A Pilot Trial of Clofarabine Added to Standard Busulfan and Fludarabine for Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation
Phase: PHASE2
Conditions: Myeloid Malignancy, Bone Marrow Failure Syndrome, Transfusion-dependent Red Blood Cell (RBC) Defect, Congenital Immunodeficiency, Metabolic Disease, Severe Immune Dysregulation
Sponsor: University of California, San Francisco

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A Pilot Trial of Clofarabine Added to Standard Busulfan and Fludarabine for 
Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation 
Protocol Number:  CC #110819 
Version Number:  7.0 
Version Date:  June 6, 2013 
Study Drug:  Clofarabine 
Principal Investigator (Sponsor-Investigator) 
Christopher C. Dvorak, MD 
 
 
 
 
Co-Investigators 
Janel Long-Boyle, PharmD, PhD 
Morton Cowan, MD 
Biljana Horn, MD 
James Huang, MD 
Robert Goldsby, MD 
Kristin Ammon, MD 
Justin Wahlstrom, MD 
Statistician 
Stephen Shiboski, PhD 
Clinical Research Coordinator 
 
 
 
 
 
 
Revision History 
Version #1.0 
9/19/11 
Version #2.0 
11/8/11 
Version #3.1 
02/23/12 
Version #4.0 
04/10/12 
Version #5.0 
04/30/12 
Version #6.0 
08/09/12 
Version #7.0 
06/07/13 
NCT#  01596699

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1.0 
Hypothesis and Specific Aims: 
 
1.1 
Hypothesis: The addition of Clofarabine to standard Busulfan and Fludarabine 
prior to allogeneic hematopoietic cell transplant (HCT) will be safe and will improve 
engraftment rates of children with non-malignant diseases or decrease relapse rates of 
patients with high-risk myeloid malignancies. 
 
1.2  
Specific Aims: 
1.2.1 Primary Objective: To determine the toxicity of the addition of Clofarabine to a 
conditioning backbone of Busulfan plus Fludarabine in patients with myeloid 
malignancies and non-malignant diseases undergoing allogeneic HCT. 
1.2.2 Secondary Objectives: 
a. To determine if the addition of Clofarabine to a conditioning backbone of 
Busulfan plus Fludarabine improves the engraftment rate of patients with non-malignant 
diseases (Stratum A) undergoing allogeneic HCT as compared to historic controls. 
b. To determine if the addition of Clofarabine to a conditioning backbone of 
Busulfan plus Fludarabine improves the full donor chimerism of patients with high-risk 
myeloid malignancies (Stratum B) undergoing allogeneic HCT as compared to historic 
controls. 
c. To evaluate the pharmacokinetics (PK) of Clofarabine and Fludarabine in a 
combination nucleoside analogue preparative regimen and define exposure-response 
relationships with clinical outcomes. 
 
2.0  
Background: 
2.1 
Clinical Need for an Improved Conditioning Regimen: 
Although outcomes following allogeneic hematopoietic cell transplantation (HCT) 
have improved during recent years due to advances in supportive care techniques, 
certain categories of patients continue to do poorly. One major group of patients with 
poor outcomes are those with non-malignant diseases for whom an increased 
immunologic barriers to engraftment exists. This includes both intrinsic barriers to 
engraftment, such as patients with Hurler’s Syndrome, or patients who are allo-
immunized pre-HCT due to administration of large numbers of blood products, as well 
as those patients for whom we have been unable to identify a 10/10 HLA-matched 
donor. Because most patients with non-malignant diseases (excluding patients with 
SCID) have at least partially-intact immune systems and, unlike most patients with 
hematologic cancers, have not been treated with immunosuppressive chemotherapy 
prior to HCT, the risk of graft rejection in these patients can be very high.  
 
The classic conditioning regimen for a patient with a non-malignant disease is the 
combination of targeted Busulfan with Cyclophosphamide. However, while 
immunoablative, the addition of Cyclophosphamide to Busulfan is associated with high 
rates of organ toxicity, especially to the liver.1 In order to eliminate the toxicities of 
Cyclophosphamide, the UCSF Pediatric BMT team has conducted two trials of Busulfan 
plus Fludarabine for pre-HCT conditioning. The first trial ran from September 2000 to 
June 2004 and evaluated Busulfan plus Fludarabine plus Thymoglobulin (rATG) in 19 
patients.2 While certainly less toxic than Busulfan plus Cyclophosphamide, a finding that 
has been confirmed by other trials3, this regimen was not sufficiently immunoablative to 
reliably establish engraftment in patients with mismatched donors. Therefore, from 2005 

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to 2010 a follow-up trial was performed in 35 patients that substituted rATG with 
Alemtuzumab, a monoclonal antibody directed against CD52, a protein found on the 
surface of most lymphocytes, with the hypothesis that it would be more effective at 
ablating the host immune system prior to HCT and would thus be associated with 
improved engraftment rates.4 Although Alemtuzumab was found to be superior to rATG 
at preventing chronic GVHD, and thus its use has been adopted by the UCSF BMT 
team as standard of care for the conditioning of patients with non-malignant diseases, it 
too failed to reliably establish engraftment in patients with mismatched donors.  
Although some patients that experience primary graft rejection are able to be 
salvaged with an emergency rescue second transplant,5 this results in a significantly 
increased use of patient resources, prolonged hospitalizations, and is not always 
successful. Due to other advances in supportive care, graft rejection is becoming the 
major cause of death in certain subgroups of patients with non-malignant diseases 
undergoing allogeneic HCT. In order to make further advances in the care of these 
patients, a novel conditioning regimen will need to be employed.    
 
Another group of patients with less than optimal outcomes following allogeneic 
HCT are those with certain types of myeloid malignancies. One group that appears to 
be at high-risk for relapse is patients with AML and detectable minimal residual disease 
at the time of initiation of HCT conditioning.6,7 Presumably these patients begin HCT 
with a large enough disease burden that the graft-versus-leukemia (GVL) effect does 
not have sufficient time to develop and thereby control the underlying AML. Similarly, 
some myeloid malignancy variants, including MDS, JMML, and CML often come to HCT 
having received little to no pre-HCT chemotherapy. Therefore, not only are these 
patients potentially at increased risk for graft rejection when a mismatched donor is 
utilized,8 but with their large disease burden they also may need an improved 
conditioning regimen in order to allow sufficient time for the GVL effect to develop. The 
UCSF Pediatric BMT team has published that relapses following HCT can be predicted 
by the degree of donor cell engraftment.9 Patients with full-donor chimerism have only a 
11% risk of relapse, as compared to a 71% in patients with mixed-donor chimerism.9 
UCSF Protocol CC# 09082: “A phase II study of preemptive fast withdrawal of 
immunosuppression and donor lymphocyte infusions for achieving complete donor 
chimerism following allogeneic transplant for pediatric hematologic malignancies” is 
currently testing whether fast withdrawal of immunosuppression plus possible donor 
lymphocyte infusions, can eliminate residual host cells and thereby convert patients to 
full-donor chimerism. However, by amplifying the early GVL effect, this approach also 
has a risk of increased rates of GVHD. Thus, a pharmacologic modification of the 
conditioning regimen that produces a greater degree of full-donor chimerism may be 
associated with lower rates of GVHD. Furthermore, since relapse following HCT can 
occur as late as 2-years out, the degree of full-donor chimerism at Day 100 post-HCT is 
a faster endpoint to utilize for a clinical trial when trying to determine whether the novel 
therapy is making a significant impact on outcomes.  
 
Finally, although dramatically different disease types, patients with both myeloid 
malignancies as well as non-malignant diseases receive Busulfan plus Fludarabine as 
the standard-of-care conditioning regimen at UCSF. Therefore, the toxicity of a common 
addition to this regimen that potentially reduces both graft rejection and relapse rates 
could be studied in a single trial with two different strata.  
 

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2.2 
Clofarabine as an Effective Agent Against Lymphocytes and Myeloid Cells: 
Clofarabine (2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine) is a rationally 
designed second-generation purine nucleoside analog FDA-approved for the treatment 
of pediatric patients 1 to 21 years old with relapsed or refractory acute lymphoblastic 
leukemia at a dose of 52 mg/m2/day for 5 consecutive days. It was designed to retain 
the antitumor properties of Fludarabine and Cladribine but to have an improved safety 
profile. It exerts its anticancer activity through the intracellular generation of triphosphate 
species, which inhibits DNA synthesis and ribonucloeotide reductase, thereby inducing 
apoptosis. The double halogen strategy confers resistance to adenosine deaminase, 
while increasing acid stability and bioavailability (in part through more rapid membrane 
transport). Clofarabine is more efficient than fludarabine at inhibiting DNA polymerase 
A, inhibiting ribonucleotide reductase (RR), and better at disrupting mitochondrial 
function leading to apoptosis via recruitment of APAF-1 (biology reviewed in 
Kirschbaum et al.10).  This latter activity may explain the increased killing of non-dividing 
lymphocytes,11,12 an advantage that would theoretically reduce the likelihood of rejection 
in the allogeneic setting, and perhaps augment the graft-versus-tumor effect of the 
donor graft.  
 
