Microbiota Transfer Therapy for Children With Both Pitt Hopkins Syndrome and Gastrointestinal Disorders
Phase: PHASE2
Conditions: Pitt Hopkins Syndrome
Sponsor: Arizona State University

1 
 
Microbiota Transfer Therapy for Children with both Pitt Hopkins Syndrome 
and Gastrointestinal Disorders 
NCT04132427   
Clinical Study Protocol Version 3 – March 28, 2022 
Previous versions: September 8, 2020 version6.i  Objectives and purpose of the study 
This will be a Phase 2 Trial to determine the safety, tolerability, and efficacy of Microbiota 
Transfer Therapy (MTT) for treating patients with Pitt Hopkins Syndrome and gastrointestinal 
disorders (chronic constipation and/or diarrhea). 
 
6.ii  Name and qualifications of sponsor, investigators and sub-investigators 
 
Sponsor and Investigator:  James B. Adams, Ph.D. 
 
Arizona State University 
 
PO Box 876106 
 
Tempe, AZ 85287-6106   
Prof. Adams is the director of the Autism/Asperger’s Research Program at Arizona State 
University, which focuses on medical causes of autism, how to treat it, and how to prevent it.  He 
has published over 150 papers in peer-reviewed journals, including over 40 on autism-related 
research.  He has led several clinical trials for ASD and assisted with several others.  He led the 
Phase 1 study on MTT, and is currently leading a study on “Microbiota Transfer Therapy (MTT) 
for Treating Gastrointestinal Problems in Adults with ASD.”  
 
 
Co-Investigator:  Rosa Krajmalnik-Brown, Ph.D.  
Biodesign Institute at Arizona State University 
P.O. Box 875701  
Tempe, AZ 85287-5701 
Prof. Krajmalnik-Brown is a Professor in the School of Sustainable Engineering and the Built 
Environment, and in the Swette Center for Environmental Biotechnology in the Biodesign Institute 
at Arizona State University. She has extensive expertise in microbial ecology with more than 60 
papers in peer-reviewed journals. She has led many studies determining the gut microflora 
structure and function.  She has worked with Prof. Adams on 4 previous autism microbiome 
studies, including the Phase 1 study on MTT for children with ASD and a current study on MTT 
for adults with ASD.   
 
 
Lead Physician: .  
 
 
Dr. Robert Hellmers 

2 
 
Arizona Allergy Associates 
705 S. Chandler Blvd. 
Chandler, AZ85224 
 
Robert Hellmers, MD, is board-certified in pediatrics and board certified in allergy and 
immunology.  He has over 40 years of clinical experience, including evaluating and treating 
many children and adults with autism.  He previously was the senior study physician for a 
randomized clinical trial of comprehensive nutritional intervention for children and adults with 
autism, in collaboration with Prof. Adams. He is now semi-retired, and this study will be one of 
his major projects. 
 
 
Research Facilities at Arizona State University 
Autism Research Program 
Arizona State University 
ECG 302 
501 E Tyler Mall 
Tempe, AZ 85287-6106 
 
Biodesign Institute 
Arizona State University 
727 East Tyler Road  
Tempe, AZ 85287-5701    U.S.A. 
 
 
Institutional Review Board 
The IRB at Arizona State University will be the IRB for this study. 
 
 
6.iii  Patient Inclusion, Exclusion, and Number 
 
Inclusion Criteria  
1) Children ages 7-17 years with Pitt Hopkins Syndrome (verified by genetic testing) 
2) GI disorder as defined below that has lasted for at least 2 years. 
3) No changes in medications, supplements, diet, or therapies in last 2 months, and no intention 
to change them during the Parts 1 and 2 of the clinical trial. 
4) Ability to swallow pills (without chewing) - this will be verified by the study staff during the 
first eligibility visit by administering a placebo capsule and ensuring that the participant can 
swallow it without chewing. 
5)  Review of last two years of medical records by the study physician. 
 
Exclusion Criteria  
1) 
Antibiotics in last 3 months (topical antibiotics are allowed) 
2) 
Probiotics in last 2 months, or fecal transplant in last 12 months  
3) 
Tube feeding 
4) 
Severe gastrointestinal problems that require immediate treatment (life-threatening) 

3 
 
5) 
Ulcerative Colitis, Crohn’s Disease, diagnosed Celiac Disease, Eosinophilic 
Gastroenteritis, or similar conditions 
6) 
Unstable, poor health (based on study physician’s opinion) 
7) 
Recent or scheduled surgeries 
8) 
Current participation in other clinical trials 
9)      Females who are pregnant or who are at risk of pregnancy and sexually active without 
effective birth control.  We will conduct a pregnancy test on all female participants as 
part of the screening and at each clinical visit. 
10) 
Allergy or intolerance to vancomycin or magnesium citrate 
11) 
Clinically significant abnormalities at baseline on two blood safety tests:  Comprehensive 
Metabolic Panel, and Complete Blood Count with Differential.  Note that some 
abnormalities may occur due to PTHS, so only those likely to significantly increase risk 
in this study would be grounds for exclusion, at the discretion of the study physician.  See 
detailed discussion at end of this section on Interpreting Laboratory Results. re. 
Eligibility for Admission to Study. 
12) 
Evidence of significant impairment of immune system, or taking medications that can 
compromise the immune system, and thus increase risk if exposed to multiple-drug 
resistant bacteria. 
 
The rational for exclusions 1-2 is that they interfere with gut flora. 
The rationale for exclusion 3 is that those individuals are probably less likely to respond to the 
proposed treatment. 
The rationale for exclusions 4-7 is that those individuals are at higher risk of safety problems 
with MTT. 
The rational for exclusion 8 is that participation in other trials would interfere with the results of 
this one. 
The rationale for exclusion 9 is to avoid risk to fetuses. 
The rationale for exclusion 10 is to avoid known allergic reactions to study medications. 
The rationale for exclusions 11 is to ensure that participants are in adequate health (aside from 
chronic GI and PTHS-related problems) at the start of the study. 
 
Definition of a GI Disorder (for this study):   
On the Daily Stool and Symptom Record, five or more abnormal days out of 14 days, where an 
abnormal day is defined as a day which involves one or more of the following symptoms: 
1) Abnormal stool:  type 1-2 (hard) or type 6-7 (soft/liquid) on the Bristol Stool Scale  
2) Three or more bowel movements in 1 day 
3) No bowel movement that day. 
4) Significant abdominal/gastrointestinal pain. 
5) GI medication or treatment is required (such as laxative, enema, etc.) 
 
Interpreting Laboratory Results re. Eligibility for Admission to Study 
Each participant will have a fasting blood draw to assess safety criteria for admission to the 
study.  Those tests include a comprehensive metabolic panel (including liver/kidney function 
tests) and complete blood count with differential (CBC). The tests will be conducted by LabCorp 
or an equivalent CLIA-certified laboratory. 

4 
 
Normal Values:  Participants who have values for all tests within the reference ranges will be 
deemed eligible to participate.   
Borderline Values (at or slightly outside the reference range limits):  Those whose values are in 
the borderline range and whose values are isolated and not consistent with a potential clinical 
concern, will also be deemed eligible.  For example, if ALT were slightly above the reference 
range, but AST was normal, then we would assume liver function is acceptable and the 
participant would be eligible for enrollment. 
Abnormal Values:  Participants who have a value clearly  outside of the reference range, but for 
a known reason, will be considered for eligibility based on the study physician’s clinical 
judgement following review of prior medical records, history from parent, and a determination 
that medical care is being provided for the cause of the abnormality and likely the lab value will 
remain stable during the study.  Examples of acceptable reasons for an abnormal value include: 
1) Participant is taking a psychiatric or anticonvulsant medication known to increase liver 
enzymes (ALT and AST) 
2) Altered CO2 due to altered respiratory function typical in PTHS and is under medical care 
 
For any applicant that has abnormal laboratory test values we will document the abnormality and 
the physician’s interpretation of the test result and why it is or is not an exclusion criteria for 
admission to the study. 
In some marginal cases the study physician may request a second blood draw before making a 
decision on eligibility, or if there is a suspicion of a laboratory error. 
 
