Background and Aims: Endometriosis is known to have detrimental effects on fertility, but there is no consensus on the optimal stimulation protocol for IVF-ET in patients with endometriosis. The study aimed to compare the IVF outcomes of gonadotropin-releasing hormone (GnRH) agonist protocols versus antagonist protocols in patients diagnosed with endometriosis. Method: We performed a meta-analysis of studies that compared IVF outcomes of GnRH agonist versus antagonist protocols in patients with endometriosis. Through literature search, we retrieved 222 articles, and the last search date was April 7, 2023. Among them, six studies which met inclusion criteria were eligible for final analysis. The primary outcome was clinical pregnancy. Random effects and fixed effects models were applied according to I2 statistics. Results: The use of GnRH agonist was associated with higher clinical pregnancy rate (Odds ratio (OR) 1.61, 95% CI 1.35–1.93, 6 studies, [Formula: see text]<0.00001, I2=16%), higher live birth rate (OR 1.75, 95% CI 1.32–2.33, 3 studies, [Formula: see text]<0.0001, I2=12%), and similar miscarriage rate. The total dose of gonadotropin did not differ between the two methods, but the GnRH agonist protocol had a longer duration of stimulation (WMD 1.34, 95% CI 0.44–2.24, 5 studies, I2=98%), retrieved more oocytes (WMD 2.23, 95% CI 0.58–3.88, 3 studies, [Formula: see text]=0.0008, I2=97%), more MII oocytes (WMD 2.81, 95% CI 2.34–3.28, 3 studies, [Formula: see text]<0.00001, I2=0), and more embryos (WMD 1.90, 95%CI 1.13–2.67, 3 studies, [Formula: see text]<0.00001, I2=68%). Conclusion: Patients with endometriosis may benefit from using GnRH agonist protocol in the IVF-ET cycle, as it may be associated with a higher clinical pregnancy rate and live birth rate. Even though the stimulation duration is longer, more oocytes, mature oocytes, and embryos may be expected. Although the findings of this study may be potentially beneficial for clinicians, it is crucial to conduct additional randomized prospective trials with larger cohorts to further validate the results.
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