll need from me to get this submitted!

Re: the prior forum post and CohortDiagnostics and cohortDefinitionSet objects, I unfortunately can’t run this definition easily through those packages.

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@tonysun I have imported your definition. It should be in next release

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