Below is a list of the LabCorp Reference Ranges for each test. 
Lab Test 
Age 
Reference Range 
(males) 
Reference 
Range 
(females) 
Reference 
Range (all) 
Comprehensive Metabolic Panel 
BUN  (mg/dL) 
1-17 years 
5-18 
same 
Creatinine, Serum 
(mg/dl) 
1-2 years 
.19-.42 
same 
3-4 years 
.26-.51 
same 
5-6 years 
.30-.59 
same 
7-8 years 
.37-.62 
same 
9-10years 
.39-.70 
same 
11-12 years 
.42-.75 
same 
13-14 years 
.49-.90 
same 
>14 years 
.76-1.27 
.57-1.00 
Glucose, Serum (mg/dl) 
all 
65-99 

5 
 
BUN/Creatine Ratio 
7mths-1year 
20-71 
same 
2-5years 
19-51 
19-49 
6-12years 
14-34 
13-32 
13 -17 years 
10-22 
same 
Sodium, Serum 
(MMOL/L) 
all 
134-144 
Potassium, Serum  
(MMOL/L) 
all 
3.5-5.2 
Chloride, Serum 
(MMOL/L) 
all 
96-106 
Carbon Dioxide, Total 
all 
17-26 
Calcium, Serum(mg/dL) 11 days- 1 year 
9.2-11.0 
same 
2-11 years 
9.1-10.5 
same 
12-17 years 
8.9-10.4 
same 
Protein, Total, Serum 
(g/dl) 
all 
6.0-8.5 
Albumin, Serum (g/dl)  
1-2years 
3.4-4.2 
same 
3-17 years 
3.5-5.5 
same 
Globulin, Total (g/dl) 
all 
1.5-4.5 
A/G Ratio ( No unit)  
all 
1.5-2.6 
Bilirubin, Total (mg/dL) all 
0.0-1.2 
Alkaline Phosphatase, S 
(IU/L) 
all 
133-309 
AST (SGOT)  ( IU/L) 
all 
0-60 
ALT (SGOT)  ( IU/L) 
1-11 years 
0-29 
0-28 
12-17 years 
0-30 
0-24 
Complete Blood Count with Differential 
WBC ( X10E3/UL) 
all 
4.3-12.4 

6 
 
RBC ( X10E6/UL) 
1-7 years 
3.96-5.30 
same 
8-12 years 
3.91-5.45 
same 
>12 years 
4.14-5.80 
3.77-5.28 
Hemoglobin (g/dl) 
1-7 years 
10.9-14.8 
Same 
8-12 years 
11.7-15.7 
Same 
13-15 years 
12.6-17.7 
11.1-15.9 
>15 
13.0-17.7 
11.1-15.9 
Hematocrit (%) 
1-7 years 
32.4-43.3 
Same 
8-12 years 
34.8-45.8 
Same 
>12 years 
37.5-51.0 
34.0-46.6 
MCV ( fL)  
1-7 years 
75-89 
Same 
8-12 years 
77-91 
Same 
>12 years 
79-97 
Same 
MCH (pg) 
1-7 years 
24.6-30.7 
Same 
8-12 years 
25.7-31.5 
Same 
>12 years 
26.6-33.0 
Same 
MCHC (g/dl) 
1-12 years 
31.7-36.0 
Same 
>12 years 
31.5-35.7 
Same 
RDW (%)  
1-7 years 
12.3-15.8 
Same 
8-12 years 
12.3-15.1 
Same 
>12 years 
12.3-15.4 
Same 
Platelets (X10E3/UL) 
all 
150-450 
Neutrophils (Absolute) 
(X10E3/UL) 
1-7 years 
0.9-5.4 
Same 
8-12 years  
1.2-6.0 
Same 
>12years 
1.4-7.0 
Same 
Lymphs ( Absolute) 
(X10E3/UL)  
1-7 years 
1.6-5.9 
Same 
8-12 years  
1.3-3.7 
Same 
>12years 
0.7-3.1 
Same 
Monocytes (Absolute) 
(X10E3/UL) 
1-7 years 
0.2-1.0 
Same 
8-12 years  
0.1-0.8 
Same 
>12years 
0.1-0.9 
Same 

7 
 
Eos (Absolute) ( 
X10E3/UL) 
1-7 years  
0.0-0.3 
Same 
>7 years 
0.0-0.4 
Same 
Baso (Absolute) 
(X10E3/UL) 
1-17 years 
0.0-0.2 
Same 
Immature Grans (Abs) 
(X10E3/UL) 
> 30 days  
0.0-0.1 
Same 
 
 
 
6.iiii  Study Design 
 
 
Summary Table of Study Design 
 
Part 1 
Part 2 
Part 3 
Group A 
Treatment 
Observation 
Observation 
Group B 
Placebo 
Treatment 
Observation 
 
Part 1:  Treatment 
The three treatments (oral vancomycin, magnesium citrate, and Fecal Microbiota) 
will be given sequentially. 
 Oral Vancomycin (an oral antibiotic) for 10 days to reduce the amount of 
pathogenic bacteria, followed by  
 Magnesium citrate (a laxative/bowel cleanse) for one day to remove the 
vancomycin and further reduce intestinal bacteria, followed by  
 Fecal Microbiota (purified intestinal bacteria from healthy, carefully-screened 
donors) for 2 weeks.  The dosage for the first four days will be approximately 
5 x 1011 cells/day.  It can be administered as a single dose or b.i.d. The 
maintenance dose for the next 12 weeks will be approximately 1x 1011 cells 
every four days. 
 
Group A:  vancomycin, magnesium citrate, FM 
Group B:  placebo vancomycin, magnesium citrate, placebo FM  (note that this 
group receives the real magnesium citrate because the bowel-emptying effects are 
obvious) 
 
 
Part 2:  Open-Label Observation and Cross-Over 
Group A:  observation only (no treatment) for 14 weeks 
Group B:  real treatment given in Part 1 to Group A; i.e, vancomycin, magnesium 
citrate, FM  
 

8 
 
 
Part 3:  Observation:  Follow-up at 14 weeks after the end of Part 2  
 
Participant duration will be 28 weeks for treatment/observation (part 1 and 2), and 14 weeks for 
follow-up after treatment ends (Part 3). 
Study duration will likely be 2-3 years, depending on the enrollment rate of participants. 
 
