Assessing the Endometrial Environment in Recurrent Pregnancy Loss and Unexplained Infertility
Phase: PHASE2
Conditions: Recurrent Pregnancy Loss, Unexplained Infertility
Sponsor: Stanford University

 
Assessing the Endometrial Environment in Recurrent  
Pregnancy Loss and Unexplained Infertility   
NCT03401918 
August 21, 2020 
Ruth Bunker Lathi, Principal Investigator 
Stanford University 
Stanford, California 94305 
1. 
PURPOSE OF THE STUDY 
a. 
Brief Summary 
Recurrent pregnancy loss and unexplained infertility are emotionaland difficult diagnoses 
for patients. Despite a thorough medicalinvestigation, most cases of recurrent pregnancy 
loss remainunexplained and unexplained infertility is by definition so.Understanding 
endometrial factors that may contribute to recurrentpregnancy loss and unexplained 
infertility are of increasinginterest. The purpose of this study was to determine if 
patientswith recurrent pregnancy loss or unexplained infertility havealtered gene 
expression in the uterus, or an altered microbiome,during the window of implantation and 
to assess whether lutealphase progesterone supplementation improves or alters 
geneexpression and to assess whether oral antibiotics followed by vaginal 
probioticsimproves an altered microbiome. 
b. 
Objectives 
The investigators hope to determine if endometrial gene expression is altered in recurrent 
pregnancy loss or unexplained infertility patients compared to healthy controls. 
Furthermore the investigators hope to learn if luteal phase progesterone support 
normalizes women with altered endometrial gene expression and if oral antibiotics and 
over the counter vaginal probiotics improve an altered uterine microbiome. This would 
give us better evidence to justify using progesterone support which is often done 
empirically without strong evidence for or against and suggest a uterine mechanism of an 
altered microbiome in infertility and recurrent pregnancy loss. This knowledge would 
provide a better means to counsel patients in these populations. 
c. 
Rationale for Research in Humans 
Human subjects must be used for this study as the purpose of the study is to understand 
human endometrial genetic expression and the human microbiome in an unexplained 
recurrent pregnancy loss and unexplained infertility patient populations. Furthermore this 
is a minimal risk study where patients are already undergoing endometrial biopsies as a 

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standard of care to rule out endometrial infection. For healthy controls this is a minimal 
risk study as the endometrial biopsy is a minimal procedure. The benefit to the healthy 
controls would be access to the information which may be relevant to them in their future 
reproductive attempts. 
2. 
STUDY PROCEDURES 
a. 
Procedures 
Patients enrolled in the study will be those presenting to the clinic for evaluation and 
treatment of recurrent pregnancy loss and infertility. Healthy controls will be patients 
presenting for elective egg freezing and elective sex selection and recruited from the 
general population by way of flier. 
 
Recurrent pregnancy loss and infertility patients will undergo the routine clinical standard 
evaluation including a uterine cavity evaluation, evaluation for endometritis, ovarian 
reserve testing, and for patients with recurrent pregnancy loss also parental chromosome 
analysis, antiphospholipid antibody blood testing and thyroid screening. Egg freezing 
patients will undergo routine clinical evaluation which includes uterine ultrasound 
evaluation and ovarian reserve testing and elective sex selection patients will undergo a 
routine evaluation which includes a uterine cavity evaluation, ovarian reserve testing and 
blood testing. 
 
For new patients presenting with no prior evaluation we will perform the uterine cavity 
evaluation as per standard of care in the follicular phase of the menstrual cycle. The 
endometrial biopsy is typically done during this same appointment however the 
endometrial biopsy will be deferred for the purposes of the study in order to perform the 
endometrial biopsy during the window of implantation after ovulation. This endometrial 
biopsy will be sent to pathology to rule out endometritis as per clinical standard of care 
and will allow us to evaluate endometrial gene expression during the window of 
implantation. The endometrial sample will be sent to Ivigen for an endometrial 
receptivity array (ERA)and microbiome analysis at no extra cost to the patient. The ERA 
provides information on the receptivity of a patient's endometrium to the implantation of 
an embryo. It is hypothesized that unexplained recurrent pregnancy loss and unexplained 
infertility patients are more likely to have a nonreceptive endometrium then healthy 
historic controls. 
 