Clofarabine appears to have reduced CNS penetration compared to older purine 
nucleoside analogs (reviewed in Long-Boyle et al.13). While this property may decrease 
its effectiveness against CNS leukemia, when being combined with two agents with 
significant CNS penetration and potential toxicity, this “downside” is likely to be minimal. 
However, from a toxicity standpoint for patients without CNS leukemia or with non-
malignant diseases, an agent like Clofarabine, with minimal CNS penetration is clearly 
optimal.   
 
Furthermore, Andersson et al. investigated the in vitro anti-AML cytotoxic 
properties of Clofarabine alone and in combination with Fludarabine and Busulfan in a 
human cell-line model of Busulfan-resistant AML.14 They demonstrated that in this 
model, as well as in additional human AML lines and primary explanted AML blasts from 
leukemic patients, on a molar basis, Clofarabine is about 50-fold more potent than 
Fludarabine, and Clofarabine synergizes to a higher degree than Fludarabine with 
Busulfan. A combination of Clofarabine and Fludarabine exerted a much higher level of 
synergy than either nucleoside analog alone when combined with the alkylating agent. 
When Fludarabine and Clofarabine were followed by Busulfan, a major enhancement of 
the anti-leukemic efficacy was seen.15 Furthermore, via three in vitro models of 
apoptosis in AML cell lines, the combination of Busulfan plus Fludarabine plus 
Clofarabine was synergistic compared to any agent alone or two agents in 
combination.16  
 
Therefore, the use of Clofarabine in combination with standard fludarabine in the 
conditioning regimen prior to allogeneic HCT may provide enhanced 
immunosuppression as well as probable increased anti-leukemia effect. 
 
2.2.3 Alternate Agents to Combine with Busulfan and Fludarabine 
 
Clofarabine is not the only possible agent to combine with Busulfan and 
Fludarabine in order to improve engraftment rates and relapse incidences following 
allogeneic HCT. 
 
Melphalan is an alkylating agent with known in vitro activity against AML. It does 
not cross the blood-brain barrier and thus does not have additive CNS toxicities to 

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Busulfan and Fludarabine. However, its addition to HCT-conditioning regimens has 
been associated with increased toxicities. Helenglass et al. reported that a combination 
of TBI plus Melphalan was superior to TBI plus Cyclophosphamide in preventing 
relapse of AML post-HCT, however, the higher rates of TRM resulted in an identical OS 
rate.17 Furthermore, although Melphalan does appear to possess immunosuppressive 
properties in addition to its myelosuppressive effects, in patients with JMML receiving 
HCT from mismatched donors, the rates of graft rejection following a Busulfan plus 
Fludarabine plus Melphalan conditioning regimen were still very high.8    
 
Thiotepa is an alkylating agent with known in vitro efficacy against both solid 
tumors as well as hematologic malignancies, and it also caused severe 
myelosuppression in phase I studies (reviewed in Rosales et al.18). It does cross the 
blood-brain barrier, and it can be combined with standard HCT conditioning agents, 
including Busulfan or Total Body Irradiation. However, one pilot trial has concluded that 
the addition of Thiotepa to Busulfan and Cyclophosphamide did not improve outcomes 
compared to Busulfan and Cyclophosphamide alone.18 Furthermore, Thiotepa has 
recently had significant supply issues that have limited its availability and use.  
Both Melphalan and Thiotepa are alkylating agents, which in combination with 
Busulfan are known to increase the risk of sinusoidal obstruction syndrome post-HCT. 
Alkylators may contribute to increased risk of late effects of HCT, including 
endocrinologic damage and infertility. Therefore, based on the relatively limited benefit 
in terms of efficacy and the potential toxicity risks, neither Melphalan nor Thiotepa 
appear to be an optimal agent for combining with Busulfan and Fludarabine. Instead, 
preliminary clinical studies suggest that the purine nucleoside analogue Clofarabine 
may be the best available agent. 
 
2.3  
Preliminary Studies: 
2.3.1 Efficacy Studies: 
There have been several published trials of adding Clofarabine to pre-HCT 
conditioning regimens. Andersson et al. performed a 4-arm clinical trial in which 
escalating doses of Clofarabine were combined with de-escalating doses of 
Fludarabine, plus standard Busulfan in 51 primarily adult (though one patient was as 
young as 6 years old) patients with high-risk myeloid malignancies.16 The dose of 
Clofarabine utilized was 10 to 40 mg/m2/day for 4 consecutive days. All 51 patients 
engrafted and there was no significant difference between the four arms in terms of 
overall or progression-free survival. A direct comparison to their historical cohort that 
received only Busulfan and Fludarabine was not performed, however, some conclusions 
can be tentatively reached. For patients receiving BU-FLU-CLO, the overall survival 
(OS) was 48% in a population where 80% of patients had active disease at the time of 
transplant, compared to an OS of 42% for patients receiving BU-FLU only, where the 
population was slightly lower risk (71% with active disease at the time of transplant). 
Therefore, BU-FLU-CLO appears at least equal to a historical BU-FLU only cohort, with 
possibly a hint towards superiority.  
Farag et al. performed a Phase I dose-escalation trial of Clofarabine in 
combination with Busulfan prior to allogeneic HCT in 15 adult patients with high-risk 
acute leukemias.19 Clofarabine dosing started at 30 mg/m2/dose, escalating to 60 
mg/m2/day, for 5 consecutive days. All patients engrafted and the maximally tolerated 

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dose (MTD) was not reached. The 1-year OS and event-free survival (EFS) were 60% 
and 53% in a high-risk population with an expected EFS of 25% or lower.  
 
Kirschbaum et al. performed a Phase I dose-escalation trial of Clofarabine in 
combination with Melphalan prior to allogeneic HCT in 16 adult patients with AML.10 
Clofarabine dosing started as 30 mg/m2/dose, escalating to 40 mg/m2/dose, for 5 
consecutive days. All patients engrafted. The 1-year OS and EFS were 73% and 61%.  
 
Srivastava et al. performed a Phase I 3+3 dose-escalation trial of Clofarabine in 
combination with high-dose Cyclophosphamide and Etoposide prior to autologous HCT 
in 16 adult patients with high-risk Non-Hodgkin Lymphoma.20 Clofarabine dosing started 
at 30 mg/m2/dose, escalating to 70 mg/m2/day, for 5 consecutive days. The MTD was 
not reached. The 1-year OS and PFS were 68% and 63%, in a high-risk patient 
population with an expected PFS of <20%.  
 
Therefore, all four trials demonstrated, in a non-randomized fashion, at least 
equivalence and potentially superiority compared to non-Clofarabine based conditioning 
regimens for patients with malignancies. 
 
There is considerably less in the literature regarding the use of Clofarabine for 
the conditioning of patients with non-malignant diseases undergoing allogeneic HCT. 
However, Long-Boyle et al. did report the pharmacokinetic data of 16 primarily pediatric 
patients (as young as 0.5 years of age) who received Clofarabine 40 mg/m2/day for 5 
consecutive days in combination with Melphalan and low-dose TBI as part of a brain-
sparing conditioning regimen for patients with metabolic diseases.13 The outcome data 
was not presented.    
 
2.3.2 Safety Studies: 
 
In general, the addition of Clofarabine to standard pre-HCT conditioning agents 
has been very well-tolerated. Andersson et al. demonstrated in 51 patients that the 
addition of Clofarabine to BU + FLU did not significantly alter the safety profile 
compared to their historic controls.16 TRM rates were 15% at Day +365, compared to 
12% in the historic BU-FLU cohort, and toxic deaths were solely limited to being caused 
by infections and GVHD, with no deaths due to direct organ toxicity. The most common 
toxicity was grade 2-3 mucositis in 80% of patients. There was only one case of 
reversible sinusoidal obstruction syndrome. Rates of grades II-IV acute GVHD were 
similar to historic controls: 31% for BU-FLU-CLO vs. 26% for BU-FLU only.  
 
Farag et al. found that the major toxicity was a reversible Grade 3-4 elevation of 
liver transaminases occurring shortly after Clofarabine administration and resolving by 
Day +3 post-HCT in 67% of patients.19 Grade 3-4 mucositis was also common (60%), 
and there was one case of hand-foot syndrome. Although two patients died of sepsis or 
cGVHD, there were no deaths due to direct organ toxicity.  
 
Kirschbaum et al. found that 1 of 15 patients at the lower-dose Melphalan level 
expired from TRM (multi-organ failure).10 Grade 1-2 liver toxicity was seen in all 
patients, though it fully resolved in all cases except the one that died of TRM.  
Srivastava et al. found that most elevations of liver transaminases were Grade 1-
2 in nature, and all resolved by Day +8 post-HCT.20 There was a 31% incidence of 
hand-foot syndrome. All toxicities were reported to have resolved by Day +30 and there 
were no treatment-related deaths.  
 
Therefore, all four trials demonstrated, in a non-randomized fashion, similar 
safety outcomes compared to non-Clofarabine based conditioning regimens for patients 

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with malignancies. TRM rates were not high, despite doses of Clofarabine that 
occasionally exceeded the FDA-approved dose, and most organ toxicities resolved 
fairly promptly. From the literature, the major toxicities that will need monitoring will be 
hepatic in nature.   
 