 
Tables describing schedule for Parts 1 and 2  (note that dates might vary by a few days due 
to patient scheduling issues, but treatment duration is fixed) 
 
 
 
Part 1:  Treatment for Groups A and B 
 
 
Part 1 
 
Baseline 
Days 1-10 
Day 11 
Days 12-
15 
Days 16-99  
 
 
 
 
 
 
Group A 
 
Vancomycin 
Magnesium 
Citrate 
High-dose 
FM 
Maintenance FM 
Group B 
 
Placebo 
vancomycin 
Magnesium 
Citrate (not 
placebo) 
Placebo 
FM 
Placebo FM 
Physical Exam, 
test for pill 
swallowing, 
and CGI.  OT 
evaluation 
Day 0 
 
 
 
Day 98 
AE monitoring 
by physician 
 
 
 
 
Day 98 
Contact with 
Study 
Coordinator 
and AE 
monitoring 
 
Day 10 
 
Day 12 
Day 16, 45 
DSR 
Daily for 
14 days 
prior to 
Day 0 
Daily 
 
Daily 
Daily 
Vancomycin 
adverse effect 
 
Days 1-10 
 
 
 
MT adverse 
effect 
 
 
 
Days 12-
15 
Days 16-18 
GSRS and PGI-
PTHS and 
FLACC 
Day 0 
Day 10 
 
 
Days 24, 38, 52, 
66, 80, 94  
Diet 
Evaluation 
Day 0 
 
 
 
 

9 
 
Blood, buccal 
swab 
Day 0 
 
 
 
Day 99 
Urine, Stool 
Day 0 
Day 8  
 
 
Day 24, 94 
 
Part 2:  Group A:  Observation 
 
 
 
Part 2:  Group B:  Open-label cross-over  
  
Days 99-198  
Treatments 
none 
Physical Exam, 
AE monitoring, 
and CGI.   OT 
evaluation 
Day 198 
Contact with 
Study 
Coordinator 
and AE 
monitoring 
Day 150 
DSR 
Days 134-148, 
180-194 
GSRS and PGI-
PTHS and 
FLACC 
Days 148,194  
Blood, buccal 
swab 
Day 198 
Urine, Stool 
Day 198 
 
Part 2 
 
Days 101-110 
Day 111 
Days 112-
115 
Days 116-199  
Treatments 
Vancomycin 
Magnesium 
Citrate 
High-dose 
FM 
Maintenance 
FM 
Physical Exam, 
AE monitoring, 
and CGI.   OT 
evaluation 
 
 
 
Day 199 
Contact with 
Study 
Coordinator 
and AE 
monitoring 
Day 110 
 
Day 112 
Day 116, Day 
145 
DSR 
Daily 
 
Daily 
Daily 
Vancomycin 
adverse effect 
Days 101-110 
 
 
 

10 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Part 3:  Follow-up at 14 weeks after end of Part 2 for Groups A and B 
 
Day 296 
 
Phone call with 
study physician 
and AE 
monitoring.  OT 
evaluation 
Day 296 
Contact with 
study 
coordinator and 
AE monitoring 
Day 245 
DSR 
Daily days 
280-294  
GSRS and PGI-
PTHS; Diet form 
Day 296 
Urine, Stool 
Day 296 
Diet Evaluation 
Day 296 
 
MT adverse 
effect 
 
 
Days 112-
115 
Days 116-119 
GSRS and PGI-
PTHS and 
FLACC 
Day 110 
 
 
Days 124, 138, 
152, 166, 180, 
194  
Blood, buccal 
swab 
 
 
 
Day 199 
Urine, Stool 
Day 108  
 
 
Day 124, 194 

11 
 
 
There will also be contact (phone, email, or text) with the study coordinator on approximately the 
following dates to check on compliance with the study protocol and to screen for possible adverse 
events.  
Part 1: Both Groups Days 10, 12, 16, 45  
Part 2, Group A:   
Day 150 
Part 2, Group B:   
Day 110, 112, 116, 145 
Part 3: Both Groups   Day 245 
 
Participants will be required to complete a medication checklist to determine their compliance 
with the study medication.  Also, they will be required to return medication containers with any 
unused medication at their clinic appointments. 
 
Physical Examinations:  The initial physical exam will be conducted by the lead study 
physicianin Arizona.  Since PTHS is a rare disorder, we think it is possible that some participants 
will be from out-of-state.  Due to the severe physical and mental challenges of the participants, 
we wish to minimize the burden of travel on out-of-state participants.  Therefore, out-of-state 
participants will have the option of having the subsequent blood draws and physical 
examinations done by their local physician, with a report being sent to the lead study physician 
for review.  The local physician will be offered a copy of the Investigator Brochure.  In those 
cases the lead study physician will also talk with the participants by Skype or similar video-
conferencing as part of the physical examination process, and to conduct the CGI evaluations.  
The physical exam will include an assessment of the characteristic signs and symptoms of Pitt 
Hopkins as listed in the international consensus statement. 
All physical examinations and discussions with the study physician will include monitoring for 
possible adverse events.  Also, the study physician will review the Vancomycin Adverse Effect 
Form, the Microbiota Adverse Effect form, the GSRS form, and the PGI-PTHS form.  At the 
3month and 6 month post treatment visits the study physician will also check for serious adverse 
events and adverse events of special interest including new onset diagnosis of obesity, glucose 
intolerance, an autoimmune condition, or metabolic syndrome. 
 
 
Sample Size Justification  
PTHS is a very rare condition, affecting approximately 1000 people (primarily children) in the 
US, and approximately 70% of those have chronic GI disorders.  This significantly limits our 
recruiting ability, even with the help of the PTHS Foundation which is funding the study and 
offering to help recruit for it.  Also, this is the first treatment study of any type for PTHS, so we 
hope to learn a lot from it.  Therefore, we plan to initially enroll 10 participants to obtain initial 
estimates of safety, tolerability, dosage, and efficacy.  We may enroll an additional 10 if results 
are promising but inconclusive for the first 10.   
If this study is successful and demonstrates good safety and efficacy with minimal adverse 
effects, then we will discuss with the FDA what are the next steps required to seek drug approval 
of MTT for individuals with PTHS.  If the study has limited success, we may need to enroll more 
participants, possibly with a modified study protocol based on the results of this initial study.   
 

12 
 
Analysis of Safety 
The primary safety analysis will be based on the following: 
• 
Rate and severity of adverse effects and serious adverse effects. 
• 
Average changes in any blood safety tests (blood chemistry panel and complete blood count 
with differential), and number of test results in abnormal reference range. 
 
Analysis of Tolerability  
The primary estimate of tolerability will be the percentage of consumption of each study 
medication, and number of dropouts from the study. 
 
Analysis of Efficacy  
The primary estimate of efficacy will be a comparison of changes in the Daily Stool Record 
(DSR). The secondary measures of efficacy include changes in the Clinical Global Impressions 
(CGI), Parent Global Impressions – Pitt Hopkins (PGI-PTHS), and Gastrointestinal Symptom 
Rating Scale (GSRS). 
 
Informed Consent 
After applications are screened and approved, the study coordinator will contact participants and 
explain the study to the participant’s parent/guardian.  If the child has a developmental age of 
approximately 7 years of age or older, then the study will be explained to them in a simplified 
manner, and given the opportunity to ask questions.  The study coordinator will provide an 
opportunity to ask questions, and then invite the parent/guardian (and child if possible) to 
participate in the study. 
 
 
Compensation for Participation 
Medications will be provided at no charge.  No compensation will be provided for participation in 
the study. 
 
 
 
6.v  Dosage of Medications 
 
Proposed dosage for this study, and Justification: 
 
Vancomycin (oral):  40 mg/kg P.O. per day, maximum of 2 gram P.O. (oral) per day, divided into 
three doses.  It is the same dosage we used for the Phase 1 study of MTT for ASD study, except 
for that study we treated for 14 days, and here we propose treatment for 10 days as we think that 
will be sufficient. 
 
Magnesium Citrate (oral):  The standard concentration is 1.75 g/30 mL solution.  The standard 
dose will be: 

13 
 
5-8 yr: 4 ml/kg-bodyweight 
8-12 yr: 150 ml 
12-15 yr: 200 ml 
15-18 yr: 300 ml 
Half the standard dose (above) will be given in the early afternoon, and followed by another ½ 
dose within 12 hours if sufficient clean out does not occur after 3-4 hours. 
 
The dosage may be modified based on the clinician’s assessment of the child’s history of GI 
problems and response to initial mag citrate dose. Evening meal to be clear liquids. 
 
Initial FM Oral Dose: The dosage for the first four days will be approximately 5 x 1011 cells/day.  
It will be administered as two capsules in the morning and 3 capsules in the evening.  
  
