Response, Resistance and Metastasis of Locally Advanced Breast Cancer (LABC, Stage 2B-3C) in a Multiethnic Cohort: A Phase II International Multicentric Study of Concurrent Paclitaxel and Radiation
Phase: PHASE2
Conditions: Breast Cancer
Sponsor: NYU Langone Health

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Version February 3, 2016
RESPONSE, RESISTANCE AND METASTASIS OF LOCALLY ADVANCED 
BREAST CANCER (LABC, stage 2B-3C) IN A MULTIETHNIC COHORT
A Phase II International Multicentric Study of Concurrent Paclitaxel and
Radiation: Correlation of tumor profiles with pathological response
VERSION:  February 3, 2016
Principal Investigator:
Nelly Huppert (practice license #207260)
(212) 731-5003
FAX:  (212) 731-5512
Nelly.Huppert@nyumc.org
Co-PI:
Robert Schneider, Ph.D.
Project director (research) 
Phone:  (212) 263-6006
Email: schner01@med.nyu.edu
Co-Investigators:
Naamit Gerber, M.D.
(practice license #262775)
             Participating Radiation Oncologist, New York
Carmen Perez, M.D.
                Participating Radiation Oncologist, New York
Freya Schnabel, M.D.
(practice license #157899)
Participating Surgical Oncologist, New York
Robert Reader, M.D.
(practice license #129232)
Participating Surgical Oncologist, New York 
Deborah Axelrod, M.D.
(practice license #151859) 
Participating Surgical Oncologist, New York
Amber Guth, M.D.
(practice license #170036)
Participating Surgical Oncologist, New York
Daniel Roses, M.D.
(practice license #106908)
Participating Surgical Oncologist, New York 
Richard Shapiro, M.D.
(practice license #178862) 
Participating Surgical Oncologist, New York
Karen Hiotis, M.D.
(practice license #214480/1)
Participating Surgical Oncologist, New York
Mary Lynn Nierodzik
(practice license #162305)
Participating Medical Oncologist, New York
 Julia Smith, M.D.
(practice license # 186341)
Participating Medical Oncologist, New York
Yelena Novik, M.D.
(practice license #195414)
Participating Medical Oncologist, New York
Sylvia Adams, M.D.
(practice license #217787)
Participating Medical Oncologist, New York 
Shubhada Dhage, M.D.
(practice license #244635) 
Participating Surgical Oncologist, New York

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Joshua Silverman, M.D.
(practice license #257075 )
Participating Radiation Oncologist, New York
James Speyer, MD.
(practice license #123865 )
Participating Medical Oncologist, New York
Joan Cangiarella, M.D.
(practice license #186338)
Chief Cell cytologist
Baljit Singh, M.D.
(practice license #232939)
Program chief pathologist
Judith Goldberg, Sc.D.
Director, Biostatistics and Data Management Core
Alan Arslan, M.D.
Director, Epidemiology and Data Collection Core
Paolo Toniolo, M.D.
Epidemiology and Data Collection Core
Medical Monitor:
Franco Muggia, M.D.
(practice license #0925891)
Phone: (212) 731-5433
Email: franco.muggia@med.nyu.edu
NYU School of Medicine 
Division of Medical Oncology 
NYU Cancer Institute
Director, Medical Oncology and medical program support
Location of Study
Lead Institution:
New York University School of Medicine
NYU Cancer Institute
160 East 34th Street
New York, NY 10016 USA 
Bellevue Hospital Center
566 First Avenue TCH 
New York, NY 10016
Woodhull Hospital
760 Broadway
Brooklyn, New York 11206
Time Required to Complete
the Study:
Start: 3/2005,  Complete: 3/2010
Collaborating Sites:
Justus Apffelstaedt, M.D.
(practice license #MP030407)
Stellenbosch University
Tygerberg Hospital, Tygerberg, South Africa
Phone: (27-21) 938-9277
Fax: (27-21) 933-7999
Email: jpa@sun.ac.za
Local project director
Medical Monitor:

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Isabel Loubser, M.D. 