2.2.3 Clofarabine Pharmacokinetics 
 
Recently, Long-Boyle et al. investigated the PK of Clofarabine in 16 pediatric 
patients undergoing HCT for the treatment of high risk inherited metabolic disorders.13 
All patients received a single nucleoside analogue preparative regimen consisted of 
Alemtuzumab, Clofarabine, Melphalan, and TBI. Parameter estimates for AUC0-   and 
Cmax were consistent with the dose-proportional PK of Clofarabine characterized in 
phase I and phase II trials of pediatric patients receiving single agent monotherapy 
doses of 11.25-52 mg/m2 daily over 5 days for treatment of refractory hematologic 
malignancies.21 There was no evidence of accumulation of Clofarabine between the 1st 
and 5th dose in the patients with stable renal function.13 This is similar to what has been 
reported when fludarabine is given daily at doses ranging from 30 to 40 mg/m2 in adult 
HCT patients with adequate renal function.22 Variability of 2-3 fold was observed in 
Clofarabine PK parameters including CL, AUC0-  , and Vd and was not sufficiently 
explained by clinical covariates of body size and renal function.13 Approximately 40-60% 
of Clofarabine is renally-eliminated unchanged in the kidneys through a combination of 
glomerular filtration and active tubular secretion via transporters.23 Several transporters 
(ENT1, ENT2, CNT2 and CNT3) have been shown to influence in vitro distribution and 
accumulation of Clofarabine.24,25 These transporters are expressed in both target 
tissues (e.g. B and T lymphocytes) and renal epithelial cells of the kidney and 
concomitant use with other nucleoside analogues such as fludarabine which share a 
similar metabolic pathway may impact PK and drug disposition through several 
mechanisms. To date, the impact the relationship between Clofarabine exposure and 
clinical outcomes in HCT remain undefined.  
 
2.3.4 Choice of Clofarabine Dosing: 
 
Although the FDA-approved dosing in children with ALL is 52 mg/m2/dose for 5 
consecutive days, this is as monotherapy. As noted above, several trials in adults 
utilized doses as high as 40 to 70 mg/m2/day for 4 to 5 consecutive days with tolerable 
toxicity rates.10,16,19 However, in order to not alter our backbone standard of care 
conditioning regimen of Busulfan plus Fludarabine, we will simply add 10 mg/m2/dose of 
Clofarabine for 4 consecutive days. Therefore, we will only be altering one component 
of the conditioning regimen, which will improve our ability to compare the results of this 
trial with our historic controls. Furthermore, there was no apparent benefit to Clofarabine 
dose escalation (with simultaneous de-escalation of Fludarabine dosing) in the trial by 
Andersson et al.16 so we chose to utilize the smallest published dose in order to 
maximize the safety of patients enrolling on this trial.  
 
 
 

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3.0 
Eligibility: 
3.1 
Inclusion Criteria: 
 
a. Patients must be ≥ 3 months and ≤30 years of age. 
 
b. Stratum A: Non-Malignant Diseases, including: 
 
 
i.  
Bone Marrow Failure Syndromes 
 
 
ii. 
Hemoglobinopathies or transfusion-dependent RBC defects 
 
 
iii. 
Congenital Immunodeficiencies 
 
 
iv.  
Metabolic Diseases known to be treatable with HCT (e.g. Hurler’s) 
v.  
Other Bone Marrow Stem Cell Defects (e.g. Osteopetrosis) 
vi.  
Severe Immune Dysregulation / Autoimmune Syndromes with at 
least transient prior response to immunosuppressive therapy 
 
c. Stratum B: Myeloid Malignancies, including: 
i.  
AML, in greater than first clinical remission, or in CR1 but with 
either (see Table 2):  
a. Detectable disease (≥0.1% Blasts by MRD or Flow, or Positive 
Cytogenetics), OR 
b. A matched sibling UCB donor , OR 
c. A mismatched unrelated donor. 
ii. 
MDS 
iii. 
JMML 
iv.  
CML, with detectable disease by PCR 
d. Patients must have a suitable donor based on the UCSF Pediatric BMT SOP. 
10/10 (HLA-A, -B, -C, -DR, -DQ) matching will be done for related and adult 
unrelated donors; 8/8 (HLA-A, -B, -C, -DR) for umbilical cord blood donors. 
Patients with non-malignant diseases will generally be eligible only if they have a 
mismatched donor, or an accepted clinical reason to be considered high-risk for 
rejection (see Table 1 for details).   
e. Liver transaminases (AST/ALT) and Direct Bilirubin less than twice the upper 
limit of normal within 2 weeks of admission.  
 
f. Cardiac Shortening Fraction ≥27% within 4 weeks of admission. 
g. Creatinine clearance by Schwartz formula, GFR or 24 hr urine collection ≥50 
cc/min/1.73 m2, within 4 weeks of admission. 
h. Pulmonary diffusion capacity ≥50% of predicted corrected for anemia/lung 
volume within 4 weeks of admission. If unable to do PFT’s, then no active lung 
disease by CXR and/or O2 Sat ≥90% on room air. 
 
 
 

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Table 1: Non-Malignant Diseases (Stratum A) 
 
Stem Cell 
Source 
Matched RD 
10/10 (8/8) URD 
< 10/10 (8/8) URD* 
BM 
BU600 + 
Fludarabine 
BU600 + Fludarabine 
BU600 + Fludarabine 
  
Alemtuzumab 
Alemtuzumab 
Alemtuzumab 
  
  
  
Clofarabine 
  
  
  
  
PBSC 
BU600 + 
Fludarabine 
BU600 + Fludarabine 
BU600 + Fludarabine 
  
Alemtuzumab 
Alemtuzumab 
Alemtuzumab 
  
  
  
Clofarabine 
  
  
  
  
UCB 
BU600 + 
Fludarabine 
BU600 + Fludarabine 
BU600 + Fludarabine 
  
rATG 
rATG 
rATG 
  
  
  
Clofarabine 
 
 * = Or Otherwise Determined to be at High Risk for Rejection Based on Clinical Criteria (i.e. 
Hurler’s Syndrome, Osteopetrosis, etc.)  
Shaded area = Low-risk patients not eligible for this trial, will receive a standard-of-care HCT. 

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Table 2: Myeloid Malignancies (Stratum B) 
 
Stem Cell 
Source 
  
AML CR1, MRD Negative 
  
  
Matched RD 
10/10 (8/8) URD < 10/10 (8/8) URD 
BM 
BU900 + Fludarabine BU900 + Fludarabine BU900 + Fludarabine 
  
  
rATG 
rATG 
  
  
  
 Clofarabine 
  
  
  
  
PBSC 
BU900 + Fludarabine BU900 + Fludarabine BU900 + Fludarabine 
  
rATG 
rATG 
rATG 
  
  
  
Clofarabine  
  
  
  
  
UCB 
BU900 + Fludarabine BU900 + Fludarabine BU900 + Fludarabine 
  
  
rATG 
rATG 
  
Clofarabine 
  
Clofarabine  
  
Stem Cell 
Source 
  
 
AML CR2 or MRD Positive; MDS; JMML; CML 
 
Matched RD 
10/10 (8/8) URD < 10/10 (8/8) URD 
BM 
BU900 + Fludarabine 
  
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
  
  
  
  
  
  
PBSC 
BU900 + Fludarabine 
rATG 
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
  
  
  
  
  
  
UCB 
BU900 + Fludarabine 
  
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
BU900 + Fludarabine 
rATG 
Clofarabine 
  
  
  
Shaded area = Low-risk patients not eligible for this trial, who will receive a standard-of-
care HCT. 
 
 

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3.2 
Exclusion Criteria: 
1. Fanconi Anemia 
2. Dyskeratosis Congenita 
3. A known syndrome with increased sensitivity to radiation or alkylating agents 
4. Severe Combined Immunodeficiency Disease eligible for a non-myeloablative 
HCT trial 
5. A mismatched donor for whom ex vivo T-cell depletion of the donor stem cells 
is planned 
 
4.0 
Procedures: 
4.1 
Study Procedures/Treatments: 
 
4.1.1 Stratum A (Non-Malignant / Stem Cell Defects) 
 
Day 
Medication 
Dose for ≥12 kg 
Dose for <12 kg 
Day -13 Alemtuzumab Test Dose (1 mg)*,  
then 0.5 mg/kg (max 15 
mg) 
Test Dose (1 mg)*,  
then 0.5 mg/kg (max 6 mg) 
Day -12 Alemtuzumab 0.5 mg/kg (max 15 mg) 
0.5 mg/kg (max 6 mg) 
Day -11 Alemtuzumab 0.5 mg/kg (max 15 mg) 
0.5 mg/kg (max 6 mg) 
Day -10 Busulfan 
TBD by Wt-based formula 
1st dose at 9 pm 
TBD by Wt-based formula 
1st dose at 9 pm 
Day -9 
Busulfan 
TBD by PK (goal CSS = 
600) 
TBD by PK (goal CSS = 600) 
Day -8 
Busulfan 
TBD by PK  
TBD by PK  
Day -7 
Busulfan 
TBD by PK 
TBD by PK 
Day -6 
Busulfan 
TBD by PK: Last dose at 3 
pm (16 doses total) 
TBD by PK: Last dose at 3 pm 
(16 doses total) 
Day -5 
Fludarabine 
Clofarabine 
40 mg/m2 
10 mg/m2 
1.33 mg/kg 
0.33 mg/kg 
Day -4 
Fludarabine 
Clofarabine 
40 mg/m2 
10 mg/m2 
1.33 mg/kg 
0.33 mg/kg 
Day -3 
Fludarabine 
Clofarabine 
40 mg/m2 
10 mg/m2 
1.33 mg/kg 
0.33 mg/kg 
Day -2 
Fludarabine 
Clofarabine 
40 mg/m2 
10 mg/m2 
1.33 mg/kg 
0.33 mg/kg 
Day -1 
Rest 
 
 
Day 0 
Transplant 
To begin ≥48 hours from 
last dose of Flu and Clo 
To begin ≥48 hours from last 
dose of Flu and Clo 
 
* The test dose of Alemtuzumab (1 mg) will be given over 2 hours on the 1st day of 
conditioning. Four hours after the test dose, the first full dose of Alemtuzumab is given. 
 