Maintenance FM Oral Dose: The maintenance dose for the next 12 weeks will be approximately 
1x 1011 cells (1 capsule) every four days. 
 
All FM doses will be given 2 hours away from meals. 
 
Justification of FM Dosing:  Our Phase 1 study of MTT for ASD (IND # 15886) used a dose of 
oral FM for  2 days of  8.3x1011, t.i.d, for a total daily dose of 2.5 x 1012 /day, and a maintenance 
FM dose of 2.5x109 CFU/day, administered 1x/day orally, for 8 weeks.   That study found that GI 
improvements were near maximal at about 5-6 weeks, and ASD improvements were initially 
maximal at 10 weeks, with greater improvement at the 2-year follow-up. Children with PTHS have 
worse phylogenetic diversity than children with ASD (see section 4.i), so we want to treat them 
for longer, and with a higher maintenance dose, to attempt to maximize their chances of clinical 
improvement. 
 
It is important to point out that the dosing of vancomycin and FM proposed here is our best 
estimate, and that the results of the proposed study will provide important guidance on dosing for 
future studies. 
 
Shipping, Handling, and Administration of Medications 
The study medications will be provided to participants by Pure Compounding Pharmacy 
(Naperville, IL).  They will individually compound vancomycin capsules for each participant.  
They will also put the FM capsules from University of Minnesota into individual bottles for the 
participants.  They will also send magnesium citrate to the participants.  The pharmacist will 
provide the medications to each participant individually after receiving the prescription from the 
study physician, using a randomization key which only they will have direct access to. 
The vancomycin, magnesium citrate, and FM will be prescribed by the study physician after 
reviewing their baseline lab safety tests (CBC and metabolic panel).   
 

14 
 
The FM will be shipped overnight from the University of Minnesota to the pharmacy in an 
insulated container with dry ice and a temperature monitor.  The pharmacy will store it in a 
temperature-monitored freezer.  The pharmacy will give the FM to individual participants in an 
insulated container with freezer packs and/or dry ice to keep it frozen (below zero oC) with a 
temperature monitor.  During storage and shipping, temperatures of 8-21 oC for up to 48 hours 
will be tolerated, but longer time periods, or temperatures above 21 oC, will result in discarding 
of the FM and replacing it with new material.  Participants will maintain the FM in their personal 
refrigerators.  Participants are given the following instructions, and any dosages which are 
unrefrigerated at room temperature for up to 24 hours, or any dosages which exceed room 
temperature (23oC) at any time, will be discarded and replaced. 
 
Instructions for Participants: 
DO NOT OPEN THE CAPSULE – it must be swallowed intact, to protect the bacteria 
from stomach acid 
Refrigeration:  Keep the microbiota in the refrigerator at all times, except to open the 
bottle and briefly remove dosage.  Take dose within 15 minutes of removing from 
refrigerator.  Do not expose to any heat.   
Keep Dry:  Keep all capsules in the container with the desiccant.  Seal the container 
tightly after each use. 
Avoid Heat:  If microbiota capsule is exposed to any heat above room temperature, or is 
left at room temperature for more than 60 minutes – CONTACT YOUR STUDY 
COORDINATOR 
Avoid placing microbiota capsules near hot spots (oven/stove/toaster, or leaving in hot 
cars), and keep refrigerated.  Even a brief dose of heat above room temperature may 
destroy the bacteria.  Request a replacement dose if there are any concerns. 
The above procedures are based on new stability data from the University of Minnesota: 
Summary of Stability Data: 
-80 oC:  at 12 months, 6.5% loss 
-20 oC:  at 12 months, 1% loss 
4 oC:  at 6 months, 4% loss 
Room temperature:  at 4 weeks, 0% loss 
 

15 
 
 
Here is the raw data on stability testing of FM samples by University of Minnesota. 
 
 
 
Labelling of Study Medications 
The following are the proposed labels for this study for the study medications. 
 
 
 
Donor 42 - 3/7/2017
Membrane integrity
replicate 1 replicate 2 replicate 3
Initial
62.4
65.5
61.1
Post lyo
58.4
62.7
61.4
replicate 1 replicate 2 replicate 3 replicate 1 replicate 2 replicate 3 replicate 1 replicate 2 replicate 3 replicate 1
replicate 2 replicate 3
1 week
56.2
62.2
57.2
55.4
51.2
58.3
61.3
55.3
59.4
51.4
49.3
57.5
2 Weeks
55.3
51.9
54.3
59.6
52.9
54.3
51
57.9
54
52.3
58.7
53.2
3 Weeks
61.2
57.4
58.3
54.3
55.2
60.4
59.8
62.1
51.7
59.3
49.4
48.4
4 Weeks
55.3
51.2
57.4
55.1
54.2
61.7
57.8
56
56.4
51.2
55.4
52.8
2 Months
49.2
55.8
59.3
51.5
60.4
62.3
53.8
52.6
53.8
3 Months
51.2
58.8
61.2
47.2
49.6
57.2
58.9
60.9
61.4
4 Months
58.4
59.3
51.3
62
50.9
47.8
49.3
57.7
58.9
5 Months
57.3
58.8
51.9
57.9
62.5
60.9
61.8
57.8
50.9
6 Months
61.3
54.3
49
50.6
60.7
47.7
52.7
51.2
57.5
12 Months
51.2
54.4
53.2
51.2
54.9
52.6 NA
NA
NA
% loss from week 1
91.1%
87.5%
93.0%
92.4%
107.2%
90.2%
86.0%
92.6%
96.8%
99.6%
112.4%
91.8%
average of 3 samples
90.5%
96.6%
91.8%
101.3%
Donor 42 - 3/8/2017
Membrane integrity
replicate 1 replicate 2 replicate 3
Initial
72.4
76.5
74.3
Post lyo
51.3
52.8
53.2
replicate 1 replicate 2 replicate 3 replicate 1 replicate 2 replicate 3 replicate 1 replicate 2 replicate 3 replicate 1
replicate 2 replicate 3
1 week
53.5
55.5
51.3
47.8
47.3
51.2
47.8
47.6
50.7
44.7
44.8
44.2
2 Weeks
53.8
47.6
53.9
46.7
47.8
49.4
47.8
48.4
43.1
41.2
42.8
43.1
3 Weeks
53.3
47.4
54.2
50.7
52
48.2
48.2
45.8
46
42.4
52.3
48.4
4 Weeks
51.3
47.5
54.1
51.1
46.9
50.9
48.8
48.7
48.3
44.6
47.2
42.3
2 Months
54.5
50.9
50.5
45.3
50
51.2
48.2
42.2
42.6
3 Months
48.4
50.4
45.6
50.5
47.5
52
44.2
47.4
48.4
4 Months
52.7
52.9
53.9
50.4
46.7
52.6
43.8
46.2
46.5
5 Months
52.9
46.1
52.7
49.4
49
50.2
42.1
47.7
49.6
6 Months
46.4
54.7
47.2
52.5
45.5
50.3
49
47
49.4
12 Months
48.2
53.9
52.3
47.7
49.9
51.4 NA
NA
NA
% loss from week 1
90.1%
97.1%
101.9%
99.8%
105.5%
100.4%
102.5%
98.7%
97.4%
99.8%
105.4%
95.7%
average of 3 samples
96.4%
101.9%
99.6%
100.3%
average from both 
donors
93.5%
99.3%
95.7%
100.8%
-80C Storage
-20C Storage
4C Storage
Room Temp
-80C Storage
-20C Storage
4C Storage
Room Temp

16 
 
Primary Label that will be on FM bottle shipped from the University of Minnesota 
 
 
 
 
 
 
 
 
 