(practice license #MP0182036)
Stellenbosch University
Tygerberg Hospital, 
Tygerberg, South Africa
Secondary medical program 
support

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TABLE OF CONTENTS
Page
1.
STUDY OBJECTIVES..........................................................................................7
2.
BACKGROUND AND HYPOTHESIS................................................................7
2.1
LABC: A Disease of the Underserved .................................................................................... 7
2.2
LABC: a Worldwide Problem ................................................................................................. 8
2.3
Conventional Approach to LABC ........................................................................................... 8
2.4
Pathological Response as a Surrogate Endpoint for Survival ................................................. 9
2.5
Pre-operative Concurrent Chemotherapy and Radiation: Preliminary Experience ................. 9
2.6
Concurrent 5-Fluorouracil (5-FU) and Radiation: A Phase I-II Study .................................... 9
2.7
Background for Combining Taxanes and Radiation ..............................................................12
2.8
Concurrent Paclitaxel and Radiation: A Phase I-II Study ......................................................12
2. 9  Hypotheses .............................................................................................................................13
3.
PRELIMINARY DATA ......................................................................................14
3.1
Association of Molecular Markers with Pathological Response: Preliminary Data ...............14
3.2
Rationale for a Single Study of Preoperative Chemo-radiation .............................................14
3.3
Establishment of an International Network of Participating Clinical Institutions ..................15
3.4
Establishment of a Research Matrix Composed of Investigators with Complementary, 
Synergistic Research Expertise ..............................................................................................17
4.
ST
4.1
UDY DESIGN/SUBJECT ELIGIBILITY ....................................................19
Study Design: Overview ........................................................................................................19
4.2
Projected Accrual ...................................................................................................................19
4.3
Inclusion Criteria....................................................................................................................19
4.4
Exclusion Criteria...................................................................................................................20
5.
D
5.1
ATA AND TISSUE STANDARDIZATION PROCEDURES ......................20
Epidemiology and Data Collection (EDC) Core ....................................................................20
5.2
Tissue Acquisition and Handling ...........................................................................................20
5.3
Protocol upon Receipt of Tissue at NYU ...............................................................................21
5.4
Protocol for Assessment of Pathologic Response ..................................................................22
5.5
5.6
Pathologic complete response: no residual invasive carcinoma in breast or axillary lymph
nodes. .....................................................................................................................................22
Peripheral Blood Sampling and Handling ..............................................................................23
5.7
Standardization of Pathology Procedures...............................................................................23
5.8
Shipment and Storage of Tissue Samples ..............................................................................23
6.
TREATMENT......................................................................................................23
6.1
Radiation Therapy ..................................................................................................................23
6.2
Chemotherapy ........................................................................................................................26
6.3
Surgery ...................................................................................................................................27
7.
STUDY PARAMETERS .....................................................................................28
8.
CRITERIA FOR EVALUATION AND ENDPOINT DEFINITIONS ...........28
9.
PRODUCT INFORMATION .............................................................................29
10.
PATIENT RECRUITMENT AND REGISTRATION ....................................34
10.1 Recruitment and Registration in New York City ...................................................................34
10.2 Recruitment and Registration at and South Africa Sites ........................................................35
11.
PROTECTION OF HUMAN SUBJECTS ........................................................35
11.1 Benefits/Risks ........................................................................................................................35
11.2 Privacy/Confidentiality ..........................................................................................................35
11.3 Non-Health Related Risks ......................................................................................................35

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11.4 Serious Adverse Events (SAE) Reporting..............................................................................36
11.5 Medical Care for Research Related Injury .............................................................................37
12.
INFORMED CONSENT .....................................................................................37
12.1 Procedure for obtaining Informed Consent ............................................................................37
12.2 Procedure for Obtaining Research Authorization ..................................................................37
12.3 Minimization of Coercion and Undue Influence ....................................................................38
13.