 
 

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4.1.2 Stratum B (Myeloid Malignancies)# 
 
Day 
Medication 
Dose for ≥12 kg 
Dose for <12 kg 
Day -10 
Busulfan 
TBD by Wt-based formula 
1st dose at 9 pm 
TBD by Wt-based formula 
1st dose at 9 pm 
Day -9 
Busulfan 
TBD by PK (goal CSS = 
900) 
TBD by PK (goal CSS = 900) 
Day -8 
Busulfan 
TBD by PK  
TBD by PK  
Day -7 
Busulfan 
TBD by PK  
TBD by PK  
Day -6 
Busulfan 
TBD by PK: Last dose at 3 
pm (16 doses total) 
TBD by PK: Last dose at 3 pm 
(16 doses total) 
Day -5 
Fludarabine 
Clofarabine 
40 mg/m2 
10 mg/m2 
1.33 mg/kg 
0.33 mg/kg 
Day -4 
Fludarabine 
Clofarabine 
rATG^ 
40 mg/m2 
10 mg/m2 
0.5 mg/kg  
1.33 mg/kg 
0.33 mg/kg 
0.5 mg/kg 
Day -3 
Fludarabine 
Clofarabine 
rATG^ 
40 mg/m2 
10 mg/m2 
2.5 mg/kg (1 mg/kg if UCB) 
1.33 mg/kg 
0.33 mg/kg 
2.5 mg/kg (1 mg/kg if UCB) 
Day -2 
Fludarabine 
Clofarabine 
rATG^ 
40 mg/m2 
10 mg/m2 
2.5 mg/kg (1 mg/kg if UCB) 
1.33 mg/kg 
0.33 mg/kg 
2.5 mg/kg (1 mg/kg if UCB) 
Day -1 
rATG^ 
2.5 mg/kg (1 mg/kg if UCB) 
2.5 mg/kg (1 mg/kg if UCB) 
Day 0 
Transplant 
To begin ≥48 hours from 
last dose of Flu and Clo 
To begin ≥48 hours from last 
dose of Flu and Clo 
 
# Because of limited data utilizing Alemtuzumab with Umbilical Cord Blood (UCB) 
Donors, this regimen will also be utilized for Stratum A Patients with UCB Donors (See 
Table 1), EXCEPT that their Busulfan goal CSS will still be 600.  
^ Because of decreased GVL effect from matched related donors when using Bone 
Marrow or Umbilical Cord Blood as the stem cell source, only patients receiving 
Peripheral Blood Stem Cells from a matched related donor will receive rATG (See Table 
1). 
UCB recipients will receive “low dose” rATG (total dose of 3.5 mg/kg) based on recent 
data suggesting that “standard dose” rATG is associated with poor immunologic 
recovery. 
 
4.1.3 Supportive Care Practices: 
 
a. All USCF Pediatric BMT Supportive Care Guidelines will be followed 
b. Premedications for Serotherapy (rATG and Alemtuzumab) will include: 
Acetaminophen (10 mg/kg), Diphenhydramine (1 mg/kg), and Dexamethasone 
(0.2 mg/kg).  
c. Appropriate Seizure prophylaxis will be administered prior to 1st dose of 
Busulfan and for at least 12 hours after the final dose. 
d. Fludarabine should be infused over 1 hour (9 am to 10 am) and Clofarabine 
should be infused over 2 hours immediately afterwards (10 am to 12 noon). 

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e. To prevent hand-foot syndrome with Clofarabine, hydrocortisone (100 mg/m2; 
100 mg max dose) will be administered 1-2 hours prior to each dose unless 
Dexamethasone has been given within the last 24 hours. 
 
f. Ursodiol (6-7.5 mg/kg/dose twice daily) will be administered to all patients 
preferably 2 weeks prior to admission and no later than the day of admission. 
Ursodiol will continue until at least Day +30 or Day of Discharge, whichever is 
sooner, except for intolerance or side effects. 
g. Standard GVHD prophylaxis per the UCSF BMT Guidelines will be 
administered starting on Day -1. If a patient is unable to receive methotrexate on 
Day +1 due to liver enzyme elevations, mycophenolate mofitil should be 
substituted until the liver enzyme elevation has resolved and methotrexate can 
be re-initiated.  
h. Standard G-CSF administration will begin on Day +14, if needed. 
 
4.2 
Study Tests: 
4.2. 1 Standard of Care Testing: 
Most tests performed on this trial will be done as standard of care for any patient 
undergoing allogeneic HCT. This will include: 
a. A minimum of twice weekly monitoring of CBC, chemistries, renal function, 
and liver enzymes during the first month post-HCT, and at least twice monthly 
for the first 100 days post-HCT. 
b. Engraftment studies by STR analysis of cell subsets beginning on ~Day +30 
and then monthly until stable.  
4.2.2 Study Tests: 
a. To monitor for liver toxicity while receiving Clofarabine, daily liver enzymes 
(AST, ALT, Total and Direct Bilirubin, Alk Phos, and GGT) will be obtained 
starting on Day -5 and continuing until at least Day +6, at which point, the UCSF 
Pediatric BMT standard operating practices resume, which includes monitoring of 
liver enzymes twice weekly. Because daily tests of electrolytes are standard of 
care, this does not requires any additional blood to be drawn. 
b. Patients will undergo pharmacokinetics (PK) to evaluate both Clofarabine and 
Fludarabine (“nucleoside analogue”) exposure.   
i. Blood volume and weight: In total, 11 blood samples will be collected 
over the entire course of nucleoside analogue treatment to evaluate drug 
exposure and pharmacogenomics. The total amount of blood volume needed for 
PK sampling is based on the weight of the child. For children weighing < 8 kg a 
total of 16 ml of blood will be drawn over a 4 day treatment course. For children 
weighing > than 8 kg, the amount of blood drawn over a 4 days treatment course 
will be a total of 24 ml. 
ii. DNA collection: To assess the impact of genetic variants on 
nucleoside drug exposure a single blood collection for DNA and genotyping will 
occur on the day of admission prior to the start of chemotherapy. One (1 ml) of 
whole blood will be drawn into a 3 ml K2EDTA tube, placed on wet ice, and sent 
to the UCSF CTSI Core DNA Bank for immediate DNA isolation, quantification, 
and storage until analysis is performed.   
iii. PK sampling: To evaluate plasma and intracellular drug 
concentrations blood samples will be obtained at 6 times over the course of 

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nucleoside treatment for a total 10 blood samples. Per protocol, Fludarabine will 
be administered intravenously over 60 minutes, followed by Clofarabine infusion 
over 2 hours. For convenience, blood collection times are based on the 
administration time of fludarabine. Plasma and intracellular drug concentrations 
are processed independently from one another and therefore require two 
different blood collection tubes at several of the PK sampling times. 
iv. Day 1 of nucleoside analogue therapy:  Following the administration 
of Fludarabine, 1ml of whole blood will be obtained at 2, 4, 8, and 24 hours after 
the start of infusion to evaluate plasma concentrations of both Clofarabine and 
Fludarabine. Blood samples for each plasma PK time point will be collected in a 
2 mL spray dried K2EDTA tube and immediately place on wet ice. Within 60 
minutes of collection all samples must centrifuged at 3400 rpm for 10 minutes at 
4ºC, the plasma removed, and stored at -70ºC until analysis. PK sampling for the 
analysis of intracellular fludarabine drug levels will occur concurrently at 2 and 24 
hours for correlation of plasma and intracellular drug concentrations. Blood 
samples for intracellular drug quantification will be collected in a 4 mL cell 
preparation tube with sodium citrate (BD Vacutainer ® CPT Tube) and processed 
for recovery of peripheral blood mononuclear cells. For children <8 kg only 2ml of 
blood will be collected for intracellular analysis.   
v. Day 2, 3, or 4 of nucleoside analogue therapy:  To evaluate drug 
accumulation over the course of treatment and assess inter-occasion variability, 
PK sampling will be repeated on Day 2, 3 or 4 of nucleoside analogue treatment. 
Blood samples will be collected at 2 and 24 hours following administration of 
fludarabine for a total of 4 blood samples. Blood samples for each plasma PK 
time point will be collected in a 2 mL spray dried K2EDTA tube and processed as 
previously described. As with Day 1 PK, blood collections for the analysis of 
intracellular nucleoside analogue drug concentrations will occur concurrently at 2 
and 24 hours and processed for peripheral blood mononuclear cells.  
vi. This PK sampling is identical to Study 10-00894 (Population 
Pharmacokinetics of Fludarabine in Pediatric Patients Undergoing Hematopoietic 
Cell Transplantation; Janel Long-Boyle, PI), thus patients will not need to co-
enroll on that trial. 
 