For return patients with prior standard evaluation they will be invited to participate in the 
study. These patients will undergo an endometrial biopsy as above. The endometrial 
sample will be sent to Ivigen to our collaborators (Dr. Carlos Simon) for an endometrial 
receptivity array (ERA)and microbiome analysis at no extra cost to the patient. Dr. 
Simon's group will perform the analysis of the sample. 
 
For patients whose ERA shows a non receptive endometrium in the subsequent menstrual 
cycle, vaginal progesterone medication which is often prescribed empirically for 
recurrent pregnancy loss will be prescribed to start 3 days after ovulation detected by 
home urine LH kits. A second endometrial biopsy will be sent for a repeat ERA at not 

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extra cost to the patient. The patient will still be able to participate in the study if they 
decline this second biopsy. 
 
For patients who microbiome is altered, a 2 week course of oral doxycycline will be 
prescribed followed by 2 weeks of over the counter vaginal probiotics. A second 
endometrial biopsy will be sent for a repeat microbiome at not extra cost to the patient. 
The patient will still be able to participate in the study if they decline this second biopsy. 
 
If on the first biopsy there is endometritis the patient will first be treated based on 
standard of care practice with routine use of oral antibiotics prior to undergoing a second 
endometrial biopsy which is also routine practice. If the microbiome or ERA is also 
abnormal (It would be for example EXPECTED that the microbiome will be altered in all 
endometritis patients) for an abnormal ERA- vaginal progesterone would be added prior 
to rebiopsy and/or vaginal probiotics would be added. 
 
The patients' follow up visits and treatment regimens will be determined by the treating 
physician according to the standard of care treatment of recurrent pregnancy loss, 
unexplained infertility or other medical comorbidities. 
 
These patients are not required to consent to any additional testing or drug treatments 
outside of that which is standard treatment of their condition(s). They will consent to 
follow up communication (phone call or email) for up to 5 years after enrollment in the 
study to allow for completion of data collection and pregnancy outcomes except for the 
healthy controls who will be followed for 1 year. 
 
The only procedures which would be considered entirely research would be sending the 
endometrial biopsy tissue for ERA testing (currently endometrial biopsy is a standard of 
care for recurrent pregnancy loss and unexplained infertility) however this is not sent for 
ERA testing. 
 
Emperic use of vaginal progesterone is often used in the setting of recurrent pregnancy 
loss and unexplained fertility however doing a repeat biopsy in this setting would be 
considered research- not standard of care. 
 
Use of antibiotics is often used in the setting of non-specific findings for endometritis in 
recurrent pregnancy and unexplained fertility however using this in the setting of an 
abnormal microbiome in combination with over the counter vaginal probiotics would be 
considered research. 
b. 
Procedure Risks 
New patients will not be exposed to any additional researchprocedures outside the 
standard of care. For return patients theywill undergo a simple uterine biopsy that they 
will have theknowledge ahead of time about as they have already undergone thesame 
procedure previously. For the healthy controls they will undergo one minorprocedure any 
may benefit from the testing in the future. The endometrial biopsy ingeneral is a low risk 
procedure with a risk of complications of less than 1 in1,000 with the most common side 

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effects of short lived (lasting afew minutes at most)of mild cramping and mild 
spottingUse of Deception in the Study 
Deception will not be used. 
d. 
Use of Audio and Video Recordings 
There will be no audio or video recording. 
e. 
Alternative Procedures or Courses of Treatment 
For unexplained recurrent pregnancy loss and unexplained infertility patients there is no 
standard of care treatment. Empirical treatment includes supplementing with 
progesterone in a subsequent pregnancy started in the luteal phase or with the first 
pregnancy test however there is little evidence based medicine behind these options. At 
most this would be a 1-2 month delay of starting this empiric treatment for patients who 
fall in the abnormal group who had the option for treatment with progesterone or 
antibiotics/probiotics and subsequent biopsy. 
 