DATA ANALYSIS/STATISTICAL CONSIDERATIONS..............................38
13.1 Study Objectives ....................................................................................................................38
13.2 Disposition of Data - Data Management and Monitoring ......................................................41
13.3 Microarray data ......................................................................................................................42
14.
DEVIATION FROM THE PROTOCOL ..........................................................42
15.
REFERENCES.....................................................................................................44

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SCHEMA
Eligibility:
Locally Advanced Breast Cancer: STAGE 2B-3C (AJCC, see Appendix
16.2), HER 2/neu negative.
Patients with inflammatory breast cancer or distant metastases are 
excluded.  Patients  with  prior  treatment  for  their  breast  cancer  are 
excluded.
Baseline Requirements:
Core biopsy for confirmation of diagnosis, assessment of tumor molecular 
characteristics and tumor banking. Blood samples for special studies and 
banking.
Staging evaluation, including PET/CT scans of chest, abdomen and pelvis. 
Baseline blood tests.
Baseline evaluation by Medical, Radiation and Surgical Oncologist
Treatment Schema:
Week
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
Pre-op
Chemo*
▼X
▼X
▼X
▼X
▼X
▼X
▼X
▼X
▼X
▼X
X
X
█
█
Radiation**
▼
▼X
▼X
▼X
▼X
▼X
X
█
█
Surgery***
▼
█X
█
*
pre-operative chemotherapy consists of Paclitaxel (Taxol or Abraxane) 30 mg/m2 twice/week
**
to the breast, axilla and supraclavicular area, concurrent with chemotherapy
***
within two months from the end of chemo-radiation

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1.
1.
STUDY OBJECTIVES
To test concurrent paclitaxel and radiation in a prospective multiethnic cohort of
patients  with  newly  diagnosed  stage  2B-3C  breast  cancer  treated  at  three
international academic centers under uniform conditions.
2. To assess the pathological response rate to concurrent paclitaxel-radiation at each 
collaborating institution and compare it to that achieved in a previous Phase I-II 
trial.
3. To obtain core biopsies of the original tumor before, and after treatment (from the 
surgical specimen) for molecular biology and genomic studies (projects 2-5, 7).
4. To  acquire  descriptive  information  on  patient  epidemiological,  cultural  and 
behavioral characteristics (for project 6).
2.         BACKGROUND AND HYPOTHESIS
2.1       LABC: A Disease of the Underserved
The term ―locally advanced breast cancer‖ (LABC) commonly includes tumors whose 
maximum diameter is 5 cm (T3) or larger, or which present with involvement of the chest 
wall or skin. Surprisingly, the simultaneous presence of clinically detectable distant 
metastases is relatively infrequent (~8%), a peculiar finding since in 73% of these large 
tumors it is possible to document shedding of tumor cells into the blood 1.
While LABC has become a rare clinical presentation of breast cancer in the general 
population  as  a  result  of  improved  early  detection  by  mammographic  screening,  it 
remains relatively common among minority women of low socioeconomic status 2. For 
instance, in a consecutive series of 363 African-American women presenting in a large 
urban hospital3, one out of three women newly diagnosed with breast cancer had LABC. 
It is well documented that although the incidence of breast cancer among African- 
Americans is lower than among white women, breast cancer mortality in African- 
Americans is significantly higher 4. In 1998, the American Cancer Society, the National 
Cancer Institute and the Centers for Disease Control and Prevention reported an overall 
downward trend in cancer incidence and mortality between 1990 and 1995 for all cancers 
combined.  Many minority and  medically underserved  populations,  however,  did  not 
share equally in these improvements. These patients have continued to encounter multi- 
factorial barriers to early detection and care, warranting interventions to improve access 5. 
At the same time, it is equally important to offer the best chance for survival to those 
underserved women who have already availed themselves of medical care. Paradoxically, 
while the medical community is aware of the inadequate accrual of minority patients to 
clinical trials, only few trials exist for LABC.