5.0 
Statistics & Sample Size: 
5.1 
Primary Objective: 
a. Severe Toxicity will be defined as death or Grade IV (by CTC AE 4.0) 
pulmonary or hepatic failure (including moderate veno-occlusive disease,aka 
VOD) related to the transplant conditioning regimen (as defined in Section 8.2) 
within 100 days post-HCT.  
i. VOD will be defined by standard criteria. Patients must have Bilirubin 
>2.0 plus Hepatomegaly and/or RUQ pain plus Weight gain >5%. 
b. The historic control will be the 37 patients detailed below, who have been 
treated with BU-FLU-Serotherapy based protocols at UCSF from 2000 – 2010 
(and who would have fit the eligibility criteria for this trial). Of these 37 patients, 1 
experienced TRM, but there were no cases of Grade IV pulmonary or hepatic 
failure, for a cumulative incidence of severe toxicity of 3% (90% upper confidence 
bound: 10%).  

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c. Sample size justification is based on establishing that observed rates of toxicity 
with the addition of Clofarabine to a backbone of BU-FLU-Serotherapy are not 
worse than historical control levels. Since formal establishment of noninferiority is 
not possible given feasible sample sizes, expected toxicity rates are compared to 
historical rates in terms of the 90% exact binomial upper confidence bound for 
the observed proportion of events. For our planned sample size of 31, 3 or fewer 
events would lead to an upper bound within 10% of the corresponding upper 
bound for historical control levels. We consider a difference of 10% or smaller as 
evidence of similar levels of toxicity. 
d. If there are more than 3 events in the first 15 patients enrolled, the trial will be 
closed early for failing to achieve its safety goal. 
 
5.2 
Secondary Objectives: 
5.2.1 Engraftment in patients with non-malignant diseases (Stratum A):  
a.  Engraftment will be defined as the development of an ANC >500 for 3 
consecutive days plus donor CD14/15 cells >70%.  
b.  The historic control for Stratum A will be as follows: 
 
 
Patients 
# of High-Risk 
Patients 
Engraftment 
Overall 
Survival 
Enrolled on BU-FLU-rATG2 
5 
2 
4 
Enrolled on BU-FLU-C4 
5 
2 
2 
Treated with BU off study (2005-10) 
5 
3 
5 
Summary 
15 
6 
11 
 
c. Therefore, the engraftment rate in this population was only 40%. If the 
observed engraftment rate of this trial is as large as 83% (10/12), we would 
need a minimum of 12 patients in Stratum A to show a significant  
improvement (alpha < 0.05) in engraftment rate compared to historic controls 
at the 5% level.  
d. If 3 patients in Stratum A experience graft rejection, we will close this stratum 
early for failing to achieve superior engraftment compared to standard-of-
care. 
 
5.2.2 Mixed-Chimerism in patients with high-risk myeloid malignancies (Stratum B):  
a.  Full-donor chimerism will be defined by as ≥99% donor cells by STR analysis 
in all cell lines (CD3, CD14/15, and CD19) in peripheral blood.  
b. The historic control for Stratum B will be the 20 patients who were 
transplanted from 2005 – 2010 with BU-based regimens and who 
retrospectively would have been eligible for the current trial. Of these 20 
patients, at 100 days post-HCT, only 8 (40%) patients had full-donor 
chimerism (B. Horn, unpublished data).  
c.  If the observed cumulative incidence of full-donor chimerism at Day 100 is at 
least 79%, we will need a minimum of 19 patients in Stratum B to show a 

Clofarabine 
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significant improvement (alpha < 0.05) in incidence of full donor chimerism 
compared to historic controls at the 5% level.   
d.  If 5 patients in Stratum B experienced mixed-donor chimerism at Day 100, we 
will close this stratum early for failing to achieve superior donor cell 
engraftment compared to standard-of-care. 
 
5.2.3 Fludarabine and Clofarabine PK 
Fludarabine and clofarabine drug levels and potential covariates influencing drug 
exposure such as renal function and genetic variants involved in drug 
metabolism, distribution, and activation will be analyzed using standard 
population pharmacokinetic methods using non-linear mixed effects modeling 
(NONMEM) software.   
 
5.3 
Sample Size: 
a. We will plan to accrue 12 patients to Stratum A and 19 patients to Stratum B, 
for a total of 31 patients. 
b. Feasibility: From 2005 to 2010, we transplanted 15 patients that would have 
met the criteria for enrollment in Stratum A, and 22 patients that would have met 
the criteria for Stratum B. Presuming at least 90% participation of future patients, 
this trial should be able to accrue in approximately 6 years if referrals for 
transplant stay constant, or faster if they increase.  
 
6.0 
Risks, Benefits, and Alternatives: 
6.1 
Risks: Risks and side effects seen with standard-dose Clofarabine are listed on 
the following table. Side-effects reported in four trials of Clofarabine use during 
the conditioning regimen prior to HCT are listed first and are bolded.  
 
Likely 
Less Likely 
Rare But Serious 
Nausea and/or vomiting 
Inflammation and/or sores in 
the mouth that may make 
swallowing difficult and are 
painful (painful mouth sores) 
Inflammation or damage to 
the liver which can be 
severe and life-threatening 
and which may lead to an 
enlarged liver and spleen, 
bleeding from the veins in 
the esophagus (the 
passage that leads from the 
throat to the stomach), a 
yellow appearance to the 
skin and fluid collection in 
the abdomen which makes 
it look larger 
Diarrhea 
Increased levels of a 
chemical (creatinine) in the 
blood which could mean 
kidney damage 
Severe loss of water from 
the body (dehydration) 
which if untreated may 
cause low blood pressure 
and severe loss of salts 
such as sodium and 
potassium from the body 
and could lead to the 
kidneys failing which could 
be life-threatening 

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Elevation in the blood of 
certain enzymes found in the 
liver and bilirubin (a 
substance that comes from 
the liver breaking down 
waste products) which may 
mean the liver is not working 
as well as normal 
The skin and the whites of 
the eyes appears yellow as a 
result of too much bilirubin (a 
substance that comes from 
the liver breaking down 
waste products) in the blood 
Capillary leak syndrome: a 
condition in which fluid and 
proteins leak out of tiny 
blood vessels and flow into 
surrounding tissues, 
resulting in dangerously low 
blood pressure. Capillary leak 
syndrome 
may lead to multiple organ 
failure such as kidney, 
heart or liver failure and 
shock 
Fever 
 
Severe rash with redness and 
pain on the palms of the hand 
and soles of the feet 
(Hand-Foot Syndrome) 
Inflammation of the 
pancreas (an organ in the 
abdomen which produces 
insulin and certain 
digestive chemicals) which 
may affect the function of 
the pancreas and which 
may cause pain in the 
abdomen (belly) which can 
be severe and may increase 
the blood sugar 
Skin rash 
 
Numbness and tingling in the 
fingers and toes 
Severe inflammation and 
damage to the large 
intestine wall which can be 
life threatening 
A fast heartbeat which may 
cause pain in the chest 
 
 
Rash with redness or red 
bumpy rash 
Abnormal clotting of the 
blood that can lead to 
formation of blood clots 
and/or bleeding with 
abnormal findings on 
neurologic exam 
A feeling of extreme 
tiredness not relieved by 
sleep 
The rapid death of large 
numbers of tumor cells which 
can cause the potassium and 
phosphate salts and the uric 
acid in the blood to rise 
quickly and this could lead to 
a life-threatening irregular 
heart beat or damage to the 
kidneys 
Severe rashes which can 
result in loss of skin and 
damage to mucous 
membranes and which may 
be life-threatening 
(occurred in combination of 
other drugs known to 
cause this effect) 
A decrease in blood pressure 
Fluid build-up in the tissues 
 
Severe kidney damage 
(which may be permanent) 
Pain in the abdomen (belly) 
Sleepiness and weakness 
Failure of the bone marrow 
to produce blood cells and 
platelets which can be life 
threatening 
Fever with a low white blood cell 
count which could mean 
that you have an infection 
and might require 
hospitalization and 
treatment with antibiotics 
Changes to your emotions such 
that you feel depressed, anxious, 
agitated, irritable or confused 
A change to the heart such 
that it does not pump the 
blood as well which may 
make you tired, weak, feel 
short of breath, and retain 
fluid 
Chills 
Shaking chills 
 

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Anxiety 
High blood pressure 
 
Loss of appetite  
Cough or shortness of breath 
 
Headache 
Reddening of the face with 
feelings of warmth when the 
drug is infusing 
 
Skin rash with inflammation 
A fast rate of respiration that 
may cause pain in the chest 
 
Itching 
Allergic reaction 
 
Red spots on the skin from 
low platelets 
A change in alertness, 
concentration, and memory 
 
Bloody nose 
Constipation 
 
Fewer white blood cells, red 
blood cells and platelets in the 
blood (may be prolonged)  
A low number of white blood cells 
can make it easier to get 
infections 
A low number of red blood cells 
can make you feel tired and 
weak 
A low number of platelets causes 
you to bruise and bleed more 
easily 
A life-threatening form of severe 
blood infection that usually 
results from the presence of 
bacteria and 
their toxins in the bloodstream 
and is 
characterized especially by 
persistent hypotension with 
reduced blood flow to organs and 
tissues and often organ 
dysfunction 
 