The following are the labels for the Pure Compounding Pharmacy 
Pure Compounding Pharmacy label for Initial FM/placebo for each patient 
    
Intestinal Microbiota for Transplant 
 
LOT # _______________________ 
 
DOM ________________________ 
 
Donor ID _____________________ 
 
# of Capsules _________________ 
 
 
Store in Freezer at 0 to  – 35o C 
 
 
 
Caution: New Drug--Limited by 
Federal Law to 
Investigational Use 
 
James B Adams 
Arizona State University 
ECG 302, 501 E Tyler Mall 
Tempe, AZ 85287-6106 
Phone: (480) 818-0741 
 
 
Fecal Microbiota (FM) or Placebo Qty: 20 caps 
Initial dose: Take 2 capsules by mouth on an empty 
stomach in early morning and 3 capsules by mouth in 
evening.  
No caloric intake (solid or liquid) for 1-2 hours prior and 
1 hour after dosing. 
Take capsules with at least 1.5 ounces (3 tablespoons) of 
water. 
For oral consumption only. Swallow capsules whole – do 
not open. 
Keep refrigerated (36-46°F) – very important. 
Prescribed by ______ and compounded by Pure 
Compounding Pharmacy (630-995-4300). 
Caution:  New Drug - Limited by Federal Law to Investigational 
Use 
Produced for: 
James B. Adams 
Arizona State University 
ECG 302, 501 E. Tyler Mall 
Tempe, AZ 85287 
Phone:  480 818-0741 

17 
 
Pure Compounding Pharmacy label for Maintenance FM/placebo for each patient 
 
 
Fecal Microbiota (FM) or Placebo Qty: 21 caps 
Maintenance dose:  Take 1 capsule by mouth on an 
empty stomach every four days for 12 weeks.  
No caloric intake (solid or liquid) for 1-2 hours prior and 
1 hour after dosing. 
Take capsules with at least 1.5 ounces (3 tablespoons) 
of water. 
For oral consumption only. Swallow capsules whole – 
do not open. 
Keep refrigerated (36-46°F) – very important. 
Prescribed by _________  and compounded by Pure 
Compounding Pharmacy (630-995-4300). 
Caution:  New Drug - Limited by Federal Law to 
Investigational Use 
Produced for: 
James B. Adams 
Arizona State University 
ECG 302, 501 E. Tyler Mall 
Tempe, AZ 85287 
Phone:  480 818-0741 

18 
 
Pure Compounding Pharmacy label for Vancomycin/placebo for each patient. 
 
 
 
Vancomycin or Placebo Qty: __ caps 
Take ___________ capsules 3 times per day (after 
waking, mid-afternoon, bedtime), for 10 days.  
For oral consumption only. 
Prescribed by __________  and compounded by Pure 
Compounding Pharmacy (630-995-4300). 
For investigational use only. 
Produced for: 
James B. Adams 
Arizona State University 
ECG 302, 501 E. Tyler Mall 
Tempe, AZ 85287 
Phone:  480 818-0741 

19 
 
 
Magnesium Citrate:  No special label will be placed on the magnesium citrate since the real 
medication will always be used. 
 
 
6.vi  Outcome Measures 
Below is a chart of the outcome measures, followed by a more detailed description of them. 
The CGI will be conducted by the study physician.  All other forms will be completed by the 
participant’s parent/guardian, after receiving instructions from the study coordinator. 
 
Primary Outcome 
Measures 
 
Daily Stool Record 
A 14-day evaluation with the Bristol Stool Form Scale. 
 
Safety Measures 
Described in section 6.vii.a  Methods to Assess Drug Safety 
 
Secondary Outcome 
Measures 
CGI for GI Disorder 
CGI for PTHS Symptoms 
PGI-PTHS 
GSRS 
FLACC pain 
Tertiary/ Exploratory 
Outcome Measures 
Microbiome Composition of Stool 
OT Evaluation 
 
Possible Future 
Exploratory Outcome 
Measures 
Metabolomics of Blood, Urine, and Stool 
Measurements of 200+ metabolites in blood, urine, and stool (we will 
be collecting samples for future testing, but do not yet have funding 
for those tests). 
 
 
Detailed description of Outcome Assessments 
 
Daily Stool Record (DSR) 

20 
 
For the Daily Stool Record, participants will record the type of stool(s) each day using the 
Bristol Stool Form Scale (see below).  We will score it as the percentage of days (over 14 days) 
with a normal stool (defined as a stool with a score of 3-5 on the Bristol Stool Form Scale; 
abnormal scores are1-2 for very hard stools, and 6-7 for soft/liquid stools).  Days without a 
bowel movement, or with 3 or more bowel movements, will be counted as an abnormal day.  
Days requiring a GI medication/treatment, such as a laxative or enema, will also be counted as an 
abnormal day.  Days with significant abdominal pain would also be counted as an abnormal day. 
The reason for this scale is that most PTHS patients have constipation, but some have diarrhea, 
and some alternate between the two.  This simple form allows us to describe either type of 
problem as an “abnormal” day, and hence use a single number to describe constipation and/or 
diarrhea symptoms.   
Subscales will include the percentage of days of types 1-2 (constipation), types 6-7 (diarrhea), 
days with no stool, days with 3 or more stools, days requiring GI medication/treatment, and days 
with significant abdominal pain. 
In our Phase 1 study for autism (Kang 2017), we found that the DSR was easy for participants to 
understand and comply with, and it was able to detect significant changes due to MTT treatment.   
 
 

21 
 
THE BRISTOL STOOL FORM SCALE 
Type 1 
 
 
 
Type 2  
 
 
Type 3 
 
 
Type 4 
 
 
Type 5 
 
 
 
Type 6 
 
 
 
Type 7 
Separate hard lumps, like nuts 
 
 
 
Sausage-like but lumpy 
 
 
Like a sausage but with cracks in the surface 
 
 
Like a sausage or snake, smooth and soft 
 
 
Soft blobs with clear-cut edges 
 
 
 
Fluffy pieces with ragged edges, a mushy 
stool 
 
 
Watery, no solid pieces 
 
 
 
 
Clinical Global Impression (CGI) 
The CGI is a widely used tool for assessing severity of symptoms, and changes after treatment.  
We will use the CGI- Severity Scale (CGI-S) at baseline, and after treatment we will use the 
CGI-S, CGI-Improvement (CGI-I), and CGI-Efficacy.  The study physician will conduct all the 
CGI evaluations.   
 
We will conduct two types of CGI evaluations.  One evaluation will focus on GI symptoms 
(CGI-GI), and one will focus on PTHS-related symptoms (CGI-PH) not including GI symptoms.  
The rationale is that we hope that MTT will result in substantial improvements in GI symptoms, 
but it is unclear if it will have any effect on PTHS symptoms.  Since GI symptoms are distinct 
from PTHS symptoms, we think it is best to separate the two by using two different assessments 
by the study physician. 
 
Parent Global Impressions – Pitt Hopkins (PGI-PTHS) 
There is no validated or unvalidated instrument for assessing symptoms in PTHS patients, as this 
is the first treatment study for PTHS.  Therefore, we adapted the Parent Global Impressions of 
Autism – Revised (PGI-R3) for patients with PTHS.  The PGI-R3 includes18 different 

22 
 
symptoms, and changes in symptoms are rated on a 7-point scale from much worse (-3) to zero 
(no change) to much better (+3).  We used this scale for our Phase 1 study of MTT for ASD, and 
found it was very sensitivity to change.  Therefore, we decided to use the PGI-R3 as an initial 
basis for the PGI-PTHS, since all of the original 18 items on the PGI-R3 have also been observed 
in patients with PTHS.  Next, we added the following 9 items that are common in PTHS patients, 
based on a discussion with the Pitt Hopkins Foundation: 
1. 
Hyperventilation  
 
 
  
 
2. 
Daytime Apnea  
 
 
 
 
3. 
Gross Motor Skills  
 
 
 
4. 
Fine Motor Skills 
 
 
 
 
5. 
Ataxia (lack of communication between brain and body) 
  
 
 
 
6. 
Food allergies  
  
 
 
7. 
Environmental allergies 
 
  
 
8. 
Flushing 
9. 
Rashes  
An advantage of this scale is that it is quick to assess (10 minutes), so parents/guardians will use 
it frequently during the study to gather a quick assessment on possible changes in any PTHS-
related symptoms. 
 
