A Study of Cyclophosphamide, Fludarabine, and Antithymocyte Globulin Followed by Matched Sibling Donor Hematopoietic Cell Transplantation in Patients With Fanconi Anemia
Phase: PHASE1
Conditions: Fanconi Anemia
Sponsor: Masonic Cancer Center, University of Minnesota

 
 
 
UNIVERSITY OF MINNESOTA BLOOD AND MARROW TRANSPLANTATION 
PROGRAM 
 
 
 
 
 
 
A STUDY OF CYCLOPHOSPHAMIDE, FLUDARABINE AND ANTI-THYMOCYTE 
GLOBULIN FOLLOWED BY MATCHED SIBLING DONOR HEMATOPOIETIC CELL 
TRANSPLANTATION IN PATIENTS WITH FANCONI ANEMIA 
CPRC# MT2000-09 
 
 
 
 
 
 
Version Date 
June 3, 2019 
 
 
 
Study Committee 
 
Margaret L. MacMillan, MD – PI 
John E. Wagner, MD - Co-Investigator 
Todd Defor, MS - Biostatistician 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 2 of 30 
 
 
 
CPRC #MT2000-09 
 
 
DATE 
PROTOCOL CHANGE 
August 7, 2012 
Section 10.4 and 10.5 - Set enrollment at an additional 20 patients beginning with the August 
2012 revision and update study stopping rules accordingly  
Resolve data collection inconsistencies: 
• 
Clarify the secondary objective/endpoint of regimen related toxicity is based on transplant 
outcomes through day 100 (engraftment, infections, treatment related mortality, etc.)  
• 
Patients will be monitored for reportable events according to the table in section 9.1.2 
• 
Add arm 4 for registration purposes – Sibling donor, without use of the CliniMACS 
March 3, 2011 
Added documentation that protocol is conducted under IND 14536 
October 8, 2010 
Remove IDE references and restore protocol to standard of care; Section 9 - update UPIRTSO 
reporting requirements to U of MN IRB. 
August 25, 2010 
Revision in conjunction with submission of IDE application for CliniMACS® Cell Selection 
System to be used for bone marrow processing. 
Establish study arms based on cell source as follows:  
arm 1:  bone marrow processed using Isolex 300i (for patients enrolled through April 2010), 
arm 2: UCB (no processing), arm 3: bone marrow processed using CliniMACS (for patients 
enrolled beginning with the August 2010 protocol version); update protocol to reflect IDE 
reporting requirements; Section 4 - update background with interim results (for arm 1); section 7 
– update to reflect change in cell processing device; added targeted event form. 
Other revisions:  Section 6.2 - update MMF administration; Section 6.4 add cell infusion 
guidelines; Section 10 – Statistical Considerations rewrite to reflect current study  
Updates: Add study synopsis/schema; Section 2.2 – delete secondary objective 2.2.2. relapse in 
patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), as these 
patients are not eligible as of November 2002; Section 5.3 add patient registration information; 
Section 6 add standard care language (delete supportive care appendix, add appendix V - Drug 
Formulation and Availability); Section 8 and Appendix I – update required observations (delete 
panorex, add CT abd, pelvis to r/o tumors, delete day 60 bm bx); Section 9 – update to current 
definition of UPRITSO and AE reporting table; add data collection and record retention sections; 
update header and footer. 
March 24, 2010 
Section 6.2, MMF will now be used for GVHD prophylaxis per current institutional standards; 
Section 7.1 Cell Processing – replace Isolex 300i System with CliniMACS® Cell Selection 
System (Miltenyi Biotec), add protocol to current  CliniMACS IDE (D. Weisdorf sponsor); add 
section SAE reporting and DSMP; Appendix VI - update risks.  Deleted appendix VII – study 
uses CTC version 2 for toxicity criteria; Additional Minor edits; Update consents 
November 5, 2007 
Further revised information on fungal prophylaxis to allow for changes based on individual 
patient needs. 
September 7, 2007 
Changed fungal prophylaxis from Itraconazole to voriconazole (Section 6.2.1) 
Dr. Norma Ramsay removed from study committee. 
Each patient is to receive 1.0 x 105/kg CD3+ cells.  An add back infusion of CD3+ cells may be 
required to achieve this prescribed cell dose (section 7.1.1).   
November 24, 2003 
Maximum enrollment raised to 24 subjects and statistical section revised accordingly (section 9). 
September 17, 
2003 
Dr. Stella Davies and Dr. Anne Goldman removed from study committee.  Todd Defor added as 
biostatistician. 
November 20, 2002 
Revised eligibility to include only patients with HLA-matched sibling donors, and exclude 
patients with advanced MDS or AML prior to transplantation (section 5.1 and 5.2) 
July 1, 2002 
1. Added Amendment page 
2. Removed the creatinine clearance > 40 mL/min from the inclusion criteria (section 5.4.1) 
because this study is the safest preparative regimen for Fanconi patients with matched 
siblings, who have severe renal disease 
January 9, 2002 
Changed title from A Phase I-II Study of Cyclophosphamide, Fludarabine, and Antithymocyte 
Globulin Followed by Matched Sibling Donor Hematopoietic Cell Transplantation in Patients 
with Fanconi Anemia to A Study of Cyclophosphamide, Fludarabine, and Antithymocyte 
Globulin Followed by Matched Sibling Donor Hematopoietic Cell Transplantation in Patients 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 3 of 30 
 
 
 
CPRC #MT2000-09 
 
DATE 
PROTOCOL CHANGE 
with Fanconi Anemia 
November 1, 2016 
Updated protocol to remove IND as all subjects will now be co-enrolled on the HUD protocol. 
Related donors will now be co-enrolled on MT2012-14 
Antifungal therapy updated to current standard of care (section 6.3) 
Removed standard of care evaluations from the trial (section 8 and Appendix 1) 
Removed day 21 bone marrow biopsy  
June 3, 2019 
Revised to clarify that post-transplant bone marrow aspirates and biopsies will only be 
performed if clinically indicated 
Section 5.1.3, eligibility criteria: definition of moderately severe SAA will no longer be different 
for patients under age 18 
Updated required observations (Section 8.0 and appendix I) to current standard of care 
Updated reporting guidelines (Section 9) to current SOPs 
Throughout protocol minor edits for spelling and clarity  

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 4 of 30 
 
 
 
CPRC #MT2000-09 
 
TABLE OF CONTENTS 
 
TABLE OF CONTENTS ..................................................................................................................... 4 
SCHEMA ............................................................................................................................................... 5 
1.0 
TITLE ......................................................................................................................................... 6 
2.0 
OBJECTIVES ............................................................................................................................ 6 
3.0 
STUDY DESIGN ........................................................................................................................ 6 
4.0 
BACKGROUND AND RATIONALE ..................................................................................... 6 
5.0 
ELIGIBILITY AND EXCLUSION CRITERIA/STUDY REGISTRATION ...................... 8 
6.0 
TREATMENT SCHEMA ....................................................................................................... 10 
7.0 
HEMATOPOIETIC STEM CELL HARVEST AND PROCESSING ............................... 12 
8.0 
REQUIRED OBSERVATIONS ............................................................................................. 13 
9.0 
EVENT REPORTING AND DATA AND SAFETY MONITORING PLAN .................... 15 
10.0 
EXPERIMENTAL DESIGN AND STATISTICAL CONSIDERATIONS .................... 18 
11.0 
CONDUCT OF THE STUDY ............................................................................................. 20 
12.0 
REFERENCES ..................................................................................................................... 21 
APPENDIX I - SCHEDULE OF ACTIVITIES FOR EACH PATIENT ...................................... 23 
APPENDIX II - GRAFT VERSUS HOST DISEASE ..................................................................... 24 
APPENDIX III - PERFORMANCE STATUS SCALE .................................................................. 25 
APPENDIX IV - EXPECTED TOXICITIES .................................................................................. 26 
APPENDIX V – DRUG FORMULATION AND AVAILABILITY .............................................. 29 
  
 
 
 
 
 
 
 
 
 
 
 
PI Contact Information: 
Margaret L. MacMillan, MD 
Pediatric BMT 
MMC 484   
420 Delaware Street SE 
Minneapolis, MN 55455 
612 626-2961 (phone) 
612-626-2815 (fax) 
macmi002@umn.edu (email) 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 5 of 30 
 
 
 
CPRC #MT2000-09 
 
SYNOPSIS/SCHEMA 
 
Study Design: 
Single institution phase II study grouped by cell source: 
Arm 1: match sibling donor marrow TCD using Isolex®300i System (for patients 
enrolled through April 2010) 
Arm 2: UCB (no processing, co-enroll on MT2011-13R for unlicensed UCB registry 
Arm 3: match sibling donor marrow TCD using CliniMACS Cell Selection System 
(effective with August 2010 protocol). Effective with November 1, 2016 protocol co 
enroll on MT2015-31 for TCD. 
Arm 4:  match sibling donor marrow without use of the CliniMACS 
 
Except for cell source, all aspects of the study treatment are identical for all patients. 
 