Another option we review with our recurrent pregnancy loss patients is in vitro 
fertilization with PGS (pre-implantation genetic screening) however this has not been 
shown to improve time to live birth and is very expensive. Again if patients decided to 
have this treatment the study would only again delay this by 1-2 months and have no 
effect on the patient's success rate of the treatment itself given a minor time delay. 
Furthermore it may allow us to better time an embryo transfer for these patients as ERA 
has been used to identify the best window of implantation after IVF. 
 
For unexplained infertility treatments in include oral fertility medications (clomid) plus 
insemination cycles or in-vitro fertilization cycles. Again this would be at most a 1-2 
month delay which we do not anticipate would change their overall prognosis or outcome 
for pregnancy. Again if patients proceed to IVF and embryo transfer the knowledge from 
the study could be used to better time an embryo transfer. 
 
For the healthy controls there is at least a 1-2 month set up to proceed with egg 
harvesting. The biopsy would be done during this set up time and would not cause a 
clinically significant delay. 
f. 
Will it be possible to continue the more (most) appropriate therapy for the 
participant(s) after the conclusion of the study? 
As there is no standard treatment of unexplained recurrent pregnancy loss, all therapy as 
described about will be possible for these patients. For unexplained infertility the 
standard appropriate therapy will resumed after the conclusion of the study. 
g. 
Study Endpoint(s) 
For patients who are found to have a receptive endometrium, the study end point will be 
after the standard medical evaluation as described. For patients who are found to have a 
non receptive endometrium or abnormal microbiome the study end point will be after the 
second endometrium biopsy. Participants will be allowed to continue any standard 

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medically indicated treatments throughout the study. For healthy controls the study end 
point will be after the first endometrial biopsy and we will not plan a repeat biopsy. The 
study will end once the anticipated total number of participants is met to complete an 
adequate power analysis. 
3. 
BACKGROUND  
a. 
Past Experimental and/or Clinical Findings 
Recurrent pregnancy loss is a difficult clinical diagnoses defined as when women have 
>2 unexplained miscarriages (not accounted for by genetically abnormal fetal tissue) <10 
weeks. After a full evaluation for genetic, endocrine, anatomic, immunologic, infectious 
and autoimmune conditions, the majority of cases remain unexplained. In unexplained 
infertility normal sperm, normal ovulatory function and patent fallopian tubes are 
documented and the reason for infertility remains unexplained. The role of endometrial 
factors in pregnancy loss and unexplained infertility is becoming of increasing interest. 
Studies have identified differences in the endometrium in protein expression and 
endometrial glandular development in women with unexplained recurrent pregnancy loss. 
Some studies have suggested that luteal phase progesterone may change the endometrial 
environment. Therefore the purpose of this study was to look at a more comprehensive 
genetic expression profile and the microbiome atmosphere during the window of 
implantation and to evaluate if luteal phase progesterone support normalizes this genetic 
expression profile for RPL patients who are found to have non- receptive endometrial 
biopsies. Understanding the genetic expression profile of the endometrium and the 
microbiome atmosphere during the window of implantation for unexplained infertility 
may help identify a previously unknown uterine factor in unexplained infertility. Prior 
studies have shown that a non receptive ERA and an abnormal microbiome (lactobacilli 
non dominant) is associated with decreased implantation rate, pregnancy rate and live 
birth rates in women undergoing IVF. 
b. 
Findings from Past Animal Experiments 
None 
4. 
DEVICES USED IN THE STUDY 
a. 
IDE-Exempt Devices 
IND-Exempt Device 1 
Name: 
ERA: Endometrial receptivity array (IVIGEN) 
Description: 
The ERA is a diagnostic tool used to evaluate the endometrial receptivity 
of a patient that determines whether or not an embryo is capable of 
implanting in the uterus.   
IND-Exempt Device 2 
Name: 
Vaginal progesterone (endometrin) (Ferring Pharmaceuticals Inc.) 
Description: 
Vaginal progesterone supplementation   
IND-Exempt Device 3 
Name: 
Doxycyline (Generic) 
Description: 
Doxycyline 
 