Abnormal levels of 
potassium or magnesium in 
the body which may require 
that you take extra 
potassium by mouth or vein 
Tremor (shakiness usually of 
the hands) 
 
An increase in an enzyme 
(called lipase) that helps 
break down fats in the body 
Difficulty sleeping or falling 
Asleep 
 
 
Fainting 
 
 
Low levels of oxygen in the 
blood which may make you 
feel short of breath 
 
 
Pain including back, bone, 
arm, or leg pain 
 
 
Weight loss 
 
 
Aches and pains in the 
muscles and joints 
 
 
Bleeding from the bladder, 
gut, mouth, or gums 
 
 
Vomiting or coughing blood 
 
 
Fluid build-up in the lungs 
that can make you feel short 
of breath 
 
 
A life threatening condition in 
which the level of oxygen in 
the blood becomes too low or 
the level of carbon dioxide in 
the blood becomes too high 
 
 
Damage to the sac around 
the heart which can lead a 
build-up of fluid around the 
heart which may be painful 
 

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and affect the ability of the 
heart to work normally but in 
most cases is only mild and 
temporary 
 
Bruising of the skin from low 
Platelets 
 
 
Occasional sudden sharp 
pain in the rectal area 
 
 
Infections including those 
caused by bacteria, virus, 
and fungus and can be found 
in the lung, the blood, the 
skin and other places in the 
body 
 
 
Dizziness 
 
 
Abnormal high level of 
potassium in the blood which 
may cause irregular heart 
beat and require drug 
treatment to lower the level 
 
 
An increase in an enzyme 
(called amylase) that helps 
break down starch and 
sugars in the body 
 
 
A problem in nerve function 
that may cause pain, 
numbness, tingling, and 
muscle weakness in various 
parts of the body and may 
affect the ability to perform 
tasks that require fine 
movements 
 
 
6.2 
Benefits: 
a. There is a possible benefit to the patient in that the addition of low-dose 
Clofarabine may decrease the risk of either graft rejection or relapse. If that 
occurs, then there would likely be a survival benefit to the patient as well. 
b. The characterization of Clofarabine PK and knowledge of associations 
between drug exposure and outcomes will facilitate the development of 
individualized dosing strategies for use in pediatric HCT. We expect 
individualized dosing strategies will lead to improved rates of stem cell 
engraftment and reduced treatment-related mortality and thus will be a potential 
future benefit to the segment of society in need of receiving these agents.    
 
6.3 
Alternatives: 
The UCSF standard of care for patients eligible for enrollment on this study 
would be to receive Busulfan and Fludarabine, without the addition of 
Clofarabine, for the pre-HCT conditioning regimen. 
 
7.0 
Subject Recruitment and Consent Process 
7.1 
Subject Recruitment 

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a. Source: Subjects are referred from outside physicians and immunology and 
hematology clinics and specialists. 
b. Initial contact: Usually, patients and parents are initially seen in the pediatric 
BMT outpatient clinic. Occasionally, the initial contact is as an inpatient. 
7.2 
Consent Process:  
There is an initial consultation evaluation in the BMT outpatient clinic for all 
prospective patients and their parents at which the basic concepts of 
transplantation are reviewed including the overall risks and benefits of the 
procedure, the donor search, and the main aspects of the transplant, i.e., the 
estimated length of hospital stay, administration of chemotherapy, and the major 
side effects and complications, both acute and long term. When it is apparent 
that a donor is available, a second outpatient meeting occurs with the family, and 
the protocol is discussed in more detail including who the likely donor will be (if 
known based upon HLA typing). This is generally within 2-3 weeks of the 
potential admission to the BMT unit. If the parents want to proceed, the 
evaluations are done on the patient and donor. Once this is complete and at least 
3 days prior to admission to the BMT unit, a final informed consent conference is 
held to review the results of the work-up and to obtain final signed agreement. At 
that meeting, the attending discusses the donation procedure with the donor (if 
related). 
 
All participants must be provided a consent form describing the study with 
sufficient information for participants to make an informed decision regarding 
their participation.  Participants must sign the IRB-approved informed consent 
form prior to participation in any study specific procedure.  The participant must 
receive a copy of the signed and dated consent document.  The original signed 
copy of the consent document must be retained in the medical record or research 
file. 
 
8.0  
Reporting and Documentation of Adverse Events 
8.1  Definitions of Adverse Events 
8.1.1 Adverse Event 
An adverse event (also known as an adverse experience) is defined as any 
untoward medical occurrence associated with the use of a drug in humans, 
whether or not considered drug related.  More specifically, an adverse event (can 
be any unfavorable and unintended sign (e.g., an abnormal laboratory finding), 
symptom, or disease temporally associated with the use of a drug, without any 
judgment about causality.  An adverse event can arise from any use of the drug 
(e.g., off-label use, use in combination with another drug) and from any route of 
administration, formulation, or dose, including an overdose.  
8.1.2 Adverse reaction 
An adverse reaction is defined as any adverse event caused by the use of a 
drug.  Adverse reactions are a subset of all suspected adverse reactions for 
which there is reason to conclude that the drug caused the event. 

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8.1.3 Suspected adverse reaction 
A suspected adverse reaction is defined as any adverse event for which there is 
a reasonable possibility that the drug caused the adverse event. For the 
purposes of IND safety reporting, “reasonable possibility” indicates that there is 
evidence to suggest a causal relationship between the drug and the adverse 
event.  A suspected adverse reaction implies a lesser degree of certainty about 
causality than an adverse reaction. 
8.1.4 Unexpected 
An adverse event or suspected adverse reaction is considered unexpected if it is 
not listed in the investigator brochure or package insert(s), 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.  
“Unexpected,” as used in this definition, also refers to adverse events or 
suspected adverse reactions that are mentioned in the investigator brochure as 
occurring with a class of drugs or as anticipated from the pharmacological 
properties of the drug, but are not specifically mentioned as occurring with the 
particular drug under investigation. 
Adverse events that would be anticipated to occur as part of the disease process 
are considered unexpected for the purposes of reporting because they would not 
be listed in the investigator brochure.  For example, a certain number of non-
acute deaths in a cancer trial would be anticipated as an outcome of the 
underlying disease, but such deaths would generally not be listed as a suspected 
adverse reaction in the investigator brochure. 
Some adverse events are listed in the Investigator Brochure  as occurring with 
the same class of drugs, or as anticipated from the pharmacological properties of 
the drug, even though they have not been observed with the drug under 
investigation.  Such events would be considered unexpected until they have 
been observed with the drug under investigation. For example, although 
angioedema is anticipated to occur in some patients exposed to drugs in the 
ACE inhibitor class and angioedema would be described in the investigator 
brochure as a class effect, the first case of angioedema observed with the drug 
under investigation should be considered unexpected for reporting purposes. 
8.1.5 Serious 
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 
 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 function 
 Congenital anomaly/birth defect 

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Important medical events that may not result in death, are 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.  Examples of such medical events include allergic bronchospasm 
requiring intensive treatment in an emergency room or at home, blood dyscrasias 
or convulsions that do not result in inpatient hospitalization, or the development 
of drug dependency or drug abuse. 
8.1.6 Life-threatening 
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. It does not include an adverse event or 
suspected adverse reaction that, had it occurred in a more severe form, might 
have caused death.  
8.2 Recording of an Adverse Event 
All Grade 3 – 5 adverse events will be entered into OnCore®, whether or not the 
event is believed to be associated with use of the study drug.  Data about these 
events and their severity will be recorded using the NCI CTCAE v4.0.   
The Investigator will assign attribution of the possible association of the event with 
use of the investigational drug, and this information will be entered into OnCore® 
using the classification system listed below:  
Relationship  
Attribution  
Description  
Unrelated to 
investigational 
drug/intervention 
Unrelated 
The AE is clearly NOT related to the 
intervention  
Unlikely 
The AE is doubtfully related to the 
intervention  
Related to investigational 
drug/intervention 
Possible 
The AE may be related to the intervention  
Probable 
The AE is likely related to the intervention  
Definite 
The AE is clearly related to the 
intervention  
 
Signs or symptoms reported as adverse events will be graded and recorded by 
the Investigator according to the CTCAE.  When specific adverse events are not 
listed in the CTCAE they will be graded by the Investigator as none, mild, 
moderate or severe according to the following grades and definitions: 