Eligible Diseases: 
Age < 60 and diagnosis of Fanconi anemia meeting one of the following disease 
requirements: 
• < 18 years of age with moderately severe aplastic anemia (AA) and having at least 
one of the following: 
o platelet count <40 x 109/L 
o absolute neutrophil count <10 x 108/L 
o hemoglobin <9 g/dL 
• ≥18 and < 60 years of age with moderately severe aplastic anemia (AA)  and 
having at least one of the following: 
o platelet count <20 x 109/L 
o absolute neutrophil count <5 x 108/L 
o hemoglobin <8 g/dL 
• early myelodysplastic syndrome with multilineage dysplasia and < 5% blasts, with 
or without chromosomal anomalies 
 
SCHEMA 
 
 
Patients will receive antifungal prophylaxis beginning 1 month prior to conditioning therapy, if possible.   
 
 
 
 
 
 
 
 
 
 
Day    -6   -5    -4   -3    -2    -1    0    1                                    30             45              60              90        100 
 
 
 
 
 
     Fludarabine 35 mg/m2 IV 
 
     Cyclophosphamide 5 mg/kg IV 
 
     Anti-thymocyte globulin (ATG) 30 mg/kg with Methylprednisolone 2 mg/kg/day as pre-med 
CSA (begin taper at day +100) 
MMF (until day +30 or 7 days after engraftment) 
HSC infusion 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 6 of 30 
 
 
 
CPRC #MT2000-09 
 
 
1.0 
TITLE 
 
A study of cyclophosphamide (CY), fludarabine (FLU) and anti-thymocyte globulin (ATG) 
followed by matched sibling donor hematopoietic cell transplantation (HCT) in patients with 
Fanconi Anemia (FA). 
 
 
2.0 
OBJECTIVES 
 
2.1 
Primary Objective 
 
To determine the probability of engraftment in FA patients treated with CY, FLU and 
ATG followed by an HLA-genotypically identical related donor HCT. 
 
2.2 
Secondary Objectives 
 
To evaluate the incidence of: 
2.2.1 acute (aGVHD) and chronic (cGVHD) graft-versus-host disease 
2.2.2 regimen-related toxicity (RRT) based on transplant outcomes through day 100 
2.2.3 one year survival 
2.2.4 late secondary malignancies (e.g. squamous cell carcinoma of head and neck, 
and cervix) 
 
 
3.0 
STUDY DESIGN 
 
This is a study designed to evaluate neutrophil engraftment in Fanconi anemia (FA) patients 
transplanted with CD34+ selected bone marrow stem cells after a chemotherapy regimen consisting 
of CY, FLU and ATG. 
 
 
4.0 
BACKGROUND AND RATIONALE 
 
HCT from an allogeneic donor is the only treatment with curative potential for patients with the 
hematological complications of FA.  Durable engraftment and long term survival has been observed 
in matched sibling donor HCT after preparative regimens consisting of limited field irradiation (LFI) 
and low dose cyclophosphamide (CY).1-7 
 
For the IBMTR, Gluckman et al. (1995) analyzed the outcome of 151 patients who received HCT for 
FA from HLA-identical siblings.5  Age at transplant ranged from 1 to 39 years (median 10 years).  
Preparative therapies consisted of low dose CY (15 to 25 mg/kg) and limited field irradiation (LFI; 
400-1500 cGy) with or without ATG (n = 75), low dose CY and total body irradiation (TBI; 300-800 
cGy) (n = 20), and high dose CY (≥100 mg/kg) with or without ATG (n = 25).  GVHD prophylaxis 
regimens included cyclosporine (CSA) (n = 82), methotrexate (MTX) (n = 10), and (3) CSA and 
MTX (n = 28).  Two year probability of myeloid engraftment was 92%.  Probabilities of grade II-IV 
acute GVHD at day 100 was 42% and of chronic GVHD at 2 years 44%.  Probability of survival at 2 
years was 66%.   In multivariate analysis, improved engraftment rates were observed with age of 
HCT ≤10 years, conditioning including ATG, and higher platelet count pretransplant.  In multivariate 
analysis, decreased mortality was observed with younger age, use of ATG in the conditioning 
regimen, conditioning with LFI and low-dose CY versus ≥100 mg/kg CY and no irradiation, and the 
use of cyclosporin with or without methotrexate for GVHD prophylaxis. 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 7 of 30 
 
 
 
CPRC #MT2000-09 
 
Long-term follow-up studies indicates that although successful HCT may cure the hematological 
complications of FA, patients are still at high risk for malignancy with approximately 40% of patients 
developing a malignancy within 15-20 years after HCT.8,9  In an analysis of 700 patients with FA 
(n=79) or aplastic anemia (n=621) treated with allogeneic HCT in Seattle or Paris, the Kaplan-Meier 
estimate developing any malignancy by 20 years after transplantation was 14%.8  The probability of 
FA patients developing a malignancy by 20 years after HCT was 42%.  For the entire cohort of 
patients, risk factors for developing malignancy identified in multivariate analysis included chronic 
GVHD and azathioprine therapy, and the diagnosis of FA.  In the non-FA group, chronic GVHD and 
azathioprine therapy, or irradiation were associated with increased risk of malignancy. 
 
The Paris group described the long-term follow-up of 50 FA patients transplanted from a related 
donor.9  With a median follow-up of >6 years, 32 patients (64%) were alive with a probability of 
survival at 100 months of 58.5%.  In multivariate analysis, the only factor significant for poor 
survival was receiving more than 20 transfusions prior to HCT.  The most important long-term 
complication in this group of patients was the occurrence of epidermoid carcinoma.  Six male 
patients developed epidermoid head and neck cancers.  All six patients had extensive chronic GVHD.  
The mean elapsed time between transplantation and the diagnosis of cancer was 8.2 years (range 5-26 
years).   A seventh patient developed a liver carcinoma 16 years after HCT.  This patient had an 
androgen-induced adenoma before HCT and chronic hepatitis C.  The 8- and 13- year projected 
incidence of malignancy in this cohort of patients was 24% and 43% respectively. 
 
In an attempt to reduce the risk of malignancy, the Seattle group used a preparative regimen of CY 
120-200 mg/kg without irradiation in 41 FA patients receiving related donor HCT (MSD in 38).10  
GVHD prophylaxis was with CSA and MTX (n=27), CSA alone (n=6) or MTX alone (n=8).  Durable 
engraftment was observed in 88% of evaluable patients.  Two patients, each conditioned with 200 
mg/kg CY developed squamous cell carcinoma of the oral cavity 9.4 and 11 years after transplant.  
One patient had been treated with azothrioprine for chronic GVHD however this medication had been 
discontinued 9 years before the diagnosis of the malignancy. 
 
Smaller doses of CY have been used in a few cases.  In Hammersmith, 3 FA patients were 
transplanted with HLA-identical sibling donor BM after a preparative regimen of CY 20 mg/kg in 2 
cases and CY 80 mg/kg in one case.11  GVHD prophylaxis consisted of CSA.  All 3 patients achieved 
myeloid engraftment and long term survival.  One patient developed grade II acute GHVD of the skin 
and gut.  
 
To potentially decrease the long-term effects of HCT, we have chosen fludarabine (FLU) to replace 
the use of irradiation.  FLU is an antimetabolite that has been shown to be an effective 
immunosuppressive agent in BMT conditioning therapy.12-15  As FLU is not a cross-linking agent, it 
will likely be well tolerated in FA patients.  The combination of FLU and CY may offer sufficient 
engraftment rates and decrease the risk of long term complications after HCT.  There are a couple of 
published case reports from Israel using a fludarabine in FA patients.16,17  In both cases, preparative 
therapy consisted of CY (10 mg/m2), FLU (150 mg/m2) and ATG (40-50 mg/kg).  GVHD 
prophylaxis consisted of CSA.  Stem cell sources were an HLA-matched cousin bone marrow in one 
case and an HLA-matched sibling umbilical cord blood in the second.  Myeloid engraftment was 
achieved on day +12 in the bone marrow recipient and day +28 in the UCB recipient.  Myeloid 
engraftment was achieved on day +28.  Acute grade II GVHD of the gut and liver developed in the 
UCB recipient and was successfully treated with CSA and steroids.16  
 
In summary, two factors appear to be associated with risk of late malignancy in FA patients: 1) TBI 
and 2) development of chronic GVHD.  Therefore, in an attempt to decrease the risk of malignancy, 
we have developed a regimen that does not include irradiation and have incorporated TCD to reduce 
the risk of chronic GVHD.  In view of the fact that we are the largest referral center for HCT for FA 
and we have considerable experience with TCD, we have the unique ability to evaluate this treatment 
plan.  We anticipate transplanting 5 patients per year with sibling donors using this new protocol. 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 8 of 30 
 
 
 
CPRC #MT2000-09 
 
 
In April 2010, Isolex®300i System were no longer available as they ceased to be manufactured and 
therefore enrolment on arm 1 has been terminated.  As of August 2010, CliniMACS Cell Selection 
System will be used for T cell depletion of all bone marrow products used in this protocol and 
recipients of BM will be enrolled on this new arm 3. 
 