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2.2       LABC: a Worldwide Problem
The need to understand LABC is especially compelling in populations and countries with 
limited resources, where breast cancer incidence is relatively low, but mortality is 
comparably high 6. In these settings access to appropriate cancer care is characteristically 
limited or often plainly nonexistent. In contrast to economically developed nations, where 
on average fewer than 20% of women present with breast cancer at advanced stages 7, 
LABC and metastatic disease are the most common stages at presentation in 50% or more 
women in Latin America, Asia and Africa. Although precise data are scarce, reports from 
areas as diverse as South America (Argentina, Brazil, Peru) 8, India 9 and South Africa 10, 
compare well with the direct clinical experience reported by our research collaborators in 
these countries. In 1996, in the city of Trivandrum, in the State of Kerala, south India, 
stage III LABC accounted for over 40% of new cases of breast cancer, and stage IV for 
an additional 12.8% 9. In South Africa, medical records of various large academic 
hospitals during the 1980s and 1990s offer a picture of striking social differences at 
presentation, with stages III and IV being the stages at presentation for 77.7% of black 
patients, as compared to 30.7% among non-blacks 10.
The experience of economically developed countries, like the U.S., show that 
these incidences can be modified resulting in markedly reduced breast cancer mortality. 
In fact, while U.S. breast cancer mortality remained constant from the 1930s to the late
1980s, beginning in the early 1990s it has started decreasing by 1-2% annually, a 
phenomenon  that  continues  11.  Although  the  causes  remain  unclear,  it  is  strongly 
suspected that it is the result of an effective combination of timely early detection and 
substantial improvements in therapy. Further gains in terms of reduced mortality in the 
U.S. and worldwide could be achieved with a deeper understanding of LABC—a multi- 
dimensional  disease  that  requires  a  multi-dimensional  approach  for  its  study  and
understanding. These components include behavioral, cultural, epidemiological, genetic, 
immunological, molecular and possibly ethnic aspects, which need to be investigated 
concurrently, as they all have the potential to contribute to our understanding. Thus, 
reaching out to populations comprising a broad range of ethnic, social, economic and 
health care characteristics—a global perspective for a global disease—is the most 
effective means for investigating, understanding and eventually impacting on LABC.
2.3       Conventional Approach to LABC
The contemporary management of LABC consists of pre-operative systemic 
chemotherapy  to  facilitate  the  surgical  removal  of  the  tumor  and  to  address  early 
systemic treatment of distant micro-metastases 12-13. This approach has the advantage of 
enabling  in  vivo  assessment  of  tumor  sensitivity  or  resistance  to  the  pre-operative 
regimen by measuring the residual disease in the pathological specimen obtained at
mastectomy (i.e., pathological response). Moreover, identification of molecular markers 
from pre-treatment tumor biopsies allows investigators to explore their association with 
the extent of pathological response 12, 14.

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2.4       Pathological Response as a Surrogate Endpoint for Survival
Evidence is emerging that pathological response after primary chemotherapy can be used 
as a surrogate endpoint for survival. Despite differences in the criteria adopted to measure 
and report the pathological findings after primary non-invasive treatment, most groups 
have shown a similar correlation between residual disease found at mastectomy and 
patient outcome. For instance, Feldman et al. reported lack of residual macroscopic tumor 
after doxorubicin-based primary chemotherapy as the strongest predictor for overall 
survival (OS) and disease-free survival (DFS) 15, while Buzdar et al. noted that lack of 
nodal involvement after therapy was associated with the best prognosis 16. The Milan 
National Cancer Institute conducted a series of studies of primary doxorubicin-based 
chemotherapy. By classifying the pathological findings of 412 consecutive patients, 
Bonadonna et al. demonstrated conclusively that patients with a pathological complete 
response  had  better  survival  than  those  who  had  residual  tumor  in  the  specimen 
(p=0.034) 17. Similarly, Kuerer et al. found a similar association in 372 LABC patients 
treated at M.D. Anderson Cancer Center 18. It has thus become clear that therapeutic 
attempts to improve pathological response to primary therapy are likely to reflect on 
patient outcomes. In addition, pathological response as a surrogate for outcome provides 
a much quicker method to evaluate treatments while also offering the opportunity to 
explore its association with biological correlates 12, 14, 19-21. In this sense, LABC offers an 
ideal opportunity to expedite clinical research on how to best ―tailor treatment‖ based on 
specific tumor characteristics. Moreover, the data derived are likely to be relevant to the 
management of all invasive breast cancers.