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5. 
DRUGS, BIOLOGICS, REAGENTS, OR CHEMICALS USED IN THE STUDY 
a. 
Commercial Drugs, Biologics, Reagents, or Chemicals 
Commercial Product 1 
Name: 
PurFem priobiotic (Bifodan A/S) 
Dosage: 
Dispense 1 capsule per vagina daily x 10 days 
New and different use? (Y/N) 
No 
Commercial Product 2 
Name: 
Probaclac Vaginal Probiotic (Nicar Laboratories) 
Dosage: 
apply 1 vaginal capsule oer vagina daily x 14 days 
New and different use? (Y/N) 
No 
Commercial Product 3 
Name: 
Lactogyn (JADRAN-GALENSKI LABORATORIJ d.d. JGL d.d) 
Dosage: 
1 application to vagina per day 
New and different use? (Y/N) 
No 
6. 
DISINFECTION PROCEDURES FOR MEDICAL EQUIPMENT USED ON BOTH HUMANS AND 
ANIMALS 
N/A 
 
7. 
PARTICIPANT POPULATION 
a. 
Planned Enrollment 
The number of participate expected to be enrolled at Stanford Medicine Fertility and 
Reproductive Health Clinic is 100 patients per patient population (100 recurrent 
pregnancy loss patients, 100 unexplained infertility patients and 100 health controls). 
Any patients eligible for the study but desiring no intervention will be offered the 
alternative of being included as an observational group only without intervention in order 
to compare pregnancy outcomes without intervention. These patients will be recurrent 
pregnancy loss and unexplained infertility patients seeking treatment at our facility. 
healthy controls will be patients presenting for elective egg freezing and sex selection. 
b. 
Age, Gender, and Ethnic Background 
All participants enrolled in this study will be female and of reproductive age 18-45 years 
old that present to our clinic for routine evaluation and treatment. Enrollment will be 
open to women of all ethnic backgrounds. 
c. 
Vulnerable Populations 
N/A 
d. 
Rationale for Exclusion of Certain Populations 
Children will not be included as recurrent pregnancy loss and infertility does not occur in 
children. 
e. 
Stanford Populations 
None 

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f. 
Healthy Volunteers 
None 
g. 
Recruitment Details 
The participants will be recruited by their treating physician if they meet the inclusion 
criteria for the study. The study be open to the public and women who are already 
presenting to Stanford Medicine Fertility and Reproductive Health clinic will be invited 
to participate. Participants will be treated the same whether or not they agree to 
enrollment in the study. Those consenting to study participation will be willing to allow 
physician follow up for up to 5 years for thorough data collection. 
h. 
Eligibility Criteria 
i. 
Inclusion Criteria 
Subjects must fulfill the following inclusion criteria to be eligible to participate in the 
study: 
1. Have a diagnosis of recurrent pregnancy loss as defined as two or more 
unexplained pregnancy losses at less than 10 weeks (miscarriages with known 
chromosomal errors excluded) OR have a diagnosis of unexplained infertility defined 
as normal ovarian reserve testing, normal ovulatory function, normal semen analysis 
defined why WHO criteria and evidence of at least one patent fallopian tube. 
2. Agree to the standard of care testing for evaluation of recurrent pregnancy loss OR 
unexplained infertility OR routine testing for preparation for oocyte freezing or 
elective sex selection. 
3. Be at least 18 years old and less than 46 years old. 
4. Have menstrual cycles that occur in 25-35 day intervals 
5. Agree to follow up for 5 years from the date of enrollment 
ii. 
Exclusion Criteria 
1. Irregular menstrual cycles 
2. Presence of untreated submucosal fibroids or polyps 
3. an unligated hydrosalpinx 
4. non-ovulatory progesterone level on the day of endometrial biopsy 
5. Women <21 or >45 years old. 
i. 
Screening Procedures 
Study staff will invite women presenting for recurrent pregnancy loss or unexplained 
infertility or healthy controls to participate in this study. The staff will explain the 
purpose of the study to interested patients and the patients will then sign an informed 
consent for their enrollment. Patients will receive a thorough evaluation of their condition 
upon presentation. It will be emphasized that their participation is entirely voluntary and 
that they will receive the standard of care even if they choose not to enroll in the study or 
discontinue participation at any time. 