 
Gastrointestinal Symptom Rating Scale (GSRS)  
The GSRS is an assessment of GI symptoms based on 15 questions, which are then scored in five 
domains: abdominal pain, reflux, indigestion, diarrhea, and constipation. We use the GSRS-
Likert, which rates each symptom on a 7-point scale.  The GSRS is somewhat limited in that the 
scale is qualitative, but we think it provides good coverage of GI symptoms common in PTHS 
patients.  Since it is not validated for PTHS patients, we are using it as a secondary outcome.  In 
our Phase 1 study for children with ASD we found it to be very sensitive to change. 
 
Revised Face Legs Activity Crying Consolability Pain Questionnaire for Children with 
Cognitive Impairment (FLACC) 
The original FLACC was slightly revised for children with cognitive impairment (Malviya et al.,   
2006) by modifying the descriptions of some items.  It assesses pain in five areas (Face Legs 
Activity Crying Consolability) using a three-point scale for each area, resulting in total FLACC 
pain scale ranging from zero to 10.  The Interrater reliability has high intraclass correlation 
coefficients (ICC, ranging from 0.76 to 0.90) and adequate kappa statistics (0.44-0.57). The 
criterion validity is supported by good correlations between FLACC, parent, and child scores 
(rho = 0.65-0.87; P < 0.001). The construct validity was demonstrated by a significant decrease 
in FLACC scores following analgesic administration (6.1 +/- 2.6 vs 1.9 +/- 2.7; P < 0.001) in a 
small study.  So, we believe it will be useful for assessing pain in children with PTHS. 
 
Diet 
The diet evaluation involves an estimate of the frequency of foods consumed during the last 
week, using the Block Brief 2000 Food Frequency Questionnaire from Nutrition Quest (child).  
Analysis of the form provides an estimate of both macro and micro nutrient intake.  This 

23 
 
information is helpful in interpreting results of microbiome measurements.  The diet form will be 
repeated at the end of the study, to determine if the treatment also results in changes in diet. 
 
PTHS Registry 
The Pitt Hopkins Research Foundation established a registry which collects a detailed 14-page 
medical history on people with PTHS.  Participants will fill out that form prior to starting the 
study, and send us a copy to provide our study physician with a detailed understanding of their 
medical history. 
 
Medical History 
This form supplements the PTHS Registry form.  It includes medical history focused on onset 
and history of PTHS and GI symptoms, other medical conditions, recent treatments, current 
medications/supplements, special diets, and level of exercise.  
 
Clinical Diagnostic Criteria for PTHS 
We will evaluate the clinical diagnostic criteria for PTHS for each participant using Table 2 of 
the Clinical Diagnostic Criteria from the International Consensus Report (Zollino et al 2019).  
This will only be used for informational purposes, as the verification of PTHS diagnosis will be 
done by review of previous genetic testing of the study participants. 
 
 
Occupational Therapy (OT) Evaluation 
At baseline (Day 0), an occupational therapist will conduct an occupational therapy evaluation 
including physical, sensory, and functional  assessments such as posture, reaching, grasping, 
playing, sensory responses, and  social/emotional behaviors.  She will conduct an assessment of 
the autonomic nerve system (ANS) with a sensor that measures heart rate variability, skin 
conductance, and surface temperature.  At the follow-ups, there will be a videocall discussion 
with the participant and their parents for approximately 15 minutes to determine if there have 
been any changes after treatment. 
 
Microbiome Assessments 
We will conduct microbiome assessments using the same approach as in our Phase 1 Study for 
ASD (Kang et al 2017).  Specifically, we will first assess the overall diversity of gut bacteria at 
baseline (before MTT treatment) and investigate how it changes after the treatment, using a non-
phylogenetic metric, Observed OTUs and a phylogenetic distance (PD) index. Next, we will 
collect individual bacterial profiles at baseline to identify specific bacteria significantly different 
between PTHS and controls (previously collected). We will also determine if there are significant 
changes in levels of either beneficial or harmful bacteria after MTT treatment. Finally, we will 
assess similarity of the gut microbiome of the recipients to that of their donor, to determine if there 
is successful engraftment.    
 
Storage of biological samples 

24 
 
 
CBC & ChemPanel: these blood samples will be sent to LabCorp or similar lab immediately 
upon collection 
 
Other blood samples, stool, urine, and buccal swab: these samples will be stored at -80oC in a 
freezer in the laboratory of Prof. Krajmalnik-Brown, in the Biodesign Center at Arizona State 
University, until we are able to conduct the tests or send them to another lab for testing.  Since 
we currently have funding for only some of the tests, it may be several years before funds are 
raised and samples can be tested.  Each sample is stored with a subject code and date of 
collection – no other identifiers. 
 
 
6.vii  Safety Considerations and Monitoring 
6.vii.a  Methods to Assess Drug Safety 
We will use several different approaches to monitor drug safety. 
1) Adverse Effect Monitoring:  Participants will be asked to report any adverse effects 
immediately if they occur.  Any possible adverse effects will be followed up by research 
staff, and reported to the study physician if a possible adverse effect has been observed.  
Physicians will ask about possible adverse effects at each clinical visit.  Research staff 
will check for possible adverse events in-between clinical visits (see section 6.iiii).  
Research staff will also review the PGI-PTHS and GSRS questionnaires to determine if 
there is any significant worsening of symptoms for any patients. 
 
For the primary outcome on safety, we will count the number of adverse effects (AE’s) 
and determine if the treatment group has more AEs than the placebo group, both in terms 
of total AE’s, and in terms of AE’s for each severity category. 
2) Vancomycin:  Minor, temporary adverse behavior reactions (irritability and/or 
hyperactivity) were observed during the first few days of administration of vancomycin in 
both our Phase 1 study and the Sandler et al 2000 study (8 weeks of oral vancomycin for 
children with ASD) in 66% and 50% of participants with ASD, respectively.  Therefore, 
participants will complete a brief Vancomycin Adverse Effect questionnaire daily during 
the vancomycin therapy, to determine if there were any adverse effects daily while taking 
the vancomycin.  If adverse symptoms continue beyond that date, they will continue filling 
out the questionnaire until adverse symptoms stop.  Similar to our Phase 1 study, this 
questionnaire will ask if there was any worsening of hyperactivity, irritability, or other 
adverse symptoms, and the severity of any symptoms, and the duration of any symptoms.  
If symptoms last longer than 2 weeks, we will continue to monitor them until they 
disappear, or until the end of Part 3 of the study. 
3) For the primary outcome on safety, we will count the number of adverse effects (AE’s) 
during vancomycin therapy, and determine if the treatment group has more AEs than the 
placebo group, both in terms of total AE’s, and in terms of AE’s for each severity category. 