As of August 2010, 23 subjects have been enrolled on this protocol.   All subjects achieved primary 
engraftment. One subject, a recipient of an HLA-matched maternal BM, developed secondary graft 
failure (had initially engrafted but later lost the graft).  He was retransplanted using the same donor 
but later died from chronic GVHD.  Two patients also died after transplant from relapsed MDS.  In 
light of these events, in November 2002, the eligibility was changed to only allow for HLA-identical 
sibling donors and to exclude FA patients with MDS or acute leukemia.  A fourth patient (age 43 
years) died from an intracranial hemorrhage shortly after transplantation. No patient has developed 
acute or chronic GVHD after an initial transplantation.  To date, 19 of 20 recipients of HLA matched 
sibling donor HCT who had aplastic anemia at the time of transplant are alive and well.  This result is 
superior to any published report of matched sibling donor HCT in FA patients.  
 
As of August 2010, we have successfully shown that neutrophil engraftment is achievable in FA 
patients transplanted with CD34+ selected bone marrow stem cells (using the Isolex®300i System) 
after a chemotherapy regimen consisting of CY, FLU and ATG (arm 1 of trial).  As the Isolex®300i 
System is no longer available we want to open a new arm of this protocol to study whether neutrophil 
engraftment is achievable in FA patients transplanted with CD34+ selected bone marrow stem cells 
(using the CliniMACS Cell Selection System) after the same chemotherapy regimen consisting of 
CY, FLU and ATG (arm 3).   We will continue to accrue patients in arm 2 of the study in which 
sibling donor UCB is used as the stem cell source.  We will also continue to follow all patients for the 
development of acute and chronic GVHD and late effects. 
 
In August 2012, arm 4 was added as it was recognized not all sibling donor bone marrow will require 
cell selection using the CliniMACS.  The decision whether or not to do CD34 selection will be made 
on an individual patient basis.  Enrollment plans were also updated.  Using the August 2010 revision 
as the starting point, an additional 20 patients will be accrued. 
 
 
 
5.0 
ELIGIBILITY AND EXCLUSION CRITERIA/STUDY REGISTRATION 
 
5.1 
Inclusion Criteria 
 
5.1.1 Patients must be <60 years of age with a diagnosis of FA. 
 
5.1.2 Patients must have an HLA-A, B, DRB1 identical sibling donor. Related donors will 
be evaluated under the University of Minnesota donor protocol MT2012-14C.  Patients and 
donors will be typed for HLA-A and B using serological or molecular techniques and for 
DRB1 using high resolution molecular typing.  If a matched sibling marrow donor is not 
available, UCB may be used as a cell source.  If unlicensed cord blood unit is used, patients 
will co-enroll on MT2011-13R: Infusion of Cell Populations from Unlicensed Umbilical Cord 
Blood Units. 
 
5.1.3 Patients with FA must have moderately severe aplastic anemia (AA), early 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 9 of 30 
 
 
 
CPRC #MT2000-09 
 
myelodysplastic syndrome (MDS) with no excess blasts with or without chromosomal 
abnormalities. 
5.1.3.1  
1) 
platelet count <20 x 109/L 
2) 
ANC <5 x 108/L 
3) 
Hgb <8 g/dL 
 
5.1.3.3  Early myelodysplastic syndrome, with multilineage dysplasia with < 5% 
blasts, with or without chromosomal anomalies. 
 
5.1.4 Adequate major organ function including: 
5.1.4.1 Cardiac: ejection fraction >45% 
5.1.4.2 Hepatic: no clinical evidence of hepatic failure (e.g. coagulopathy, ascites) 
5.1.4.3 Karnofsky performance status >70% or Lansky >50 (for patients < 16 years) 
 
5.1.5  Women of child bearing age must be using adequate birth control and have a negative 
pregnancy test. 
 
5.1.6 
Written consent. 
 
5.2 
Exclusion Criteria 
 
5.2.1 Active bacterial infection within one week of HCT. 
5.2.2 Active fungal infection at time of HCT. 
5.2.3 Late MDS with greater than 5% blasts in bone marrow. 
5.2.4 AML or history of AML. 
5.2.5 Malignant solid tumor (e.g. squamous cell carcinoma of the head/neck/cervix) within 
2 years of HCT. 
5.2.6 Pregnant or lactating female. 
 
5.3 
Patient Registration  
To be eligible for registration to this study, the patient must meet each criteria listed on the 
eligibility checklist based on the eligibility assessment documented in the patient’s medical 
record. 
5.3.1 Registration with the Clinical Trials Office 
Upon completion of the screening evaluation, eligibility confirmation and obtaining informed 
consent, a designated study staff person will enroll the patient into OnCore.  At the time of 
registration, the patient’s cell source/processing will be indicated in OnCore as one of the 
following study arms: 
Arm 1:  bone marrow processed using Isolex 300i (for patients enrolled through April 2010) 
Arm 2: UCB – no processing. If one or both of the cord blood units used for the graft is 
unlicensed, the participant will co-enroll on University of Minnesota protocol MT2011-13R 
“Infusion of Cell Populations from Unlicensed Umbilical Cord Blood Units.” 
Arm 3: bone marrow processed using CliniMACS (for patients enrolled beginning with the 
August 2010 protocol version). Subjects enrolled on the November 1, 2016 version of the 
protocol will co-enroll on University of Minnesota Protocol MT2015-31 “CliniMACS CD34 
Reagent System as a HUD for Obtaining CD34+ Cell-Enriched Products” 
Arm 4:  match sibling donor marrow without use of the CliniMACS 
 
5.3.1 Patients Who Are Registered and Do Not Receive Study Treatment 
If a patient is registered to the study, and is later found not able to begin the preparative 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 10 of 30 
 
 
 
CPRC #MT2000-09 
 
regimen (beginning with the first dose of fludarabine), for whatever reason, the patient will be 
removed from study and treated at the physician’s discretion.  The patient will be considered a 
screen/baseline failure and the reason for removal from study will be clearly indicated in 
OnCore. 
 
 
 
6.0 
TREATMENT SCHEMA 
In order to provide optimal patient care and to account for individual medical conditions, investigator 
discretion may be used in the prescribing of all supportive care therapy (i.e. acetaminophen, 
diphenhydramine, G-CSF, antimicrobials, etc). 
 
Patients will receive antifungal prophylaxis beginning 1 month prior to conditioning therapy, if 
possible.  Refer to section 6.3. 
 
See appendices IV and V for preparative and prophylaxis drug information including expected 
toxicities.    
 
 
Day 
Treatment 
-6 
CY 5 mg/kg IV 
FLU 35 mg/m2 IV 
ATG 30 mg/kg/day IV 
MP 2 mg/kg IV 
-5 
CY 5 mg/kg IV 
FLU 35 mg/m2 IV 
ATG 30 mg/kg/day IV 
MP 2 mg/kg IV 
-4 
CY 5 mg/kg IV 
FLU 35 mg/m2 IV 
ATG 30 mg/kg/day IV 
MP 2 mg/kg IV 
-3 
CY 5 mg/kg IV 
FLU 35 mg/m2 IV 
ATG 30 mg/kg/day IV 
MP 2 mg/kg IV 
-2 
FLU 35 mg/m2 IV 
ATG 30 mg/kg/day IV 
MP 2 mg/kg IV 
-1 
Rest day 
0 
HCT 
+1 
Initiate G-CSF 5mcg/kg per day 
IV (continue until ANC ≥2.5 x 
109/L) 
 
The administration of the preparative regimen will follow the institutional dosing 
and supportive care guidelines.  Dose and/or schedule adjustments consistent with 
the standard of care may be made on an individual patient basis as needed for 
safety.     
 
6.1 
Preparative Therapies 
The preparative cytoreductive therapy will be identical for all patients.  Toxicities related to 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 11 of 30 
 
 
 
CPRC #MT2000-09 
 
the preparative regimen are defined in Appendix IV. 
 
6.1.1 Cyclophosphamide 
CY 5 mg/kg is to be given as a 2 hour infusion with strict attention to vigorous hydration, 
fluid balance and maintenance of good urine output.  Mesna (5 mg/kg) in divided doses may 
be given in the first 24 hours after CY. 
 
6.1.2 Fludarabine 
FLU 35 mg/m2 will be given IV over 30 minutes.  Preparation, administration and monitoring 
will be according to standard practice procedures. 
 