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j. 
Participation in Multiple Protocols 
Patients will be asked if they are participating in any other studies on their consent forms. 
They may be enrolled in other studies concurrently with this study as long as it does not 
impact the outcome of this study. 
k. 
Payments to Participants 
No payment will be provided. Patients are receiving standard of care evaluation and 
management of recurrent pregnancy loss and unexplained infertility. 
l. 
Costs to Participants 
Standard recurrent pregnancy loss and unexplained infertility evaluation and treatment 
costs will be charged to the patient or her insurance. Similarly standard evaluation prior 
to oocyte freezing or sex selection cycles will be charted to the patient or her insurance. 
m. 
Planned Duration of the Study 
The probable duration of the study will be approximately 3-5 years to complete the 
patient's treatment of recurrent pregnancy loss and unexplained infertility and follow up 
the outcome of their pregnancies (if applicable) for up to 5 years. 
8. 
RISKS 
a. 
Potential Risks 
i. 
Investigational devices 
The ERA and microbiome tests pose no risks or injury to the subject. Participants will 
receive standard of care at the study site which includes an endometrial biopsy. A portion 
of this specimen will be sent free of charge for the endometrial receptivity array and 
microbiome evaluation. 
ii. 
Investigational drugs 
N/A 
iii. 
Commercially available drugs, biologics, reagents or chemicals 
Vaginal progesterone supplementation is often used empirically as an available treatment 
for patients with recurrent pregnancy loss. This will be offered to all patients who desire 
this empirical treatment if their ERA shows a non-receptive endometrium. These patients 
will be offered a repeat ERA biopsy to determine whether progesterone improves their 
endometrial receptivity. 
Vaginal progesterone risks are considered minimal but patient's have reported in clinical 
trials to report symptoms such as abdominal pain (12%) nausea (8%) abdominal bloating 
(4%), constipation (2-3%) vomiting (3%), fatigue (2%), UTIs (2%) headache 4%, vaginal 
bleeding of 3%. Vaginal progesterone may also have similar side effects compared to 
other drugs containing progesterone including breast tenderness, bloating, mood swings, 
irritability, and drowsiness. If patients experience bothersome side effects that are not 
easily treated (for example a headache that resolves with a dose of Tylenol) we would 
stop vaginal progesterone treatment as is our current clinical practice. 

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Oral doxycycline is considered minimal risk but patients have reported in clinical trials to 
report symptoms such as nausea, decreased appetite, vomiting, diarrhea, hives and 
anemia. If these symptoms developed and didn't resolved with minimal intervention 
(taking food with medicine) the treatment would be stopped as is our current clinical 
practice. 
iv. 
Procedures 
Minimal risk to patients with non-invasive procedures. Patients will only receive standard 
of care diagnostic testing during their duration of treatment in our office. This will 
include ultrasounds, blood tests and a uterine cavity evaluation. A patient may experience 
mild discomfort at the venipuncture site and some lower abdominal cramping and light 
bleeding (spotting) associated with a uterine cavity evaluation. There are extremely low 
risks of infection or other complications associated with these minimally invasive 
procedures. 
v. 
Radioisotopes/radiation-producing machines 
N/A 
vi. 
Physical well-being 
Minimal risks to a patient's physical well-being. Patients are receiving standard medical 
treatment. Repeat biopsies will be offered to patients whose initial testing is not 
receptive. The risk of the repeat biopsy is again minimal physical risk and patients will be 
allowed to decline the repeat testing. 
vii. 
Psychological well-being 
Minimal risks to a patient's psychological well-being. Potential improvement to 
psychological well being as the information from the ERA may help explain a previously 
unexplained diagnosis of recurrent pregnancy loss or unexplained infertility. 
viii. 
Economic well-being 
Participants will not be responsible for any costs associated with this study. The are 
receiving standard medical care and if they agree to the endometrial biopsy, the ERA and 
microbiome testing will be done for no additional cost. 
ix. 
Social well-being 
x. 
Participation in this study should not effect a patient's social well-being. Overall 
evaluation of risk 
Low 
b. 
International Research Risk Procedures 
N/A 
c. 
Procedures to Minimize Risk 
Clinical study staff will explain all procedures thoroughly to consented subjects and why 
each diagnostic test is being done during their evaluation. There are no anticipated 

