It included following changes: - Increased the target enrollment number from 200 to 250 to account for potential dropouts; - Clarified IBD nonresponders as those with a decrease in pMCS of < 2 points or an increase in pMCS; - After the Week 13 visit, IBD nonresponders discontinued study drug and commenced OL filgotinib 200 mg once daily; and at Week 26, if they did not have a ≥ 50% decrease in sperm concentration from baseline, had the option to continue receiving OL filgotinib as part of the LTE; - Any participants who demonstrated a ≥ 50% decrease in sperm concentration from baseline entered the MP regardless of when it occurred; - Clarified that participants would be allowed on conventional immunomodulators as defined by the inclusion criteria; - LTE defined as Week 26 to Week 221; - Updated the 30-day follow-up visit and the posttreatment visit to a safety follow-up visit; - Added a required safety follow-up visit 30 days after last dose of study drug at the end of the LTE and after an ET visit; - Clarified the inclusion criteria for tumor necrosis factor alpha (TNFα) antagonists; - Clarified for participants at screening who were taking allowed therapies for UC that they had to remain on stable doses for the noted times; - Excluded ustekinumab 12 weeks prior to screening; - Updated the inclusion criteria to require that semen volume be ≥ 1.5 mL, total sperm per ejaculate to be ≥ 39 M, and that participants be up to date on colorectal cancer surveillance as per local guidelines prior to screening; - Updated participants meeting the disease worsening criteria to be offered the option to commence OL filgotinib; - End of study defined as when the last participant completed the Week 225 visit or the last participant completed their last visit, whichever was sooner; - Updated study visit windows to ± 5 days for the primary study and ± 10 days during the LTE.

It included following changes: - Revised study title from UC to IBD to encompass CD; - Increased the number of study centers from approximately 150 centers to approximately 175 centers worldwide; - Broadened the age range from 25 to 55 years of age (inclusive) to 21 to 65 years of age (inclusive); - Included ≥ 50% decrease in sperm total motility and/or sperm morphology as decision criteria for participants to enter the MP; - Removed Week 28 and Week 32 visits from LTE; - Amended the definition of evaluable participants; - Added the option of pooling the results of this study with a separate study being conducted in participants with rheumatic diseases (Study GLPG0634-CL-227 [2018-003933-14]) with the same objective, and having the total planned number of participants in both studies combined of up to approximately 250 participants.

It included following changes: - Updated ejaculation-free period from ≥ 48 hours and < 5 days to ≥ 48 hours and ≤ 7 days, per the recommendation of the updated Food and Drug Administration (FDA) guidance for industry on testicular toxicity studies; - Clarified OL Week 13 study visit and visit schedule of LTE; - Amended lower threshold of baseline sperm concentration for inclusion (≥ 10 million sperm cells/mL changed to ≥ 15 million sperm cells/mL) in line with FDA recommendation, and amended corresponding sperm concentration randomization strata (lower range of stratum changed from 10 to 20 million sperm cells/mL to 15 to 25 million sperm cells/mL); - Added the option for an unblinded interim analyses when 200 participants (eg, pooled data from Studies GS-US-418-4279 and GLPG0634-CL-227) and/or when some defined subset(s) of participants had completed their Week 13 assessments.

It included following changes: - Included discontinuation criteria for thromboembolic events; - Included a criterion to trigger an ad-hoc data monitoring committee (DMC) meeting; - Clarified that the CDAI score calculation excluded days that involved an endoscopy procedure or preparation for that procedure; - Added section on blinding procedures.

The primary reason for this amendment was to change sponsorship from Gilead Sciences, Inc. to Galapagos NV.

It included following changes: - Text was revised to specify the decommissioning of the DMC and transfer the role of the DMC to the Sponsor Safety Management Team (SSMT). All planned DMC reviews were completed, and no additional reviews were expected. At this advanced stage of the study, treatment assignments were unblinded for the majority of subjects, no longer requiring an external unblinded review committee in addition to the blinded Sponsor study team. Oversight by the SSMT included regular reviews of safety summary updates and provided similar options for escalated issue review as described in the DMC charter by following the SSMT standard procedures; - Text about blinding was revised to allow publication of the treatment assignments of subjects who completed the study before IA2; - A study drug interruption criterion for subjects experiencing moderate renal failure (estimated creatinine clearance ≥35 mL/min and <60 mL/min per Cockcroft-Gault formula) was added to align with the current Investigator’s Brochure; - Text was added to specify the decommissioning of the Internal Independent Safety Review Team as of this amendment. The internal independent SSMT covered the objectives of the DMC and the Internal Independent Safety Review Team.