6.1.3 Anti-thymocyte globulin 
ATG (ATGAM; Upjohn Corporation) 30 mg/kg/day will be administered after MP on days -
6, -5, -4, -3 and -2.  ATG will be diluted in sterile normal saline or half normal saline for 
intravenous infusion to a concentration of 1-2 mg/mL and will be infused through the 
Hickman catheter over 4 - 6 hours. In the event of a significant reaction to ATGAM, the agent 
will not be administered; instead patients will receive thymoglobulin (rabbit ATG) 1.5 mg/kg 
every 12 hours diluted in sterile normal saline or half normal saline for intravenous infusion to 
a concentration of 0.5 mg/mL and will be infused through the central venous line over 4 - 6 
hours.  In the event of a significant reaction to thymoglobulin, the agent will not be 
administered. 
 
Methylprednisolone (MP) 2 mg/kg/day intravenously every 24 hours will be given from day -
6 until day -2 as a premedication for ATG. 
 
6.2 
GVHD Prophylaxis 
 
Patients will receive cyclosporine A (CSA) and mycophenylate mofetil (MMF) as GVHD 
prophylaxis. 
 
6.2.1 CSA 
Patients will receive CSA therapy beginning on day -3 with a taper commencing on day +100.  
For adults with normal baseline renal function (creatinine <1.2 mg/dL), the initial dose will be 
2.5 mg/kg IV over 2 hours every 12 hours; for children <40 kg, the initial dose will be 2.5 
mg/kg IV over 2 hours every 8 hours.  CSA dosing will be monitored and altered as clinically 
appropriate per University of Minnesota Medical Center - Fairview pharmacy guidelines.  
Dose adjustments will be made on the basis of toxicity and low CSA levels with a trough 
level of <200 mg/L.   
 
Once the patient can tolerate oral medications and has a normal gastrointestinal transit time, 
CSA will be converted to an oral form at a dose of 5.0 mg/kg PO every 12 hours.  Beginning 
on day +100 or 1 month after control of GVHD (whichever is later), CSA will be tapered by 
10%/week. 
 
6.2.2 MMF 
Patients will receive MMF therapy beginning on day -3 through day +30 or for 7 days after 
engraftment, whichever day is later, if no acute GVHD.  Engraftment is defined as 1st day of 
3 consecutive days of absolute neutrophil count [ANC] > 0.5 x 109/L. 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 12 of 30 
 
 
 
CPRC #MT2000-09 
 
 
MMF will be given at a dose of 15 mg/kg/dose every 8 hours PO (to a maximum dose of 1 
gram).  The MMF dose may be adjusted to tablet sizes of 250 mg and 500 mg or administered 
using the suspension.  MMF may be given IV at the same dose if PO not tolerated.  MMF 
dosing is to be monitored and altered as clinically appropriate based on Pharmacist orders. 
  
If the patient has acute GVHD requiring systemic therapy, MMF may be stopped 7 days after 
initiation of systemic therapy for acute GVHD (e.g. resolution of skin rash, vomiting, and 
diarrhea). 
 
6.3 Antifungal Therapy 
Patients will receive anti-fungal prophylactic therapy with itraconazole, posoconazole, 
caspofungin or micofungin beginning up to 1 month prior to conditioning therapy. Antifungal 
prophylaxis will be given until at least 100 days after HSCT. 
 
6.4 
Stem Cell Infusion (day 0) 
Bone marrow and UCB grafts will be evaluated for sterility, cell viability, nucleated cell 
count, CD34 and CD3 counts. 
 
 
6.4.1 Bone Marrow (arm 1 and 3) 
Refer to Section 7 for bone marrow collection and processing information. Related donors 
will be evaluated and collected per MT2012-14C.  Infuse per University of Minnesota 
institutional guidelines for bone marrow. 
 
6.4.2 Umbilical Cord Blood (arm 2) 
Selection of UCB will be based upon institutional guidelines. The selection of the UCB unit 
will be based on level of HLA match and cell doses following a University of Minnesota 
specific UCB Selection Algorithm. The ideal body weight will be determined for all patients. 
 
The UCB will not be manipulated.  If one or both of the cord blood units used for the graft is 
unlicensed, the participant will co-enroll on University of Minnesota protocol MT2011-13R 
“Infusion of Cell Populations from Unlicensed Umbilical Cord Blood Units.” 
 
The hydration regimen will be given following institutional guidelines. Patients should 
receive pre-medication acetaminophen and diphenhydramine hydrochloride 15 to 30 minutes 
before infusion.  
 
After proper identification and crosschecking according to institutional guidelines, the UCB 
unit will be infused through a central line without in-line filtration per institutional guidelines. 
 
 6.5 G-CSF 
Initiate G-CSF 5mcg/kg per day IV day +1 and continue until ANC ≥ 2.5 x 109/L. 
 
 
 
7.0 
HEMATOPOIETIC STEM CELL HARVEST AND PROCESSING 
 
Donor marrow will be collected in the usual sterile manner.  The harvested marrow (prior to TCD) 
should contain a minimum of 2.5 x 108 nucleated cells/kg recipient body weight with a goal of >5.0 x 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 13 of 30 
 
 
 
CPRC #MT2000-09 
 
108 nucleated cells/kg recipient body weight. The ideal body weight will be determined for all 
patients. 
 
With the August 2010 protocol revision and the addition of study arm 3 (bone marrow processing 
using CliniMACS), CD34+ cells will be isolated from the bone marrow with the CliniMACS® Cell 
Selection System (Miltenyi Biotec). Each patient is to receive 1.0 x 105/kg CD3+ cells.  An add back 
infusion of CD3+ cells may be required to achieve this prescribed cell dose.  Refer to the CMC for 
additional processing information and lot release criteria.  With the August 2012 revision, arm 4 was 
added for bone marrow not using the CliniMACS. In August 2016, the University of Minnesota 
received approval to use the CliniMACS CD34 Reagent System as a Humanitarian Use Device 
(HUD) as protocol number MT2015-31. With the November 2016 amendment, we will be using 
MT2015-31 to co-enroll subjects needing CD34+ cell isolation. 
 
Prior to activation of the August 2010 amendment, cell selection was done using the Isolex®300i 
System (Nexell Therapeutics, Inc.) under treatment arm 1 (bone marrow processing using 
Isolex®300i System).  
 
 
 
 
8.0 
REQUIRED OBSERVATIONS 
 
8.1 
Schedule of Activities  
 
(See Appendix I) 
 
8.2 
Pre Study Screening Procedures 
 
 
 
8.2.1 
Chest radiograph and other radiographic studies (as clinically indicated) 
 
8.2.2 High resolution CT of chest, abdomen and pelvis  
 
 
8.2.3 Bone marrow aspirate and biopsy 
 
 
8.2.4 Karnofsky or Lansky performance status (Appendix IV) 
 
8.2.5 Ultrasound of liver and kidneys 
 
8.2.6 Pulmonary function tests if capable (children >6 years, adults) 
 
8.2.7 ECG; ECHO 
 
8.2.8 Hematology with differential 
 
 
8.2.9 Urinalysis and 24 hour urine creatinine clearance or GFR.  
 
 
8.2.10 Pregnancy test (urine) - as clinically indicated 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 14 of 30 
 
 
 
CPRC #MT2000-09 
 
 
8.2.11 CMV Titer (donor/recipient) 
 
 
 
8.3 
Evaluation During Therapy Until Engraftment 
 
8.3.1 CBC with platelet count daily until one week after ANC > 5 x 108/L, PLT >20 x 109/L 
then twice weekly or as indicated 
 
 
8.3.2 After stem cell infusion, GVHD evaluation weekly and as clinically indicated 
 
 
8.4 
Evaluation Post Engraftment To Discharge 
 
8.4.1 Physical examinations weekly until discharge 
 
8.4.2 CBC with platelet count weekly until discharge 
 
8.4.3 GVHD evaluations as clinically indicated 
 
8.4.4 Test peripheral blood and/or bone marrow for chimerism as clinically indicated 
 
8.4.5 Review for events per section 9 and for the BMT database 
 
8.5 
Evaluation Post Engraftment at Day 60, 90-100 and 180 Then Once Yearly for 2 
Years 
 
8.5.1 CBC, differential and platelet 
 
8.5.2 GVHD score 
 
8.5.3 Physical exam 
 
8.5.4 Peripheral blood Chimerism assay on day 21-30, 90-100, and 180 days, 1 and 2 years  
 
8.5.5 Review for events per section 9 and for the BMT database  
 
 
8.6 
Engraftment Evaluation 
 
Peripheral blood CBC counts will be monitored daily after transplantation until engraftment 
and weekly after engraftment while hospitalized.  CBC counts will be evaluated at follow-up 
visits in the outpatient clinic.  Chimerism assay of the blood will be sent on day 21-30, day 
90-100, day 180, and 1 and 2 years post transplant.     
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 15 of 30 
 
 
 
CPRC #MT2000-09 
 
 
 
9.0 
EVENT REPORTING AND DATA AND SAFETY MONITORING PLAN 
 
Toxicity and adverse events will be classified according to NCI's Common Terminology Criteria for 
Adverse Events V 4.0 (CTCAE). A copy of the CTCAE can be downloaded from the CTEP home 
page: 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm#ctc_40 
 
FOR UNLICENSED UCB UNITS ONLY: Selected expected adverse reactions determined to be 
caused by or at least possibly caused by the UCB units based on objective evidence will be reported 
in an expedited manner to the FDA under University of Minnesota IND BB-14797 (C. Brunstein, 
MD, PhD –sponsor/investigator). 
 