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additional risks to a patient who is involved in this study as compared to a 
nonparticipating patient in the same clinical setting. Subject identity will be kept 
confidential. 
d. 
Study Conclusion 
The study will terminate once the desired number of participants has been reached and 
each patient has been followed for 5 years from the date of enrollment. 
e. 
Data Safety Monitoring Plan (DSMC) 
i. 
Data and/or events subject to review 
Since we will be performing endometrial biopsies in patients enrolled in this study, 
there is a small risk of bleeding and infection that can occur as result of this 
intervention (<1%) We will keep track of all patients that experience complications 
as a result of this procedure. 
 
For patients who use vaginal progesterone there is a small risk of side effects from 
systemic absorption of the progesterone: Bloating, stomach/abdominal pain, nausea, 
breast tenderness, headache, drowsiness, mood swings, irritability, or vaginal 
discomfort. In our experience we have found that <1% of our patients have 
bothersome side effects with vaginal progesterone which we routinely use for many 
infertility and recurrent pregnancy loss patients. We will keep track of all patients 
that experience side effects on this medication. 
 
For patients using oral doxycycline there is a small risk of side effects including 
decreased appetite, nausea, vomiting, diarrhea, allergic reaction and anemia. In our 
experiences we have found that <1% of our patients have bothersome side effects 
with oral doxycycline which we routinely use for many of these patients. . We will 
keep track of all patients that experience side effects on this medication. 
 
Vaginal probiotics is an over the counter supplement that is not expected to have side 
effects other then difficulty with insertion or change in typical vaginal discharge. 
None the less we will keep track if any patient reports any bothersome side effect and 
discontinue its use if there are any. 
ii. 
Person(s) responsible for Data and Safety Monitoring 
The protocol director will be monitoring all unanticipated problems and adverse 
events. 
iii. 
Frequency of DSMB meetings 
N/A 
iv. 
Specific triggers or stopping rules 
The risk of complications with an endometrial biopsy in the general population is 
approximately 1%. If we experience a higher complication rate then this we will 
terminate the procedure. 

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If any patient reports persistent side effects while on vaginal progesterone this will be 
stopped for this patient as it would be based on standard of care practice. 
v. 
DSMB Reporting 
N/A 
vi. 
Will the Protocol Director be the only monitoring entity? (Y/N) 
Yes 
vii. 
Will a board, committee, or safety monitor be responsible for study monitoring? 
(Y/N) 
No 
f. 
Risks to Special Populations 
N/A 
9. 
BENEFITS 
Participants will benefit by receiving a thorough evaluation of theirrecurrent pregnancy loss and 
unexplained infertility or baseline fertility testing for thoseundergoing egg freezing or sex 
selection. Participantswill be informed of their endometrial receptivity array andmicrobiome 
results which may lead to improvements in their futurecare. For example many of our patients do 
go on to have in vitrofertilization with subsequent embryo transfers (also the sex selection 
patients or thosepatients who froze eggs who are coming back to use them). During these 
embryotransfers the ERA is used to personalize and improve the embryotransfer success rate. The 
ERA has been shown to be consistent intime across menstrual cycles over many years. 
Knowledge of the ERAwould help patients as they would not have to go through or pay forthis 
testing at a later time.  
10. 
PRIVACY AND CONFIDENTIALITY 
All participant information and specimens are handled in compliance with the Health Insurance 
Portability and Accountability Act (HIPAA) and privacy policies of Stanford University, Stanford 
Health Care, and Stanford Children’s Health.