25 
 
Microbiota Transplant Adverse Effect form:  For the first seven days of microbiota 
transplant, participants will complete a daily questionnaire which includes questions on 
body temperature (to check for a fever) and changes in severity of any symptoms including 
abdominal pain, vomiting, diarrhea, constipation, bloating, flatulence, hyperactivity, 
irritability, and any other symptom.   
For the primary outcome on safety, we will count the number of adverse effects (AE’s) 
during microbiota transplant, and determine if the treatment group has more AEs than the 
placebo group, both in terms of total AE’s, and in terms of AE’s for each severity category. 
4) Blood Tests:  Complete Blood Count with differential (CBC) and a comprehensive blood 
metabolic panel including kidney and liver function will be assessed at baseline, the end of 
treatment, and at 2 and 12 months post-treatment.   Since oral vancomycin and FM are 
generally well-tolerated, we believe this frequency is sufficient.  However, if there is a 
worsening of symptoms the study physician may request additional measurements of CBC, 
chemistry panel, and/or other tests.  
For the primary outcome on safety, we will determine if the treatment group has any 
significant changes in any of the blood tests compared to baseline.  Also, for each test,  we 
will count the number of participants who have a test result outside the reference range for 
that test, and determine if the treatment group has more abnormal results than the placebo 
group, both for each test individually and also for a total of all of the tests. 
5) Microbiome assessments:  We will assess changes in the microbiome, and for safety 
purposes we will focus on decreases in bacterial diversity (associated with a worsening of 
GI health) and increases in any known pathogens (such as C. Difficile).  These analyses 
require much more time (many weeks) than the other three assessments, but at the end of 
the study they will provide insight into whether or not there were any concerning changes 
in the microbiome of some individuals. 
For the primary outcome on safety, we will determine if the treatment group has a decrease 
(worsening) in bacterial diversity compared to the placebo group.  We will also determine 
if the treatment group has an increase in levels of any known pathogen compared to the 
placebo group. 
 
 
6.vii.b Adverse event monitoring 
Adverse event means any untoward medical occurrence associated with the use of a drug in 
humans, whether or not considered drug related. 
An adverse event is considered "serious" if, in the view of either the investigator or sponsor, it 
results in any of the following outcomes: Death, a life-threatening adverse event, inpatient 
hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or 
substantial disruption of the ability to conduct normal life functions, or a congenital 

26 
 
anomaly/birth defect. Important medical events that may not result in death, be life-threatening, 
or require hospitalization may be considered serious when, based upon appropriate medical 
judgment, they may jeopardize the patient or subject and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition. 
All adverse events, regardless of severity, will be monitored for and reported to the FDA. 
1.1.1.1.1.1.1.1 Participants and their Evaluators will be trained to contact the Study Coordinator 
if they experience any adverse events.  
 
The severity of an adverse event will be determined using the DAIDS Table for Grading the 
Severity of Adult and Pediatric Adverse Events (available at http://rsc.tech-
res.com/Document/safetyandpharmacovigilance/Table_for_Grading_Severity_of_Adult_Pediatri
c_Adverse_Events.pdf).  Special focus will be given to symptoms relating to gastrointestinal 
symptoms, infections, and neurological conditions, but any other symptoms will also be 
evaluated for severity.   
Reporting Procedures for all Adverse Events 
Unexpected and related fatal or life-threatening events must be reported to the FDA by 
telephone or FAX within seven (7) calendar days. The FDA Medwatch 3500A mandatory 
form will be completed and submitted (www.fda.gov/medwatch). 
 
We will send a written report to FDA within 15 calendar days for any serious unexpected 
adverse event considered related to study drug including those which have already been 
reported under the 7-day rule). 
 
All adverse events occurring during the study, regardless of severity, and whether or not 
attributed to study drug, will be included in the investigator’s annual IND report to FDA. 
 
We will use a standardized form for evaluating and reporting any withdrawal from the study 
(see Appendix). 
 
Criteria for Determining Causal Relationship between Adverse Events and Study 
Treatment. 
It will generally be assumed that changes in gastrointestinal symptoms, PTHS symptoms, 
or neurological symptoms are due to the study treatment, unless another explanation is 
clearly present.   
Adverse Events involving other symptoms will be assumed to be possibly due to the 
study treatment unless another cause is known.  Based on our clinical experience, the 
type of event, and the temporal occurrence of the event, we will attempt to rate all 
Adverse Events as to their likelihood of being related to the study treatment, using a scale 
of unrelated, possibly related, probably related, or definitely related. 
The following criteria will be used to assess the relationship of the Adverse Event to the 
study treatment: 

2 7  
 
� Unrelate d: t he a d v erse e ve nt is clearl y n ot relat e d t o t he a d mi nistrati o n of  t he st u d y 
treat me nt. A n ot her ca use of t he e ve nt is m ost pla usi ble, a n d/ or a cli nicall y pla usi ble 
te m p oral se q ue n ce is i nc o nsiste nt wit h t he o nset of t he e ve nt a n d t h e st u d y treat me nt; 
a n d/ or a ca usal rel ati o ns hi p is c o nsi dere d bi ol o gicall y i m pla usi ble;  
� P ossi bl y relate d: A n ot her ca us e of t he e ve nt is pla usi ble; h o we ver, a ca usal 
relati o ns hi p is c o nsi dere d cli nicall y/ bi ol o gicall y pla usi ble a n d t here is a pla usi ble 
te m p oral se q ue n ce bet w ee n o nset of t he a d v erse e ve nt a n d a d mi nistrati o n of t he st u d y 
treat me nt. 
� Pr o ba bl y relate d: A n ot her ca us e of t he e ve nt is less li kel y, a n d a ca usal  relati o ns hi p is 
cli nicall y/ bi ol o gicall y pla usi ble a n d t here is a pla usi ble  te m p oral se q ue nce bet wee n o nset 
of t he a d verse e v e nt a n d  a d mi nistrati o n of t he st u d y treat me nt.  
� Defi nitel y relate d: t he a d verse e ve nt is te m p orall y relate d t o t he  a d mi nistrati o n of t he 
st u d y treat me nt, a ca usal relati o ns hi p is c o nsi dere d bi ol o gicall y pla usi ble, a n d t here is n o 
alter nati ve ca use t hat pr o vi des a  m ore li kel y e x pla nati o n. 
I n a d diti o n, we will c o m pare t he re p orts of a d vers e e ve nts bet w ee n t he treat me nt a n d 
place b o gr o u ps i n Part 1, t o deter mi ne if t here is a si g nifica nt differe nce b et wee n t he 
gr o u ps. 
  
L o n g -Ter m F oll o w -U p of A dverse Eve nts  
F or a n y A d vers e E ve nts a n d Seri o us A d vers e E ve nts t hat occ ur, t he y will b e f oll o we d b y 
t he st u d y p h ysicia n o n at least a bi- wee kl y basis f or t he first 2 m o nt hs, a n d t he n at least 
m o nt hl y f or u p t o 6 m o nt hs, or u ntil t he s y m pt o ms disa p pear, w hi c he ver occ urs first.  
P h o ne f oll o w- u p ma y be use d f or s o me c o nt acts, a n d t he st u d y c o or di nat or ma y hel p wit h 
c o m m u nicati o n bet wee n t he fa mil y a n d t he st u d y p h ysicia n .  T hese e v e nts will be 
re p orte d t o t he Saf et y M o nit ori n g B oar d. 
 
 
6. vii.c Wit h dra wal fr o m t he St u d y 
Reas o ns  f or Wit h dr a wal 
A st u d y s u bject will be disc o nti n ue d fr o m f urt her st u d y a g e nt/i nter ve nti o ns i n t he st u d y 
f or: 
•  C o m pleti o n of t he st u d y; 
•  Re q uest b y s u bject’s par e nt/le gal g uar dia n t o ter mi nate partici pati o n; 
•  Re q uire me nt f or pr o hi bit e d c o nc o mita nt me dicati o n or treat me nt; 
•  U na ble t o c o m pl y wit h re q uire me nts of t he pr ot oc ol; 
•  L ost t o f oll o w- u p; 
•  At t he re q uest of t he I R B; 
•  T he s u bject’s w ell - bei n g, base d o n t he o pi ni o n of t he st u d y p h ysicia n or t he Safet y 
M o nit ori n g B oar d.  