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Grade 
0 
No AE (or within normal limits) 
Grade 
1 
Mild; asymptomatic or mild symptoms; clinical or diagnostic observations 
only; intervention not indicated 
Grade 
2 
Moderate; minimal, local, or noninvasive intervention (e.g., packing, 
cautery) indicated; limiting age-appropriate instrumental activities of daily 
living (ADL) 
Grade 
3: 
Severe or medically significant but not immediately life-threatening; 
hospitalization or prolongation of hospitalization indicated; disabling; 
limiting self-care ADL 
Grade 
4: 
Life-threatening consequences; urgent intervention indicated 
Grade 
5: 
Death related to AE 
8.3 Follow-up of Adverse Events 
All Grade 3 – 5 adverse events will be followed with appropriate medical 
management until resolved.  Patients removed from study for unacceptable 
adverse events will be followed until resolution or stabilization of the adverse 
event.  For selected adverse events for which administration of the investigational 
drug was stopped, a re-challenge of the subject with the investigational drug may 
be conducted if considered both safe and ethical by the Investigator. 
8.4 Adverse Events Monitoring  
All Grade 3 – 5 adverse events, whether or not unexpected, and whether or not 
considered to be associated with the use of the study drug, will be entered into 
OnCore®, as noted above. 
The Investigator will assess all adverse events and determine reportability 
requirements to the UCSF Data and Safety Monitoring Committee (DSMC) and 
UCSF’s Institutional Review Board, the Committee on Human Research (CHR); 
and, when the study is conducted under an Investigational New Drug Application 
(IND), to the Food and Drug Administration (FDA) if it meets the FDA reporting 
criteria. 
All adverse events entered into OnCore® will be reviewed by the Helen Diller 
Family Comprehensive Cancer Center Site Committee on a weekly basis.  The 
Site Committee will review and discuss at each weekly meeting the selected 
toxicity, the toxicity grade, and the attribution of relationship of the adverse event to 
the administration of the study drug(s). 
In addition, all adverse events and suspected adverse reactions considered 
“serious,” entered into OnCore® will be reviewed and monitored by the Data and 
Safety Monitoring Committee on an ongoing basis, discussed at DSMC meetings 
which take place every six (6) weeks, and prior to dose escalation.   
8.5 Expedited Reporting  
Reporting to the Data and Safety Monitoring Committee 
If a death occurs during the treatment phase of the study or within 30 days after 
the last administration of the study drug(s) and it is determined to be related either 
to the study drug(s) or to a study procedure, the Investigator or his/her designee 

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must notify the DSMC Chair (or qualified alternate) within 1 business day of 
knowledge of the event.  The contact may be by phone or e-mail. 
Reporting to UCSF Committee on Human Research (Institutional Review 
Board) 
The Principal Investigator must report events meeting the UCSF CHR definition of 
“Unanticipated Problem” (UP) within 10 business days of his/her awareness of the 
event.  
 
9.0  
Data and Safety Monitoring Plan 
 
9.1 
The UCSF-HDFCCC Data Safety Monitoring Committee (DSMC) is responsible 
for monitoring data quality and patient safety for all UCSF-HDFCCC institutional 
clinical studies.  A summary of DSMC activities for this study includes:  
 
• 
Review of subject data • 
Review of suspected adverse reactions 
considered “serious” 
 Monitoring every six months (depending on study accrual) 
 
• 
Minimum of a yearly audit 
 
9.1.2 Monitoring and Reporting Guidelines 
 
Investigators will conduct continuous review of data and patient safety at monthly 
study group or site committee meetings where the results of each patient’s 
treatment are discussed and the discussion is documented in the minutes. The 
discussion will include the number of patients, significant toxicities as described 
in the protocol, doses adjustments, and observed responses.  
 
All institutional Phase 2 studies are designated with a moderate risk assessment.  
The data is monitored twice per year with twenty percent of the subject’s 
monitored (or at least three subjects if the calculated value is less than three).   
.   
AEs, subject participation data, deviations and clinical data from electronic case 
report forms (CRFs) will be reviewed and signed off by the Investigator 
quarterly/monthly. 
 
9.1.3 Adverse Event Review and Monitoring 
 
 
All grade(s) 3-5 adverse events, whether or not unexpected, and whether or not 
considered to be associated with the use of the study drug, will be entered into 
OnCore®, UCSF’s Clinical Trial Management System.   
All grade(s) 3-5 adverse events entered into OnCore® will be reviewed on a 
monthly basis at the Site Committee meetings.  The Site Committee will review 
and discuss the selected toxicity, the toxicity grade, and the attribution of 
relationship of the adverse event to the administration of the study drug(s).   

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In addition, all adverse events or suspected adverse reactions considered 
“serious,” entered into OnCore® will be reviewed and monitored by the Data and 
Safety Monitoring Committee on an ongoing basis and discussed at DSMC 
meetings, which take place every six (6) weeks. 
If a death occurs during the treatment phase of the study or within 30 days after 
the last administration of the study drug(s) and it is determined to be related 
either to the study drug(s) or to a study procedure, the Investigator or his/her 
designee must notify the DSMC Chair within 1 business day of knowledge of the 
event.  The contact may be by phone or e-mail. 
 
9.1.4  Increase in Adverse Event Rates 
If an increase in the frequency of Grade 3 or 4 adverse events (above the rate 
reported in the Investigator Brochure or package insert) is noted in the study, a 
report should be submitted to the DSMC at the time the increased rate is 
identified.  The report will indicate if the incidence of AEs observed in the study is 
within the range stated in the Investigator Brochure or package insert.   
If at any time the Investigator stops enrollment or stops the study due to safety 
issues the DSMC Chair and administrator must be notified within 1 business 
day via e-mail.  The DSMC must receive a formal letter within 10 business days 
and the CHR must be notified. 
 
Data and Safety Monitoring Committee Contacts: 
DSMC Chair:
 
Phone 
 
Email  
 
Box 
 
 
 
DSMC Monitors 
Box 1297 
UCSF Helen Diller Family Comprehensive Cancer Center 
 
 
 
9.2 
Assessment of Risk:  This study is deemed to be a pilot phase II clinical trial that 
present a moderate degree of risk to the study subjects. Because this study will enroll 
pediatric HCT patients using an agent with limited experience when combined with 
Busulfan and Fludarabine, safety monitoring will be conducted by the UCSF Data and 
Safety Monitoring Committee (DSMC).  Utilizing the UCSF DSMC will enable the data to 
be reviewed and thus any serious adverse events can be linked to the pharmacological 
agent being investigated.   
 
9.2.1  Anticipated Adverse Events: Clofarabine has previously been demonstrated to be 
safe for human therapy in pediatric cancer patients, further supporting the assignment 
of a moderate degree of risk to this study. However, like most chemotherapy agents, 
Clofarabine does have many known side-effects (see Section 6.1). Some “side-effects,” 
such as hematologic toxicity and immunosuppression, are actually desired effects of 

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Clofarabine on this HCT trial. Some potential side-effects of Clofarabine, such as 
vomiting or mucositis, will be very difficult to distinguish from known side-effects of the 
simultaneously administered agents Busulfan and Fludarabine, and thus their incidence 
will not be tracked. Other potential side-effects of Clofarabine, such as Hand-Foot 
Syndrome, may be relatively unique to this agent but are not of sufficient severity to 
dissuade future use of this agent in the HCT setting if it shows potential benefit for 
prevention of graft rejection or relapse, potentially fatal outcomes. In the primarily adult 
trials of Clofarabine use as part of a HCT conditioning regimen, the most notable and 
commonly seen adverse event was the development of an early and reversible hepatic 
transaminitis. The trial has been designed to specifically monitor for this adverse event, 
but unless it leads to the development of Grade IV hepatic failure or moderate VOD, this 
will not be considered a significant event for the safety analysis of the trial. 
Myeloablative HCT in general, whether done as part of a clinical trial or as a standard-
of-care treatment, is a inherently risky procedure, with a known risk of TRM and many 
non-fatal toxicities, independent of the potential addition of novel agent(s). Given that 
only patients at high risk of graft rejection or relapse (frequently fatal events) are eligible 
for this trial, only a significant increase in TRM or very severe (Grade IV hepatic or 
pulmonary) toxicities would be sufficient cause to suspend further development of 
Clofarabine to potentially improve overall outcomes following HCT. 
 
9.3. 
Safety Monitoring Plan: Subjects will remain in the hospital for at least 3 weeks 
following administration of the study medication Clofarabine. This will allow sufficient 
time to monitor for the development of severe adverse events potentially attributable to 
Clofarabine. During this time, as part of routine post-HCT standard of care, patients will 
have daily physical exams, frequent vital sign monitoring, and laboratory testing at least 
twice weekly (and daily during the initial period). The safety laboratory studies (i.e. 
hepatic transaminases) will be reviewed on a continuous basis by the investigators. 
Following discharge from the hospital and until Day +100, patients will be followed 
closely in clinic at least twice monthly, with laboratory studies done at least once 
weekly, all per the UCSF Pediatric BMT SOP. Patients will also have a contact number 
to report any potential adverse events that occur in between scheduled clinic visits.  
Should a serious adverse event occur during the course of the study, it will be reported 
immediately to the Committee on Human Research (Institutional Review Board) at the 
University of California San Francisco (UCSF) in accordance with current University 
guidelines for reporting possible adverse events.   
 
9.3.1 Frequency of Safety Reviews: Safety monitoring will be conducted monthly on 
each patient. 
 
10.0 Study Management 
10.1 Prestudy Documentation 
This study will be conducted in accordance with the ethical principles that have 
their origin in the Declaration of Helsinki as stated in 21 CFR §312.120(c)(4); 
consistent with GCP and all applicable regulatory requirements. 
 

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Before initiating this trial, the Investigator will have written and dated approval 
from the Institutional Review Board for the protocol, written informed consent 
form, subject recruitment procedures (e.g., advertisements), and any other 
written information to be provided to subjects before any protocol related 
procedures are performed on any subjects.   
 