2.5       Pre-operative   Concurrent   Chemotherapy   and   Radiation:   Preliminary
Experience
Over  the  past  decade  we  have  investigated  the  combination  of  up-front  concurrent 
chemo-radiation as a pre-operative treatment, the extent of pathological response of the 
primary tumor then being used as a principal endpoint to measure tumor resistance to the 
tested chemo-radiation regimen. Radiation had traditionally played a role in the 
management of LABC since local control is also an important endpoint in this disease. 
However, it is usually added after surgery 13, 15-18. We have selected concurrent chemo- 
radiation based on the promising results witnessed in other tumors (cervix, nasopharynx, 
stomach, lung, etc.) where both local control and distant metastases are significant causes 
of  treatment  failure.  Moreover,  original  primary chemotherapy trials  reported 
pathological response rates of less than 10% 13, 17, providing the impetus to investigate the 
combination of chemotherapy with radiation to increase the proportion of patients who 
might derive a potential survival benefit associated with a pathological response. We 
have conducted two sequential studies in LABC: the first one combined continuous
infusion 5-FU and radiotherapy while the second combined semiweekly paclitaxel with 
radiotherapy 14, 19-20, 22.
2.6       Concurrent 5-Fluorouracil (5-FU) and Radiation: A Phase I-II Study
Inspired by the translational research of Leichman and co-workers in gastrointestinal 
cancers 21   and  by  the  known  radio-sensitization  properties  of  5-FU 23,  the  first  trial

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combined radiotherapy with concurrent continuous infusion (c.i.) 5-FU to optimize drug 
exposure during the course of radiation. The study included tumor biopsies to study 
molecular  determinants  of  response  (NIH  Grant  #1ROI  CA  60859-01A1,  1994-97.
―Response Determinants in Advanced Breast Cancer.", P.I, Drs. Peter Dannenberg and 
Silvia Formenti). Figure 3 displays the original study design of this trial 14. The eligibility 
criteria for this study pre-selected patients with particularly advanced LABC insofar as all 
patients were deemed ―inoperable,‖ i.e., in order to resect the primary tumor the wound 
could be closed only with the interposition of a skin graft or a myo-cutaneous flap. For 
each  
patient,  
pre-treatment  breast  cancer biopsies  
were  
analyzed  
by 
immunohistochemistry for ER/PR hormonal receptors, HER-2/neu, and p53 over- 
expression.  p53  protein  over-expression  at  immunohistochemistry  was  used  as  a 
surrogate for p53 gene mutation 24. Moreover, initial tumor core biopsies were analyzed 
by reverse transcriptase quantitative PCR (RT-PCR) to measure expression of genes
expected to be associated with response to 5-FU and radiation, e.g., the main target 
enzyme of 5-FU, thymidylate synthase. Pre-operative c.i. 5-FU, 200 mg/m2/day was 
delivered for 8 weeks with radiotherapy, weeks 3-8, to 50 Gray in 2-Gray fractions. The 
first lesson derived from this study was a definition of pathological response to chemo- 
radiation.  At  mastectomy,  pathological  findings  were  classified  on  the  basis  of 
persistence of invasive cancer. Pathological complete response (pCR) defined the finding 
of no residual invasive cells in the breast and axillary contents; pathological partial 
response described the presence of <10 microscopic foci of invasive cells in either the 
breast or nodal specimens. All other cases were classified as no pathological response 
(pNR). This trial achieved a high response rate in large, inoperable LABC with an 
objective clinical response rate of 71% and a pathological response rate (pCR+pPR) of
34%. The pathological response rate of 5FU-RT compares favorably with that of any 
reported contemporary chemotherapy neo-adjuvant trial in this patient population, as 
displayed in Table 1 below 18, 25-30.