FOR CD34+ SELECTED CELLS ONLY: Any clinically significant safety issues associated with cell 
processing failure or device malfunction regarding the CliniMACS® system must be 
reported to the PI (Dr. Margaret MacMillan) and Miltenyi (boston@miltenyibiotec.com) per 
institutional procedures under protocol MT2015-31. 
 
 
Note:  throughout this section the generic term “study drug” is used to refer to the study related 
treatment. 
 
9.1   
Adverse Event Reporting 
 
9.1.1  Definitions 
 
The following definitions are based on the Code of Federal Regulations Title 21 Part 312.32 
(21CFR312.32(a)). 
  
 
Adverse Event:  Any untoward medical occurrence associated with the use of a drug in 
humans, whether or not considered drug related.  
 
Suspected Adverse Reaction:  Any adverse event for which there is a reasonable possibility 
that the drug caused the adverse event.  
 
Life-Threatening Adverse Event Or Life-Threatening Suspected Adverse Reaction: An 
adverse event or suspected adverse reaction is considered “life-threatening” if, in the view of 
either the investigator or sponsor, its occurrence places the patient or subject at immediate risk 
of death. 
   
Serious Adverse Event Or Serious Suspected Adverse Reaction:  An adverse event or 
suspected adverse reaction is considered “serious” if, in the view of either the investigator or 
sponsor, it results in any of the following outcomes:  
• Death 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 16 of 30 
 
 
 
CPRC #MT2000-09 
 
• 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 
• A congenital 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.  
 
Unexpected adverse event or unexpected suspected adverse reaction: An adverse event or 
suspected adverse reaction is considered “unexpected” if it is not listed in the investigator 
brochure or is not listed at the specificity or severity that has been observed; or, if an 
investigator brochure is not required or available, is not consistent with the risk information 
described in the general investigational plan or elsewhere in the current application, as 
amended.  Thus, adverse events that occur as part of the disease process or underlying 
medical conditions are considered unexpected; however, they will not be reportable per 
section 9.1.2. 
 
Expedited (Rapid) Reporting: Certain events may require rapid notification to entities 
providing patient safety oversight (e.g. IRB) as detailed in section 9.1.2.   
 
Stopping rule events:  The following events count toward a study stopping rule per section 
10.5 and must be reported to the MCC Study Coordinator using the Early Stopping Rule 
Report Form found OnCore under the reports tab: 
• 
graft failure at day +42 
• 
death by day 100  
 
Events that count toward an early stopping rule do not necessarily constitute a serious adverse 
event requiring expedited reporting and should be reported as such only if they meet the 
criteria for expedited reporting as defined in the above table. 
 
In addition, the IRB considers any of the following problems/situations as meeting the 
definition of UPIRTSO: 
• 
Any accidental or unintentional change to the IRB-approved protocol that increases risk or 
has the potential to recur  
• 
Any deviation from the protocol taken without prior IRB review to eliminate apparent 
immediate hazard to a research subject  
• 
Any publication in the literature, safety monitoring report (including Data and Safety 
Monitoring Reports), interim result or other finding that indicates an unexpected change to 
the risk/benefit ratio of the research  
• 
Any breach in confidentiality that may involve risk to the subject or others  
• 
Any complaint of a subject that cannot be resolved by the research staff  
• 
Any other possibly related event which in the opinion of the investigator constitutes an 
unanticipated risk  
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 17 of 30 
 
 
 
CPRC #MT2000-09 
 
FOR UNLICENSED UCB UNITS ONLY:  These patients will be co-enrolled on 
University of Minnesota protocol MT2011-13R.  Selected expected adverse reactions 
determined to be caused by or probably caused by the UCB unit based on objective evidence 
will be reported in an expedited manner to the FDA under University of Minnesota IND BB-
14797 (C. Brunstein, MD, PhD – sponsor/investigator). Included are the following: 
• The unit is mislabeled or failure to pass local lot release 
• Serious infusion reaction within first 24 hours after infusion 
• Recipient bacteremia with clinical signs and symptoms related to a contaminated UCB 
within 24 hours after infusion 
 
FOR CD34+ SELECTED CELLS ONLY: These patients will be co-enrolled on University 
of Minnesota protocol MT2015-31. Adverse events determined to be caused by or probably 
caused by the CD34+ enriched cell product for hematopoietic reconstitution based on 
objective evidence will be reported to the IRB and Miltenyi Biotech per institutional 
procedures under protocol MT2015-31. 
 
9.1.2 Event Monitoring and Required Reporting 
Patients will be monitored from the start of the preparative regimen through day 100 for events that 
are reportable according to the below table.    
*downloadable from http://www.research.umn.edu/irb/forms.html  
 
The SAE Coordinator will provide the Masonic Cancer Center’s Data and Safety Monitoring 
Council (DSMC) with the SAE in an appropriate format depending on the individual SAE (as 
reported or in a summary format). 
 
 
9.2 
Study Data Collection and Data and Safety Monitoring Plan 
 
9.2.1 Data Collection 
 
Specific transplant related endpoints will be recorded in the University of Minnesota Blood 
and Bone Marrow Database as part of the historical database maintained by the department. 
 
9.2.2 Data and Safety Monitoring Plan 
 
Agency 
Criteria for reporting 
Timeframe 
Form 
to 
Use 
Submission address 
Copy AE to: 
U of MN 
IRB 
 
Unanticipated death of a locally enrolled subject(s); 
New or increased risk; Any adverse event  that require 
a change to the protocol or consent form – refer to the 
IRB website for complete details 
5 Working 
Days 
 
IRB report 
form 
irb@umn.edu  
Masonic Cancer 
Center SAE 
Coordinator 
mccsaes@umn.edu  
Clinical deviations per current IRB reporting requirements 
OnCore 
Deviation 
Form 
MCC SAE 
Coordinator 
Any event that counts toward a study stopping rule 
(refer to section 10.3) 
At time of 
reporting 
Event Form 
SAE Coordinator 
mccsaes@umn.edu  
Not applicable 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 18 of 30 
 
 
 
CPRC #MT2000-09 
 
The study’s Data and Safety Monitoring Plan will be in compliance with the University of 
Minnesota Masonic Cancer Center's Data & Safety Monitoring Plan (DSMP), which can be 
accessed at http://z.umn.edu/dmsp . 
 
For the purposes of data and safety monitoring, this study is classified as moderate risk.  
Therefore the following requirements will be fulfilled: 
 
 The Masonic Cancer Center Data and Safety Monitoring Council (DSMC) will 
review the trial’s progress twice yearly 
 The PI will comply with at least twice yearly monitoring of the project by the 
Masonic Cancer Center monitoring services. 
 The PI will oversee the submission of all reportable adverse events per the 
definition of reportable in section 9.1.2 to the Masonic Cancer Center’s SAE 
Coordinator and the University of Minnesota IRB.   
 
In addition, at the time of the continuing review with the University of Minnesota IRB, a copy 
of the report with any attachments will be submitted to the Cancer Protocol Review 
Committee (CPRC). 
 
9.2.3 Record Retention 
The investigator will retain study records including source data, copies of case report form, 
consent forms, HIPAA authorizations, and all study correspondence in a secured facility for at 
6 years after the study file is closed with the IRB.   
 
In addition, the Clinical Trials Office (CTO) will keep a master log of all patients 
participating in the study with sufficient information to allow retrieval of the medical records 
for that patient.  
 
Please contact the CTO before destroying any study related records. 
 
10.0 
EXPERIMENTAL DESIGN AND STATISTICAL CONSIDERATIONS 
Recent experience has demonstrated that among patients using a stem cell source from 
processed bone marrow using Isolex 300i, the primary graft failure rate is 0%. Therefore we 
expect that graft failure will be observed in very few patients. 
10.1Statistical Endpoints 
10.1.1 Primary Endpoint 
The proportion of patients with primary neutrophil engraftment by day 42 post-transplant 
10.1.2 Secondary Endpoints 
• The cumulative incidence of acute and chronic GvHD 
• The cumulative incidence of regimen-related toxicity based on transplant related 
outcomes by day 100 post-transplant 
• Probability of survival by one year post-transplant 
• The proportion of late second malignancies 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 19 of 30 
 
 
 
CPRC #MT2000-09 
 
10.2  Statistical Analysis 
Simple proportions along with 95% confidence intervals will be used to evaluate the 
incidence of primary neutrophil engraftment. Medians and ranges for time to engraftment will 
also be given. A competing risk of early death is not expected among these patients. 
Cumulative incidence will be used to estimate regimen-related toxicity and GvHD; treating 
non-event deaths as competing risks. Kaplan-Meier curves will be used to estimate overall 
survival. Additional descriptive statistics will be used for safety parameters and to evaluate 
data from the UCB cohort. 
10.3 
 Sample Size Justification 
The maximum sample size will be 39 patients (29 for arm 3 using bone marrow processing 
using CliniMACS and 10 or fewer patients receiving UCB). Twenty-nine patients are 
sufficient to maintain an overall type I error of 5% while providing 80% statistical power. The 
sample size calculation is based on the Simon method using a minimax two-stage design 
(Simon, R [1989], Optimal two-stage designs for phase II clinical trials. Controlled Clinical 
Trials, 10; 1-10).  
 