28 
 
• We will discontinue administration of the study product in any subject that develops a 
Grade 3 or higher adverse event or serious adverse event that is assessed as possibly, 
probably or definitely related to the study product. 
 
 
Subjects who are discontinued from further study agent/interventions will be followed for 
safety until completion of the normal visit schedule. 
 
Handling of Withdrawal 
Subjects will be encouraged to complete the study; however, they may voluntarily 
withdraw at any time.  The sponsor-investigator will provide a written explanation of the 
reason for withdrawal in a source document and the reason will be recorded on a case report 
form.  Subjects will be asked for permission to continue scheduled evaluations, complete 
an end-of-study evaluation, and be given appropriate care under medical supervision until 
the symptoms of any Adverse Event resolve or the subject’s condition becomes stable.  
Subjects who drop out of the study will not be replaced. 
 
 
6.vii.d  Study-Wide Halting Criteria 
If there is a major safety concern that is study-wide, enrollment and dosing for the entire study 
may be halted.  Possible criteria for stopping all enrollment and dosing pending review of safety 
data include:   
a.   Any serious adverse event assessed as at least possibly related to study treatment; and; 
b.  Any infection with an organism acquired from the Fecal Microbiota product. 
c. Two or more subjects develop the same or similar Grade 3 adverse event that is considered 
related to the study product 
d. An anaphylactic reaction that is considered possibly, probably, or definitely related to the 
study product. 
The decision to halt enrollment and dosing study-wide may be made by the PI, the study 
physicians, the Data Safety Monitoring Board, the Research Monitor, the IRB, or the FDA. 
 
6.vii.e  Data Safety Monitoring Board 
The primary goal of the DMSB is to review the data from the study, with a focus on data related 
to participants’ safety.   

29 
 
We will use an external Data Safety Monitoring Board (DSMB) consisting of two physicians and 
one biostatistician:  Dr. Alexander Khoruts (adult gastroenterologist at University of Minnesota 
who is experienced with FMT and helped develop the FM product we are using), Dr. Jessica 
Mitchell (naturopathic physician who is leading our study of MTT for adults with autism), and 
Prof. Juergen Hahn (chair of bioengineering at Rensselaer Polytechnic Institute, and experienced 
with biostatistics and with FMT research).   
The DSMB will meet at least 1x prior to enrollment of subjects to review safety criteria, and then 
at least once every three months while patients are enrolled and being treated, until all treatments 
are completed.  They will also meet at least once every six months while participants are in the 
follow-up phase (Part 3).   The DSMB, the study physicians or the PI may call additional 
meetings if there is a safety concern, or if a Serious Adverse Event is reported.   
The DSMB will review the lab safety tests and a summary of evaluations on GI and PTHS 
symptoms at each meeting.  If any participant has a significant worsening of their GI or PTHS 
symptoms, the study physicians will report that to the DSMB. All Adverse Events will be 
reported to the Safety Board.  If there is a Serious Adverse Event then they will report it to the 
Safety Board and the IRB within 24 hours.  
The DSMB will have the right to stop treatment of an individual, or to order a halt to the entire 
study, by majority vote. 
6.vii.f  Site Monitor 
The site monitor will perform oversight functions regarding recruitment, enrollment procedures, 
and the consent process for participants; oversee study interventions and interactions; review 
monitoring plans; and oversee data matching, data collection, and analysis; and report their 
observations and findings to the Study Sponsor (who will then notify the IRB and FDA if 
needed). 
The Site Monitoring will be done by FDA Connections which is a 3rd party FDA consulting 
alliance specializing in analytical, clinical, regulatory, and compliance affairs specific to FDA 
(GCP/GMP/QSR/ISO) requirements in the Pharmaceutical, Medical Device, and Biologic 
industries. They are located 3104 E. Camelback Road, Suite 571, Phoenix, Arizona  85016   and 
their website is www.FDAConnection.com.    Their work will be performed in accordance with 
all applicable United States Food and Drug Administration (FDA) regulations, Good Clinical 
Practice (GCP) regulations, and International Committee for Harmonization (ICH) guidelines.  
These duties will include, but may not be limited to: 
1. 
Site Monitoring Visits - these activities will include: 
a) 
Site Visit Scheduling 
b) 
Mailing of Visit Confirmation Letters 

30 
 
c) 
Review completed Case Report forms and compare with source data 
d) 
Track status of data queries generated by data management personnel 
e) 
Track Serious Adverse Events occurring during the conduct of clinical trial(s) to ensure 
appropriate reporting to Sponsor and Institutional Review Board (IRB). 
f) 
Function as a communication liaison between site(s) and sponsor to expedite conduct of 
the clinical trial(s). 
g) 
Prepare and submit Site Monitoring Visit reports  
h) 
Ensure that all outstanding data queries have been satisfactorily resolved and 
documented. 
i) 
Ensure that all Clinical Trial Material and/or supplies have been accurately accounted for 
and either returned or properly destroyed. 
j) 
Ensure that all regulatory documents are complete and appropriately maintained by site 
personnel 
 
The site visits will include: 
One Site Initiation Visit (SIV)  
One monitoring visit, at the end of Part 2 of the study. 
 
Activities at site: 
a. 
Source data verification 
b. 
Queries / query resolution 
c. 
Unblinded Pharmacy review 
d. 
Regulatory documents review 
e. 
Report & Follow-up Letter 
f. 
Conference calls – as needed 
 
 

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6.viii   Mechanisms in place to protect subjects’ confidentiality 
 
1)  All study staff interacting with participants or with their identifiable info are required to 
complete the CITI training course, and sign a Confidentiality Statement, which reads: 
“As a researcher working on the above research study at Arizona State University, I 
understand that I must maintain the confidentiality of all information concerning research 
participants.  This information includes, but is not limited to, all identifying information 
and research data of participants and all information accruing from any direct or indirect 
contact I may have with said participants.  In order to maintain confidentiality, I hereby 
agree to refrain from discussing or disclosing any information regarding research 
participants, including information described without identifying information, to any 
individual who is not part of the above research study or in need of the information for 
the expressed purposes on the research program.” 
 
2)  In order to maintain participant confidentiality, each participant will be assigned a code 
number, and their information will be stored by code number in our electronic database which is 
HIPPA certified.  All study forms will use only the code number for the form.  All of our 
computers are pass-word protected.  Hard copies of data will be kept in a locked file cabinet in a 
locked office, accessible only by research team staff.   
 
6-ix. – Temporary changes to study protocol due to Coronavirus/COVID-19 
Due the disruption of travel and other activities due to the COVID-19 virus, we propose the 
following temporary changes be made to the study protocol on an “as-needed” basis as 
determined by the PI’s and the study physician.  These changes are being made to increase the 
safety of the participants.   
1) Physical Exam:  The physical exams will be done with the participant’s personal 
physician, and he/she will be asked to report the results to the study physician Dr. 
Hellmers,who will also have telehealth consults with each participant at those times. 
2) Blood draw:  The blood draw can be done by a local laboratory.  The blood draw will 
include our standard safety tests (comprehensive metabolic panel and complete blood 
count with differential).  In addition, if possible the lab will also draw the extra blood 
samples for additional tests, and those samples will be shipped frozen to ASU. 
3) There may be some delays in scheduling different evaluations and sample collections, so 
the schedule of events may change somewhat, but the treatment duration for each 
medication will remain unchanged. 
4) The occupational therapy exam will be done via telehealth. 
 
 
End of Protocol 1