FAQs EMMA. 8. Endometrial Biopsy collection

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1 FAQs EMMA 1. How will the test be called? EMMA (Endometrial Microbiome Metagenomic Analysis), which will determine whether the uterine microbial environment is optimal or not for embryo implantation. EMMA provides a 360º view of the endometrial bacterial composition, including pathogens causing chronic endometritis that are specifically investigated in ALICE. 2. Indications for EMMA The impact of the endometrial microbiome in patients with RIF have been demonstrated (Moreno et al. Am J Obstet Gynecol, 2016). However, EMMA can be beneficial to any patient wishing to conceive to assess the microbiological environment that the embryo will encounter at implantation. 3. Methodology. What does the change imply for the methodology? Endometrial sample contains endometrial cells and bacterial cells that can be analyzed using deep sequencing for the prediction of the endometrial receptivity and endometrial microbiome using the same sample. This assessment offers an extended view of the endometrial factor to improve the clinical management. 4. Which are the benefits of NGS microbiome vs. microbial culture Microbial culture is the current method for the identification of bacteria and infection. However, it has been demonstrated that between 20 and 60% of bacteria (depending on their location) cannot be cultured. Among them, Gardnerella vaginalis, Mycoplasma or Ureaplasma spp., some of the most common pathogens of the reproductive tract, are not culturable under the standard microbiological methods. The molecular assessment of the microbiome using NGS allows to detect culturable and non-culturable bacteria (Moreno et al., Am J Obstet Gynecol, 2018). 5. How to collect the EB? Endometrial biopsies are collected from the uterine cavity with the use of Pipelle catheters from Cornier Devices (CCD Laboratories) or similar, under sterile conditions either in a natural cycle or in an HRT cycle. 6. How to prepare the patient to collect the EB? When ERA test is analyzed together with EMMA, the same endometrial biopsy will be used. In this case, please refer to ERA protocol for sample collection. If only EMMA is requested endometrial biopsy should be obtained either following the ERA protocol or between days in a natural cycle. 7. Does any drug affect or interfere with EMMA analysis? Yes. Specifically, the antibiotics, so they should not be administrated to the patient during the last 3 months prior to the sample collection. If the patient has taken any antibiotic during this time frame, the name of the active substance, dosage, administration way and duration must be informed in the TRF, including prophylactic antibiotics for egg retrieval. Other drugs as those which alter the immunological condition could also affect the result. Please record any drug taken by the patient in the TRF. 8. Endometrial Biopsy collection

2 Which type of pipelle should be used to take the endometrial biopsy? o We recommend the Pipelle de Cornier from Genetics. It is needed to cut the tip and then expel the sample into the vial/solution provided? o No, this is not needed. Just leave the tissue inside the cryotube. How the endometrial biopsy should be taken? o Once the catheter is into the endometrial cavity, scratching can be done many times from the fundus in each endometrial wall. Aspiration should be maintained during scratching, that way you can see the tissue entry into the catheter. Is it possible to do a biopsy for EMMA during a hysteroscopy? o Yes, it is, but it is recommended to perform it at the beginning of the procedure, before distending the uterine cavity. What happens if the doctor hasn t an EMMA kit in the moment of the sample collection? o First option: Igenomix Customer Support could contact a local clinic to request they borrow a kit. o Second option: Perform biopsy and place sample immediately in a sterile, DNAse & RNAse free, dry tube (no solution). This tube must be resistant to freezer. Place in the freezer immediately at -20ºC. Once clinic receives a kit, introduce the sample (without thawing it) inside our cryotube and refrigerate at 4ºC for a minimum of 24 hours. This method is not highly reliable and there is a strong chance that an Invalid RNA result will be obtained. o Third option: Perform the biopsy the following day (if first biopsy) and send a kit overnight to clinic. In this case medication must be continued the same and it s important to note the exact progesterone impregnation time (only applicable if the ERA is also being analysed in the same sample). How to avoid having too much blood or mucus in the biopsy sample? o It is imperative not to introduce an excessive amount of blood or mucus into the cryotube as this can interfere with the Stabilizing Buffer from properly preserving the endometrial tissue sample. For that, do not go too deep inside the tissue when collecting the biopsy, it is better to take the sample more superficially (important to make sure there is enough tissue). Can it be analyzed endocervical samples? o The EMMA test has been validated for endometrial tissue from the uterine cavity, so we cannot process endocervical samples. Can be a sample split on two different tubes? o A clinic with a high rate of Invalid RNA (due to too large sample size) asked if they can split samples into two different cryotubes. We would analyse the first sample only, if Invalid, then analyse the second sample. It is important that there is sufficient sample size in each cryotube and that the clinic indicates this is what they want to do. o We recommend do not take much tissue, as the sample get the mark label on the tube (around mg). Can be lidocaine used when taking the biopsy? o It is not recommended to use it. Can be Cytotec used when taking the biopsy? o It shouldn t.