The two-stage design uses a two-step enrollment procedure with early stopping if less than 
80% of patients fail to engraft. More than 95% engraftment shows evidence that this 
procedure is worthy of further investigation.  
 
The first enrollment will include 9 patients with an early stop if 7 or fewer patients engraft. If 
8 or more engraft, the study will continue to enroll patients until 29 patients are enrolled.  
 
After 29 patients are enrolled, the regimen will not be considered worthy of further study if 26 
or fewer patients engraft. If 27 or more engraft, this regimen will be considered worthy of 
further study.  
10.4 
 Enrollment Plan  
An additional 20 patients will be enrolled on this study beginning with the August 2012 
version.  
10.5  Monitoring Guidelines: Stopping Rules  
Based on the enrollment of 20 additional patients beginning with the August 2012 version of 
the protocol, the stopping rules are as follows: 
 
Day 100 Mortality 
Mortality will be continuously monitored so that the study will stop and the protocol will be 
re-evaluated if early mortality exceeds the boundary. Monitoring will take place separately for 
both arms. Given a hypothesized mortality rate of 30%, a maximum tolerated rate of 50% and 
a maximum sample size of 20 patients, the trial will be stopped and reviewed if: 6/6, 7/9, 
8/11, 9/14, 10/16, or 11/19 patients die prior to day 100. This has a type I error rate of 5% and 
a power of 80%. 
 
Graft failure By Day 42 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 20 of 30 
 
 
 
CPRC #MT2000-09 
 
Graft Failure will be continuously monitored so that the study will stop and the protocol will 
be re-evaluated if graft failure exceeds the boundary. Monitoring will take place separately for 
both arms. Given a hypothesized graft failure rate of 10%, a maximum tolerated rate of 20% 
and a maximum sample size of 20 patients, the trial will be stopped and reviewed if: 4/4, 5/10, 
6/17, or 7 patients have graft failure. This has a type I error rate of 5% and a power of 80%. 
 
 
 
11.0 
CONDUCT OF THE STUDY 
 
11.1 
Ethical Considerations 
 
While there will be every effort to seek out and include females and minority patients, the 
patient population is dependent upon the referral pattern and the ability to locate a matched 
sibling donor or a UCB unit.  Females and minority patients are eligible for all aspects of the 
study and their participation will be actively encouraged.   
 
11.2 
Good Clinical Practice 
 
The study will be conducted in accordance with the appropriate regulatory requirement(s).  
Essential clinical documents will be maintained to demonstrate the validity of the study and 
the integrity of the data collected.  Master files should be established at the beginning of the 
study, maintained for the duration of the study and retained according to the appropriate 
regulations.   
 
11.3 
Informed Consent 
 
All potential study participants will be given a copy of the IRB-approved consent to review. 
The investigator or designee will explain all aspects of the study in lay language and answer 
all questions regarding the study. If the participant decides to participate in the study, she/he 
will be asked to sign and date the consent document. Patients who refuse to participate or who 
withdraw from the study will be treated without prejudice. 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 21 of 30 
 
 
 
CPRC #MT2000-09 
 
 
12.0 
REFERENCES 
 
1.  Hows JM, Chapple M, Marsh JCW et al. Bone marrow transplantation for Fanconi's anemia: the 
Hammersmith experience 1977-89. Bone Marrow Transplant 4: 629-634, 1989. 
 
2.  Di Bartolomeo P, Di Girolamo G, Olioso P et al. Allogeneic bone marrow transplantation for Fanconi 
anemia. Bone Marrow Transplant 10:53-56, 1992. 
 
3.  Flowers MED, Doney KC, Storb R et al. Marrow transplantation for Fanconi anemia with or without 
leukemic transformation: an update of the Seattle experience. Bone marrow Transplant 9, 167-173, 1992. 
 
4.  Kohli-Kumar M, Morris C, DeLaat C, et al. Bone marrow transplantation in Fanconi anemia using matched 
sibling donors. Blood 84, 2050-2054, 1994. 
 
5.  Gluckman E, Auerbach AD, Horowitz MM, Sobocinski KA, Ash RC, Bortin MM, Butturini A, Camilla BM, 
Champlin RE, Friedrich W, Good RA, Gordon-Smith EC, Harris RE, Klein JP, Ortega JJ, Pasquini R, Ramsay 
NKC, Speck B, Vowels MR, Zhang M-J, Gale RP: Bone marrow transplantation for Fanconi Anemia. Blood 
86:2856, 1995 
 
6.  Zanis-Neto J, Ribiero RC, Medeiros C et al. Bone marrow transplantation for patients with Fanconi anemia: a 
study of 24 cases from a sinlge institution. Bone Marrow Transplant 15, 293-298, 1995. 
 
7.  Guardiola P, Socie G, Pasquini R, Dokal I, Ortega JJ, van Weel-Sipman M, Marsh J, Locatelli F, Souillet G, 
Cahn JY, Ljungman P, Miniero R, Shaw J, Vermylen Ch, Archimbaud E, Bekassy AN, Krivan G, Di 
Bartolomeo P, Bacigalupo A, Gluckman E: Allogeneic stem cell transplantation for Fanconi Anaemia. Bone 
Marrow Transplant 21:S24, 1998 
 
8.  Deeg, HJ, Socié G, Schoch M et al. Malignancies after marrow transplantation for aplastic anemia and 
Fanconi anemia: A joint Seattle and Paris analysis of results in 700 patients. Blood 87:386-392, 1996 
 
9.  Socié G, Devergie A, Girinski T et al. Transplantation for Fanconi's anaemia: long-term follow-up of fifty 
patients transplatned from a sibling donor after low-dose cyclophosphamide and thoraco-abdominal irradiation 
for conditioning. Br J Haematol  103:249-255, 1998 
 
10.  Flowers MED, Zanis J, Pasquini et al. Marrow transplantation for Fanconi anaemia: conditioning with 
reduced doses of cyclophosphamide without radiation. Br J Haematol 92:699-706, 1996 
 
11.  Dokal IS, Roberts IAG. Bone marrow transplantation for Fanconi's anaemia: conditioning with reduced 
doses of cyclophosphamide without irradiation. Br J Haematol 94:422-424, 1996 
 
12.  Terenzi A, Aristei C, Aversa F, Perruccio K, Chionne F, Raymondi C, Latini P, Martelli MF: Efficacy of 
fludarabine as an immunosuppressor for bone marrow transplantation conditioning: Preliminary results. 
Transplant Proceedings 28, 3101, 1996  
 
13.  Slavin S, Nagler A, Naparstek E, Kapelushnik Y, Aker M, Cividalli G, Varadi G, Kirschbaum M, 
Ackerstein A, Samuel S, Amar A, Brautbar C, Ben-Tal O, Eldor A, Or R: Nonmyeloablative stem cell 
transplantation with lethal cytoreduction for the treatment of malignant and nonmalignant hematologic diseases. 
Blood 91, 756, 1998 
 
14.  Nagler A, Or E, Naparstek G, Varadi G, Brautbar C, Slavin S: Matched unrelated bone marrow 
transplantation (BMT) using a non-myeloablative  conditioning regimen. Blood 92:289a, 1998 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 22 of 30 
 
 
 
CPRC #MT2000-09 
 
15.  Spitzer TR, McAfee SL, Sackstein R, Toh HC, Saidman S, Weymouth D, Preffer F, Colby C, Sachs DH, 
Sykes M: Induction of mixed chimerism and potent anti-tumor responses following non-myeloablative 
conditioning therapy and hla-matched and mismatched donor bone marrow transplantation (BMT) for refractory 
hematologic malignancies (HM). Blood 92:519a, 1998 
 
16.  Kapelushnik J, Or R, Slavin S, Nagler A. A fludarabine-based protocol for bone marrow transplantation in 
Fanconi's anemia. Bone Marrow Transplant 20:1109-1110, 1997 
 
17.  Aker M, Varadi G, Slavin S, Nagler A. Fludarabine-based protocol for human umbilical cord blood 
transplantation in children with Fanconi anemia. J Ped Hematol/Onol 21:237-239, 1999 
 
 
18.  Traycoff CM, Broun ER, Burgess J et al. Evaluation of the hematopoietic potential of CD34-enriched 
autologous bone marrow grafts prepared with the Baxter Isolex 300.  Experimental Hematology 22, 554a, 1994 
(abstr) 
 
19.  Cornetta K, Gharpure V, Mills B, Hromas R, Abonour R, Broun ER, Traycoff CM, Hanna M, Wyman N, 
Danielson C, Gonin R, Kunkel LK, Oldman F, Srour EF: Rapid engraftment after allogeneic transplantation 
using CD34-enriched marrow cells.  Bone Marrow Transplant 21, 65-71, 1998 
 
20.  Goldman AI and Hannan PJ: Toxicity monitoring in Phase II clinical trials, 1998 (submitted) 
 
21.  Goldman AI. Issues in designing sequential stopping rules for monitoring side effects in clinical trials, 
Controlled Clinical Trials 8:327-337, 1987 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 23 of 30 
 
 
 
CPRC #MT2000-09 
 
 
APPENDIX I - SCHEDULE OF ACTIVITIES FOR EACH PATIENT 
Scheduled evaluations prior to engraftment (day 30) may be performed +/-3 days from the targeted date; 
assessments to be performed between engraftment and day 100 may be done +/-7 days of the targeted date; 
assessments after day 100 may be performed +/-30 days of the targeted date.  In addition, targeted days may be 
altered as clinically appropriate. 
 