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Table 1: Pathological Response and Outcome In Phase I-II Studies of LABC
AUTHOR
# PTS
TREATMENT
% PATH 
RESPONSE
5Y DFS
5Y OS
Powles 25
1995
Schwartz 26
1994
Merajver 31
1997
Formenti 14, 27
1997
105
Chemo-Endocrine
Therapy/Surgery/RT*
158
Doxorubicin-Based
CT**/Surgery/RT
89
Prolonged Chemo- 
Hormonal Therapy/ 
Surgery Or RT
35
Concurrent FU/RT/ 
Surgery/ Post-Op AC
10%
NA
NA
10%
61%
69% 
NA
44%
54%
35%
58%
74% 
pCR 90% 
Others 65%
Karlsson 28
1998
128
FEC/Surgery/FEC/RT
NA
36% 
(actuarial)
49% 
(actuarial)
Morrell 29
1998
49
Doxorubicin-Based CT, 
Surgery/Rt
16%
51%
63%
Ayash 30
1998
Kuerer 18
1999
37
High Dose CT With 
Stem Cell Support/ 
Surgery /Radiation
372
Doxorubicin-Based CT, 
Surgery/Rt
14%
64% At 30
Months
12%
p CR 87% 
Others58%
NA
pCR 89% 
Others 64%
Zambetti 32
1999
Formenti 20
2001
88
Doxorubicin-Based CT 
Surgery / CMFX6/RT
44
Concurrent paclitaxel- 
RT / Surgery / 
Doxorubicin-Based CT
2%
52%
62%
35%
NA
NA
* RT= radiation therapy **CT= chemotherapy.
Eighty-four percent of the patients (32/38) in the trial were minority women. Importantly, 
the 5-FU/RT regimen was very well tolerated with no grade III or IV acute toxicities or 
increased toxicities during post-operative doxorubicin and cyclophosphamide (AC). With 
a median follow-up of 5 years, overall survival of the entire group of 38 patients is 74% 
and disease-free survival is 58% (Table 1), which compares favorably with neo-adjuvant 
chemotherapy.
We then asked whether a pathological response to chemo-RT could also be a 
surrogate endpoint for survival in LABC. The patients who achieved a pathological 
response (pCR+pPR) to 5-FU/RT have both a better DFS and OS than non-responders 
(p=0.023, and p=0.08, respectively), with only one failure among the women who 
achieved  pathological  response 20,   27.  In  addition,  no  isolated  chest  wall  or  nodal
recurrences have occurred to date.
In addition to achieving promising clinical results, this study proved the feasibility 
of using biological correlates from pre-treatment tumor biopsies to explore associations 
with pathological response: patients whose tumors had no evidence of p53 over- 
expression on immunohistochemistry were significantly more likely to achieve a 
pathological response to the regimen, compared to patients whose tumors over-expressed 
p53 (p=0.010, Fisher exact text). On multivariate analysis, lack of p53 over-expression

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was the only independent predictive factor for pathological response, generating indirect 
evidence that wild type p53 tumors were more likely to respond to the 5FU/RT regimen. 
Since the majority of patients who over-expressed p53 failed to achieve a pathological 
response, it made sense to investigate the use of agents like taxanes, which are differently 
affected by p53 status 14.
2.7       Background for Combining Taxanes and Radiation
In vitro and pre-clinical models support the combination of taxanes with radiation. For 
instance, Wahl et al. have shown that loss of normal p53 function actually confers 
sensitivity to paclitaxel in some cell types because of an increased G2/M arrest leading to 
p53 independent cell death 33. This observation may underlie the preferential activity of 
paclitaxel against cancer cells compared to normal cells as well as its activity against 
tumors that are p53 mutated 34. Moreover, accumulation of cells at the G2/M checkpoint 
explains some of the in vivo radio-sensitizing effects of the drug 35. Interestingly, our 
group was able to document the kinetics of paclitaxel-induced apoptosis and mitotic 
arrest in human tumor tissue 36. These findings support the use of a semiweekly regimen 
as the optimal radio-sensitizing schedule in the clinic 19-20.