The clinical investigation will not begin until either FDA has determined that the 
study under the Investigational Drug Application (IND) is allowed to proceed or 
the Investigator has received a letter from FDA stating that the study is exempt 
from IND requirements.  
 
The Investigator must comply with the applicable regulations in Title 21 of the 
Code of Federal Regulations (21 CFR §50, §54, and §312), GCP/ICH guidelines, 
and all applicable regulatory requirements.  The IRB must comply with the 
regulations in 21 CFR §56 and applicable regulatory requirements. 
10.2 Institutional Review Board Approval 
The protocol, the proposed informed consent form, and all forms of participant 
information related to the study (e.g. advertisements used to recruit participants) 
will be reviewed and approved by the Committee on Human Research (CHR) 
(UCSF’s IRB).  Prior to obtaining CHR approval, the protocol must be approved 
by the Helen Diller Family Comprehensive Cancer Center Site Committee and by 
the Protocol Review Committee (PRC).  The initial protocol and all protocol 
amendments must be approved by the IRB prior to implementation.   
10.3 Changes in the Protocol 
Once the protocol has been approved by the UCSF Committee on Human 
Research (CHR), any changes to the protocol must be documented in the form of 
an amendment.  The amendment must be signed by the Investigator and 
approved by PRC and the CHR prior to implementation.   
 
If it becomes necessary to alter the protocol to eliminate an immediate hazard to 
patients, an amendment may be implemented prior to CHR approval.  In this 
circumstance, however, the Investigator must then notify the CHR in writing 
within five (5) working days after implementation. 
10.4 Handling and Documentation of Clinical Supplies 
The Investigator shall maintain complete records showing the receipt, 
dispensation, return, or other disposition of all investigational drugs.  The date, 
quantity and batch or code number of the drug, and the identification of patients 
to whom study drug has been dispensed by patient number and initials will be 
included.  The sponsor-investigator will maintain written records of any 
disposition of the study drug. 
The Investigator shall not make the investigational drug available to any 
individuals other than to qualified study patients.  Furthermore, the Investigator 
will not allow the investigational drug to be used in any manner other than that 
specified in this protocol. 
10.5 Case Report Forms (CRFs) 
The Principal Investigator and/or his/her designee, will prepare and maintain 
adequate and accurate participant case histories with observations and data 

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pertinent to the study.  Study specific Case Report Forms (CRFs) will document 
treatment outcomes for data analysis (see Appendix 1).  All study data will be 
entered into OnCore®, UCSF’s Clinical Trial Management System (CTMS) via 
standardized CRFs in accordance with the CTMS study calendar, using single 
data entry with a secure access account.  The Clinical Research Coordinator 
(CRC) will complete the CRFs as soon as possible upon completion of the study 
visit; the Investigator will review and approve the completed CRFs.  
 
The information collected on CRFs shall be identical to that appearing in original 
source documents.  Source documents will be found in the patient’s medical 
records maintained by UCSF personnel.  All source documentation should be 
kept in separate research folders for each patient. 
 
In accordance with federal regulations, the Investigator is responsible for the 
accuracy and authenticity of all clinical and laboratory data entered onto CRFs.  
Each CRF must be reviewed for accuracy by the Investigator, corrected as 
necessary, and then approved.  Alternatively, the Investigator may sign 
individual, printed CRFs.  These signatures attest that the information contained 
on the CRFs is true and accurate.  
 
All source documentation and CTMS data will be available for review/monitoring 
by the Data and Safety Monitoring Committee (DSMC) and regulatory agencies. 
 
The Principal Investigator will be responsible for ensuring the accurate capture of 
study data.  At study completion, when the database has been declared to be 
complete and accurate, the database will be locked.  Any changes to the 
database after that time can only be made by joint written agreement among the 
Principal Investigator, the Trial Statistician, and the Protocol Project Manager. 
10.6 Oversight and Monitoring Plan 
The Helen Diller Family Comprehensive Cancer Center Data and Safety 
Monitoring Committee (DSMC) will be the monitoring entity for this study.  The 
DSMC will monitor the study in accordance with the NCI-approved Data and 
Safety Monitoring Plan (DSMP).  The DSMC will regularly review all adverse 
events and suspected adverse reactions considered “serious” and protocol 
deviations associated with the research to ensure the protection of human 
subjects.  The DSMC will audit study-related activities to ensure that the study is 
conducted in accordance with the protocol, local standard operating procedures, 
FDA regulations, and Good Clinical Practice (GCP).  Significant results of the 
DSMC audit will be communicated to the IRB and the appropriate regulatory 
authorities at the time of continuing review, or in an expedited fashion, as 
applicable.  
10.7 Record Keeping and Record Retention 
The investigator is required to maintain adequate records of the disposition of the 
drug, including dates, quantity, and use by subjects, as well as written records of 
the disposition of the drug when the study ends.   
 

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The investigator is required to prepare and maintain adequate and accurate case 
histories that record all observations and other data pertinent to the investigation 
on each individual administered the investigational drug or employed as a control 
in the investigation. Case histories include the case report forms and supporting 
data including, for example, signed and dated consent forms and medical 
records including, for example, progress notes of the physician, the individual's 
hospital chart(s), and the nurses' notes. The case history for each individual shall 
document that informed consent was obtained prior to participation in the study. 
Study documentation includes all Case Report Forms, data correction forms or 
queries, source documents, Sponsor-Investigator correspondence, monitoring 
logs/letters, and regulatory documents (e.g., protocol and amendments, IRB 
correspondence and approval, signed patient consent forms). 
 
Source documents include all recordings of observations or notations of clinical 
activities and all reports and records necessary for the evaluation and 
reconstruction of the clinical research study. 
 
In accordance with FDA regulations, the investigator shall retain records for a 
period of 2 years following the date a marketing application is approved for the 
drug for the indication for which it is being investigated; or, if no application is to 
be filed or if the application is not approved for such indication, until 2 years after 
the investigation is discontinued and FDA is notified. 
 
 

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Appendix I. Case Report Form: 
 
Patient's Medical Record Number:   
 
 
Patient Name (last, first):   
 
 
Date of Birth:   
 
_____/_____/_____                               Gender   
 
 
Date of Transplant:   
_____/_____/_____ 
 
1. 
Toxicities Through Day +100 
a. 
Treatment-Related Mortality:  
 
Date: ___________________ 
b. 
Grade IV Pulmonary Toxicity: 
 
Date of onset: ___________________ 
(Life-threatening respiratory or hemodynamic compromise; intubation or urgent intervention indicated) 
c. 
Grade IV Hepatic Toxicity:   
 
Date of onset: ___________________ 
(Moderate to severe encephalopathy; coma; life-threatening consequences) 
d. 
Moderate or Severe VOD:  
 
Date of onset: ___________________ 
(Bilirubin >2.0 plus Hepatomegaly and/or RUQ pain plus Weight gain >5%; typically requires treatment 
with Defibrotide) 
e. 
Required Liver Enzyme Studies: 
 
AST 
ALT 
TBili 
DBili 
AlkPhos 
GGT 
Day -5 
 
 
 
 
 
 
Day -4 
 
 
 
 
 
 
Day -3 
 
 
 
 
 
 
Day -2 
 
 
 
 
 
 
Day -1 
 
 
 
 
 
 
Day 0 
 
 
 
 
 
 
Day +1 
 
 
 
 
 
 
Day +2 
 
 
 
 
 
 
Day +3 
 
 
 
 
 
 
Day +4 
 
 
 
 
 
 
Day +5 
 
 
 
 
 
 
 
2. 
Outcomes 
a. 
First Engraftment Study (~Day +30): Report % Donor Cells   
Date: ___________ 
a. 
Whole Blood 
_________ 
b. 
CD3  
_________ 
c. 
CD14/15 
_________ 
d. 
CD19  
_________ 
b. 
~Day +100 Engraftment Study: Report % Donor Cells 
 
Date: ____________ 
a. 
Whole Blood 
_________ 
b. 
CD3  
_________ 
c. 
CD14/15 
_________ 
d. 
CD19  
_________ 
 

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Appendix II. IND Exemption Determination: 
 
This is a new use of an already approved drug. Clofarabine’s FDA label is that it is 
indicated for the treatment of pediatric patients 1 to 21 years old with relapsed or 
refractory acute lymphoblastic leukemia after at least two prior regimens. The 
recommended pediatric dose and schedule is 52 mg/m2 administered by intravenous 
(IV) infusion over 2 hours daily for 5 consecutive days. This trial meets the requirements 
for exemption from the Investigational New Drug regulations, 21 CFR 312, specifically 
because: 
1. This drug is lawfully marketed in the United States. 
2. This investigation is not intended to be reported to the FDA as a well-controlled 
study in support of a new indication for use of the drug product. 
3. The investigation is not intended to support a significant change in advertising to 
an existing lawfully marketed prescription drug product. 
4. The investigation does not involve a route of administration or dosage level or 
use in a patient population or other factor that significantly increases the risks (or 
decreases the acceptability of the risks) associated with the use of the drug 
product, as detailed in the preliminary data section. 
5. The investigation will be conducted in compliance with the requirements for 
institutional review set forth in FDA regulations 21 CFR 56, and requirements for 
informed consent as set forth in FDA regulations 21 CFR 50.  
 
 
 

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