 
Activity 
Pre-BMT 
Day +1 to 
Engraftment 
Post-
engraftment 
to Discharge 
(days <30 
minimum) 
Short-term Post-
engraftment 
Follow-up (days 
31-100 minimum) 
Long-term Post-
engraftment Follow-up 
(>day 100) 
Informed consent 
x(admission) 
 
 
 
 
Clinical evaluation 
Karnofsky/Lansky score 
 
x(admission) 
 
x(2) 
 
x(2) 
 
x(2, discharge 
home) 
 
x(day 180, 360, , 720) 
CXR 
x(admission) 
 
 
 
 
PFT (> 6 years of age) 
x(admission) 
 
 
 
x(3) 
ECG/ECHO 
x(admission) 
 
 
 
 
US liver & kidneys 
x(admission) 
 
 
 
 
CT chest, abdomen, 
pelvis 
x(admission) 
 
 
 
 
Cr/Cr clearance 
x(admission) 
 
 
 
 
Laboratory evaluation 
 
 
 
 
 
CBC/differential 
x(admission) 
x(1) 
x(1) 
x(2) 
x(day 180, 360, , 720) 
Blood chimerism 
PBLpatient for 
DNA 
BMdonor for 
DNA 
 
x(3) 
x(day 90-100) 
x(day 180, 360, 720) 
Monitoring for 
reportable events and 
stopping rules (section 
9.1.2) 
 
x 
x (day 30) 
x(day 60, 90-100) 
 
GVHD evaluation 
 
x(1) 
x(1) 
x(3) 
x(3) 
x(1)=perform test daily 
x(2)=perform test weekly 
x(3)=perform test as clinically indicated 
x(day)=perform test on day indicated 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 24 of 30 
 
 
 
CPRC #MT2000-09 
 
APPENDIX II - GRAFT VERSUS HOST DISEASE 
 
Patients will be considered evaluable if they demonstrate donor cell engraftment and survive to day 
42.  Organ involvement will be staged using the criteria outlined in the table below.  Biopsy of each 
organ site at diagnosis or major change in disease activity will be performed unless clinical 
circumstances make it impossible. 
 
Grading for Treatment Criteria 
 
a. 
Mild GVHD = Skin stage I-II only (Equivalent to Seattle Grade I). 
 
b. 
Moderate GVHD = Skin stage I-III and/or liver I-IV and/or Gastrointestinal tract (GI) I-III 
and/or Upper GI (UGI).  (Equivalent to Seattle Grade II, III). 
 
c. 
Severe GVHD = Any stage IV along with severe clinical illness. 
 
Patients progressing during initial therapy or not improving sufficiently after 2 courses of therapy are 
to be treated as severe GVHD. 
 
Criteria for staging acute graft-versus-host disease. 
 
 
Stage 
 
Skin 
 
Liver 
 
GI Tract 
 
I 
 
Maculopapular rash 
<25% of body surface 
 
T Bili 2-3 mg/dL or 
 T Bili <2 mg/L with 5'nuc 
or 
alk phos 2 x NL and 
liver bx consistent 
with GVHD 
 
>500 mL diarrhea/day 
(300 mL/m2/day+); 
 Nausea; anorexia 
 
II 
 
Maculopapular rash  
25-50% of body surface 
 
T. Bili 3-6 mg/dL 
 
1000 mL diarrhea/day 
(>600 mL/m2/day+); 
 Vomiting; food 
intolerance 
 
III 
 
Generalized 
erythroderma 
 
T. Bili 6-15 mg/dL 
 
>1500 mL 
diarrhea/day 
(>1000 mL/m2/d+) 
 
IV 
 
Generalized 
erythroderma 
with bullous formation 
and desquamation 
 
T. Bili >15 mg/dL 
 
Severe abdominal pain 
with or without 
ileus 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 25 of 30 
 
 
 
CPRC #MT2000-09 
 
APPENDIX III - PERFORMANCE STATUS SCALE 
 
KARNOFSKY PERFORMANCE STATUS SCALE 
 
Percentage 
 
100 
Normal, no complaints, no evidence of disease 
90 
Able to carry on normal activity; minor signs or symptoms of disease 
80 
Normal activity with effort; some signs or symptoms of disease 
70 
Cares for self; unable to carry on normal activity or do active work 
60 
Requires occasional assistance, but is able to care for most of his/her needs 
50 
Requires considerable assistance and frequent medical care 
40 
Disabled; requires special care and assistance 
30 
Severely disabled, hospitalization indicated.  Death not imminent 
20 
Very sick, hospitalization necessary, active supportive treatment necessary 
10 
Moribund, fatal processes, progressing rapidly 
0 
Dead 
 
Reference 
Karnofsky DA.  Editorial: Meaningful clinical classification of therapeutic responses to anti-cancer drugs. Clin Pharmacol Ther 2:709-
712, 1961. 
 
LANSKY PLAY PERFORMANCE STATUS SCALE 
Percentage 
 
100 
Fully active, normal 
90 
Minor restrictions in physically strenuous activity 
80 
Active, but tires more quickly 
70 
Both greater restriction of, and less time spent in, play activities 
60 
Up and around, but  minimal active play; keeps busy with quieter activities 
50 
Gets dressed but lies around much of the day, no active play; able to participate 
in all quiet play and activities 
40 
Mostly in bed; participates in quiet activities 
30 
In bed; needs assistance even for quiet play 
20 
Often sleeping; play entirely limited to very passive activities 
10 
Unresponsive 
0 
Dead 
 
REFERENCE 
Lansky SB, List MA, Lansky LL, Ritter-Sterr C, Miller DR (1987). "The measurement of performance in childhood cancer patients". 
Cancer 60 (7): 1651–6.  
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 26 of 30 
 
 
 
CPRC #MT2000-09 
 
APPENDIX IV - EXPECTED TOXICITIES 
 
A. 
Toxicities associated with the preparative therapies: 
 
Cyclophosphamide 
Common 
Occurs in 21-100 people out of 100 
Less Frequent 
Occurs in 5-20 
people out of every 
100 
Uncommon 
Occurs in <5 people out of every 100 
hypotension 
nausea and vomiting 
diarrhea 
hemorrhagic cystitis 
leukopenia 
amenorrhea 
 
 
syndrome of inappropriate ADH  
hemorrhagic myocardopathy 
Stevens-Johnson syndrome 
toxic epidermal necrolysis 
azoospermia 
oligozoospermia 
interstitial pneumonia  
 
Adequate diuresis must be maintained before and after Cyclophosphamide (CY) administration to 
help prevent hemorrhagic cystitis.  Hemorrhagic cystitis is a serious and potentially life-threatening 
toxicity of Cytoxan therapy.  The incidence varies but has a relationship to dose.  The toxicity is 
related to the direct contact of CY metabolites with the uroepithelium.  The recommended 
maintenance fluid is 3000 cc/m2/24 hours.  This rate should be started at least six hours before the CY 
dose.  Bolus furosemide can be administered to maintain urine output.  Patients should be weighed 
bid from day -2 to day 0 of HCT. High urine volume with frequent voiding (q 1-2 hour) is important 
to decrease the toxic exposure.  Mesna (total 60 mg/kg/day in 5 divided doses) may be given before 
CY, and 3, 6, 9 and 12 hours after CY to reduce the risk of hemorrhagic cystitis. 
 
CY has an antidiuretic effect that appears approximately 4 hours after and is maximal 10-14 hours 
after CY administration.  This can be controlled with furosemide.  In any patient with urine output 
inappropriate relative to the high volume IV input, furosemide should be given.  It is critical to 
closely monitor electrolytes during this diuresis.  See standing orders for administration of CY. 
 