Another reason for studying taxanes in a chemo-RT approach to LABC is the fact 
that several potential markers of sensitivity to taxanes have been identified. Since the 
microtubule is also a target of paclitaxel, biochemical mediators that could affect 
microtubule stability are expected to affect paclitaxel activity. For instance, the 
components of mammalian microtubules are   and   -tubulin: the latter is the main target 
of paclitaxel action 37 and elevated class III and class IV   -tubulin iso-forms were found 
in paclitaxel-resistant ovarian tumor cells 38. Metablastin (also termed p19 and stathmin)
is  also  a  regulator  of  MT  dynamics 39   and  thus  could  influence  paclitaxel  activity. 
Similarly, MAP4 protein over-expression, which is known to stabilize microtubules and
thus would be expected to antagonize paclitaxel, was found to predict for paclitaxel- 
resistance in vitro 40. Interestingly, MAP4 is one of the few genes known to be down- 
regulated by wild type p53, possibly explaining the observed inverse relationship of p53 
status and paclitaxel activity. Other potential determinants for response to paclitaxel are 
genes associated with the apoptotic or cell-cycle regulation pathways. Paclitaxel has been 
demonstrated to cause the phosphorylation of bcl-2, which is believed to abrogate the 
anti-apoptotic function of bcl-2 by dissociating it from the pro-apoptotic molecule bax 41.
Finally,  HER-2/neu  over-expression  was  shown  both  to  alter     -tubulin  iso-form 
expression  and  to  confer  resistance  to  paclitaxel 42.  Finally,  Pietras  et  al.  reported 
resistance to radiation when HER-2/neu over-expression was induced in vitro and in 
vivo, in a breast xenografts tumor model. They demonstrated that a monoclonal antibody
directed against the HER-2/neu receptor affects repair of radiation-induced DNA damage 
and  enhances  radio-sensitivity  of  human  breast  cancer  cells  over-expressing  HER-
2/neu 43.
2.8       Concurrent Paclitaxel and Radiation: A Phase I-II Study
Based on the background described above, the second concurrent chemo-RT study 
combined  a  taxane  with  RT.  For  each  patient  studied,  pre-treatment  breast  cancer 
biopsies were prospectively analyzed by immunohistochemistry for p53 over-expression.

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Estrogen receptor (ER), HER-2/neu, metablastin,   -tubulin III and IV, MAP 4, blc-2, bax 
gene expression were measured using RT-PCR. The regimen consisted of pre-operative 
concurrent paclitaxel (30 mg/m2 semiweekly) for a total of 8 weeks, while radiation was 
delivered to the breast and regional nodes during weeks 2-7 to a dose of 45 Gy at 1.8 Gy 
per fraction. Eighty-nine per cent of the patients were minority women. Pathological
response (pCR + pPR) occurred in 33%. Concurrent chemo-radiation was well tolerated 
(with acceptable toxicities) and did not worsen the toxicity profile of post-operative AC 
or AT. When associations between pathological response and molecular markers were 
explored, tumors with low HER-2/neu gene expression by RT-PCR and negative estrogen 
receptors were more likely to respond to the tested regimen (p=0.009 and p=0.006, 
respectively). The findings suggest that tumors without HER-2/neu over-expression 
are more likely to respond to paclitaxel/RT. Conversely, p53 protein expression 
measured by IHC did not appear to be associated with pathological response (p=0.67) 14.