3 Can be betadine used when taking the biopsy? o Betadine is not necessary. How to proceed if the cervical canal is very narrow and difficult to access? o The cervical canal should be accessible for final embryo transfer since they are patients undergoing ART cycles. Therefore, regular protocols should be used to prepare it in advance. A mock transfer should be done in the first appointment to assure the accessibility of the endometrial cavity. If it is not possible, cervicohisteroscopy should be peformed. In this case of minimal mechanical difficulties is better to try to enter with a smaller catheter (i.e. embryo transfer catheter with or without the guide inside). o If the last recommendation does not work, it can be possible to relax a little the os with a laminaria s branch, taking into account that this procedure should be never performed in the transfer cycle. Can be performed the EMMA in an atrophic endometrium (considering atrophy as an endometrium with < 6mm)? o The EMMA can be performed on a patient with an atrophic endometrium without any problem. 9. EMMA Sample storage and shipment At what temperature and how much time should be the sample stored immediately after taken it? o It is important that the sample be placed in the refrigerator at 4-8ºC for a minimum of 4 hours immediately after taken it. How much time can be the sample stored in a fridge? o Once the sample has been 4 hours at 4-8ºC then it can be stored at 4-8ºC for up to 3 weeks. How much time can be the sample stored in a freezer? o Once the sample has been 4 hours at 4-8ºC then it can be stored at 20ºC for up to 1 year. How much time can be the sample at RT? o If samples are delayed during shipping, keep in mind that they are typically stable at room temperature for 5-7 days. We will always try extracting DNA and performing the analysis, but there is no guarantee that results will be valid. Can be analysed samples that have been preserved in a paraffin block? o We cannot analyse samples in a paraffin block. 10. Which is the turnaround time for the test? TAT is the same than ERA, 15 days. 11. Reports. Will Igenomix release new reports? A report will be released to provide information about EMMA (which will include pathogens reported in ALICE). Igenomix will release an additional ERA report if both tests are ordered. 12. Information in EMMA report: EMMA report will inform about the overall microbial health of the uterine cavity. It will include: - Percentage of Lactobacilli. - Abundance (percentages) of the ten most abundant bacteria detected in the endometrial sample. - Also, the endometrial microbiome profile will be reported in terms of normal or abnormal microbiota. If the microbiota is abnormal, the report will show if pathogenic

4 or dysbiotic bacteria have been detected accompanying a low percentage of Lactobacilli. The report will include the suggested probiotic/antibiotic therapy. The recommendation of antimicrobial therapy will be always guided by an expert clinical microbiologist that will counsel the patient or the doctor in a personalized manner. Please find below an example of the report that Igenomix will release for EMMA: 13. In case of an abnormal microbiome. Do we recommend cancelling the embryo transfer? Do we recommend repeating the test? EMMA report will show the recommended treatment for each case based on the EMMA results to personalize the management of patients. Please refer to the decision tree. 14. Suggested clinical solution in case of abnormal microbiota A list with the recommended antibiotics and/or probiotics will be provided at the end of the report based on the EMMA results: Probiotics: vaginal suppositories containing Lactobacillus strains (L. rhamnosus, L. crispatus, L. reuterii, L. plantarum, etc.) Antibiotics: please see the document Antibiotic therapy. In complex cases, the recommended therapy will be guided and personalized through specialized microbiology counselling. 15. In case that the patient has already performed an ERA test, do we need to collect a new endometrial biopsy for this test?

5 We recommend performing the test EMMA with a new sample, because microbiome is variable over time. However, special cases, and only if the piece of tissue is still stored at Igenomix, can be analysed individually. However, there is a risk that old samples present deviations from the initial microbiota due to previous manipulation of the sample. 16. In case of a second sample, will it be collected under the same cycle/day (i.e. HRT, P+5)? is it included in the price? If only the EMMA test has to be repeated, the sample can be collected between days of the natural cycle, or during the secretory phase in HRT cycle. Nonetheless, it s recommended to collect in similar conditions. EMMA will include a second analysis for patients with a previous EMMA after recommended treatment to confirm the normal flora restoration. This is expected in up to 40% of patients. If the ERA test has also to be repeated, then the sample should be obtained following the recommendations of the ERA report. 17. Is there any previous scientific evidence related to this test? There is a paper published by Igenomix in American Journal of Obstetrics and Gynecology (Moreno et al, Am J Obstet Gynecol, 2016), showing the impact of endometrial microbiota on ART success in a pilot study with 35 RIF patients. This paper was published as Report of Major Impact. Moreno I, Codoñer FM, Vilella F, Valbuena D, Martinez-Blanch JF, Jimenez-Almazan J, Alonso R, Alama P, Remohi J, Pellicer A, Ramon D, Simon C. Evidence that the endometrial microbiota has an effect on implantation success or failure. Am J Obstet Gynecol. 2016; 215: Endometrial pathologies and EMMA The patient is going to have a uterine surgical intervention prior to the transfer. When should be performed the EMMA test? o If any surgical interventions are necessary, they should be performed before the sample collection. It is recommendable that the endometrium be in the similar and nearest conditions as this could be for the embryo transfer. Does the Endometriosis affects the EMMA result? o There are some papers supporting a higher prevalence of microbiota alterations in patients with endometriosis. However, these evidences need further research and this relation is currently under investigation by our group. For this reason, we recommend performing EMMA test in these types of patients. We will appreciate if clinicians report cases of endometriosis in the TRF for EMMA. If the patient has fluid in the lining, could be the biopsy taken? o This fluid is most likely caused by an infection of the endometrium. In these cases, is quite convenient to perform the EMMA test. Could be performed the biopsy if there is no trilaminar appearance? o Yes, this is not a problem. 19. Is the EMMA result still valid after D&C? o If a D&C occurs after an EMMA cycle, the results could change. So, it is recommended to repeat the EMMA after D&C procedures, ideally in the cycle immediately before the embryo transfer.

6 20. Does the chemotherapy/radiation affects the EMMA result? o We have no data about the effect of chemotherapy or radiation over the endometrial microbiota, but we think it could change. For that, in case that a patient has undergone chemotherapy or radiation after the EMMA test, we would recommend that endometrial biopsy be repeated to validate the results once treatment is complete and patient is close to transfer. 21. Non-endometrial pathologies and EMMA Does the chronic thyroiditis increase the risk of abnormal microbiota? o We do not have any cases of this to our knowledge, so we are unaware of the effects of this disease over the endometrial microbiota. Does PCOS increase the risk of an abnormal microbiota? o We do not have data on this.