Fludarabine 
Common 
Occurs in 21-100 people 
out of 100 
Less Frequent 
Occurs in 5-20 people 
out of every 100 
Uncommon 
Occurs in <5 people out of every 
100 
severe suppression of blood counts 
diarrhea  
anorexia 
mucositis 
nausea/vomiting 
stomatitis 
osteoporosis 
dysuria 
chills 
fever 
GI bleeding 
peripheral edema 
neurotoxicity 
agitation and confusion 
blurred vision 
peripheral neuropathy 
hearing loss  
headache 
cerebellar syndrome 
blindness 
coma  
weakness 
depression 
insomnia 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 27 of 30 
 
 
 
CPRC #MT2000-09 
 
Common 
Occurs in 21-100 people 
out of 100 
Less Frequent 
Occurs in 5-20 people 
out of every 100 
Uncommon 
Occurs in <5 people out of every 
100 
hemorrhagic cystitis (except in FA) 
abnormal renal function test 
autoimmune hemolytic anemia 
deep venous thrombosis 
aneurysms 
pruritic skin rash 
abnormal liver function/liver failure 
constipation 
transient ischemic attack 
dysphagia 
myalgia 
arthralgia 
renal failure 
 
Thymoglobulin (ATG) 
Common 
Less Frequent 
Uncommon 
fever 
chills 
leukopenia 
pain 
headache 
abdominal pain 
diarrhea 
hypertension 
nausea 
thrombocytopenia 
peripheral edema 
dyspnea 
asthenia 
hyperkalemia 
tachycardia 
malaise 
dizziness 
severe allergic reaction 
(anaphylaxis) 
 
Methylprednisolone (MP) - possible side effects include weight gain and water retention, puffiness of 
the face, high blood pressure, high blood sugar, bleeding from the stomach and intestines due to 
ulcers, and personality changes including depression. High blood pressure and water retention can be 
treated with medications and very high levels of blood sugar can be corrected with insulin. 
 
Long-term use (which is not planned) has been associated with reversible muscle weakness and 
muscle thinning and cataracts.  It has also been associated with bone thinning; this has sometimes 
progressed to areas of bone death, called “avascular necrosis” or “AVN”, especially at the knees and 
hips.  In addition, methylprednisolone or prednisone makes patients prone to infections. 
 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 28 of 30 
 
 
 
CPRC #MT2000-09 
 
B. 
Toxicities associated with T cell depletion of bone marrow 
 
The toxicities and complications that could potentially result from the removal of lymphocytes from 
the donated bone marrow are failure of bone marrow engraftment (due to loss or damage to 
hematopoietic progenitor cells), an increased risk of relapse, and an increased risk of EBV-associated 
lymphoproliferative syndrome. 
 
C. 
Toxicities associated with Hematopoietic Stem Cell Transplantation 
• nausea and vomiting  
• possible allergic reaction (including itching, hives, flushing [red face], shortness of breath, 
wheezing, chest tightness, skin rash, fever, chills, stiff muscles, or trouble breathing) 
• graft-versus-host-disease (GVHD) 
• veno-occlusive disease,  
• mucositis,  
• infections (sepsis)  
 
D. 
Toxicities associated with GVHD Prophylaxis 
 
Cyclosporine (CSA)  
 
 
Mycophenolate Mofetil (MMF) 
nephrotoxcity 
seizures 
hypertension 
hirsutism 
increased risk of relapse 
thrombotic thrombocytopenic purpura 
electrolyte imbalances 
paresthesias/neuropathy 
gingival hyperplasia 
increased risk of opportunistic infection 
pancytopenia 
headache 
insomnia 
electrolyte imbalances 
leg cramps/bone pain 
hypertension 
dizziness 
hyperglycemia 
rash 
nausea/diarrhea 
 
.E.  G-CSF 
In general, this drug has few serious side effects.  Side effects include fever, feeling tired, bone 
pain, and enlargement of the spleen.  Additionally, there is a rare risk of allergic reaction to this 
drug. 
 
 
 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 29 of 30 
 
 
 
CPRC #MT2000-09 
 
APPENDIX V – DRUG FORMULATION AND AVAILABILITY 
 
Cyclophosphamide 
Cyclophosphamide is a nitrogen mustard-derivative, polyfunctional alkylating agent.  Cyclophosphamide for injection is 
commercially available as a sterile solution in sodium chloride or as a powder that is reconstituted in sterile or 
bacteriostatic water.  Institutional guidelines for handling, reconstitution and administration should be followed.  
Cyclophosphamide can cause temporary hair loss, nausea, vomiting, diarrhea, and lowering of the blood cell counts or 
hemorrhagic cystitis.  Anti-emetics should minimize nausea and vomiting.  At the dose of cyclophosphamide used in this 
study, these symptoms are expected to be modest in severity.  
Formulation:  Parenteral 100 mg and 500 mg vials.  Commercially available. 
Storage:  Room temperature. 
Mixing:  I.V. drug should be mixed with sterile water for I.V. use.  Dissolves very slowly with cold water.  It helps to 
warm the water or to warm the vial after adding water. 
Stability:  I.V. solution should be used within 12 hours of mixing. 
Administration:  Cyclophosphamide is added to D5W and administered I.V. 
 
Fludarabine 
Fludarabine is an antimetabolite.  Fludarabine for injection is commercially available as a lyophilized cake that is 
reconstituted in sterile water.  Institutional guidelines for handling, reconstitution and administration should be followed.  
Fludarabine can cause lowering of blood counts, suppression of the immune system, nausea and vomiting, fever, 
hypersensitivity reaction, tumor lysis, transient elevation in serum transaminases, and neurotoxicity at doses generally 
higher than administered in this study. 
Formulation:  50 mg vial as a white lyophilized cake for IV use.  Commercially available. 
Storage:  Room temperature. 
Mixing:  Add 2 mL sterile water to vial to give a final concentration of 25 mg/mL. 
Stability:  I.V. solution should be used within 8 hours of mixing. 
Administration: Fludarabine is further diluted in 100 mL of 5%dextrose or 0.9% sodium chloride 
 
Thymoglobulin (anti-thymocyte globulin) 
Thymoglobulin (Genzyme) is a purified pasteurized, gamma immune globulin obtained by immunization of rabbits with 
human thymocytes.  This immunosuppressive product contains cytotoxic antibodies directed against antigens expressed 
on human T-lymphocytes.  Institutional guidelines for handling, reconstitution and administration should be followed.  
Common toxicities include fever, chills, leukopenia, pain, headache and nausea. 
Formulation:  Intravenous Lyophilized Powder 
Storage: Store in refrigerator between +2 degrees C to +8 degrees C, protect from light, do not freeze 
Mixing: 5-ml sterile water for injection as diluent. 
Stability: Should be used within 4 hours of reconstitution if kept at room temperature. 
Administration:  Infusion – deliver Thymoglobulin doses per current University of Minnesota BMT unit horse ATG 
infusion procedures.    
 
Methylprednisolone (MP) 
Availability:  Commercially available. 
Storage: Store at controlled room temperature 20° to 25°C (68° to 77°F) 
Administration:  MP will be administered at the dose of 2 mg/kg/day intravenously every 24 hours day -6 until day -2 as 
a premedication for ATG.  MP may be given as an IV push. 
 
Cyclosporin A (CSA) 
Availability:  Commercially available. 
Storage:  Store the unmixed drug and oral formulation at room temperature below 86 degrees F (30 degrees C) away 
from heat and light.   
Stability:  I.V. solution should be used within 24 hours of mixing. 
Administration: Cyclosporin A (CSA) will start day -3 per section 6.2.1.  CSA dosing will be monitored and altered as 
clinically appropriate per University of Minnesota Medical Center - Fairview pharmacy guidelines. Dose adjustments will 
be made on the basis of toxicity and/or low CSA levels. 
 
 

MT2000-09 – Matched Sibling Donor HCT in FA 
June 3, 2019 
 
 
 
Page 30 of 30 
 
 
 
CPRC #MT2000-09 
 
Mycophenolate Mofetil (MMF) 
Availability:  Commercially available. 
Storage:  Store powder and reconstituted/infusion solutions at 25°C (77°F); excursions permitted to 15° to 30°C (59° to 
86°F). 
Administration: MMF will start day -3 MMF therapy beginning on day -3 through day +30 or for 7 days after 
engraftment, whichever day is later, if no acute GVHD per section 6.6.2.  
 
 
G-CSF 
Availability:  Commercially available. 
Storage:  G-CSF should be stored in the refrigerator at 2° to 8°C (36° to 46°F). Avoid shaking. Prior to injection‚ 
NEUPOGEN® may be allowed to reach room temperature for a maximum of 24 hours. Any vial or prefilled syringe left 
at room temperature for greater than 24 hours should be discarded. 
Administration: Initiate G-CSF 5mcg/kg per day IV day +1 and continue until ANC ≥ 2.5 x 109/L.