Our two consecutive chemo-RT phase I-II studies proved the feasibility of 
concurrent chemotherapy and radiation as primary treatment for LABC. With the 
limitations associated with a Phase I-II study, 5-year DFS and OS data from the FU/RT 
study are better than those reported by other investigators that have employed sequential 
treatment with post-operative radiation in this disease. In both trials one out of three 
patients  achieved  a  pathological  response  (pCR  or  pPR,  as  per  our  definition), 
significantly higher than the 5-15% pathological response rates reported in contemporary 
studies of preoperative systemic chemotherapy alone.
2.9       Hypotheses
LABC remains a challenging presentation of breast cancer that is particularly common 
among underserved, minority women in the United States and is the most common 
presentation of breast cancer in developing countries. We have hypothesized that:
1. An international, multi-disciplinary approach is essential for the study and 
development of more successful intervention in LABC, a global, multi- 
dimensional disease.
2.   Many  components  are  likely  to  contribute  to  LABC,  including  behavioral, 
cultural, epidemiological, genetic, molecular, immunological and possibly ethnic 
factors.
3.   To understand LABC, which varies in incidence and progression in a worldwide 
manner, these components need to be studied concurrently, under standardized 
conditions applied to the same multi-ethnic cohort of patients, treated consistently 
by the same treatment regimen.
4.   Pathological   response   to   the   same   treatment   regimen   will   provide   an 
understanding of the molecular and genetic profiles of the tumors and surrounding 
tissues that contribute to tumor response to treatment or progression. There is also 
a need to investigate the epidemiological, cultural and behavioral characteristics 
of LABC to develop more effective treatment strategies.

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3.         PRELIMINARY DATA
3.1       Association of Molecular Markers with Pathological Response: Preliminary
Data
The two preliminary studies which combined taxanes and radiation (sections 2.7-2.8) also 
demonstrated that different molecular markers are associated with pathological response, 
supporting the hypothesis that different drugs combined with concurrent radiation are 
effective on different tumor types. In the 5FU/RT study, lack of p53 over-expression (i.e. 
wild  type  p53  tumors)  was  significantly  associated  with  the  achievement  of  a 
pathological response, while in the paclitaxel/RT study p53 status had no relevance, but 
tumors without HER-2/neu over-expression were more likely to respond to paclitaxel/RT. 
Based on these findings, selecting a particular chemo-RT regimen based on the molecular 
characteristics of the tumor should improve pathological response rates, thus potentially 
improving survival.
While intriguing, the data reported require validation in a much larger sample of 
patients, ideally in a multi-institutional fashion that represents the multiethnic 
characteristics of LABC. Moreover, the availability of a modern, comprehensive basic 
research matrix of collaborating researchers enables the multi-dimensional research 
strategy necessary to the understanding of the complexity associated with LABC.
3.2       Rationale for a Single Study of Preoperative Chemo-radiation
The publication in JCO of our Phase I-II trial of concurrent paclitaxel and radiation 44 has 
generated interest from a number of groups of investigators, including those from 
developing countries interested in adopting this regimen. Similarly, the two foreign 
academic institutions participating in the COE were among those that had originally 
contacted us to develop a common preoperative trial for LABC.
The current choice for a common pre-operative regime is the result of a careful 
assessment of the available resources for clinical care at each of the institutions outside 
the U.S. State of the art radiology, pathology and radiation oncology equipment are 
available. In addition, a qualified medical oncology clinic is in place at each site. To cope 
with the reality of the existing health system of the two institutions outside the U.S., the 
current protocol was developed from the preliminary work published in the Phase I-II 
study of pre-operative paclitaxel and radiation 44. This protocol proved to be the most 
realistic and feasible common approach to LABC. The advantages of adopting this 
preoperative regimen of concurrent chemo-radiation consist of: 1) availability of safety 
and toxicity data, demonstrating only grade 3 toxicity consisting of skin desquamation; 2) 
the pathological response rate achieved (34%), which was at least comparable to that of 
much more prolonged, costly, multi-agent pre-operative chemotherapy regimens; 3) 
independent evidence that the use of neo-adjuvant single agent paclitaxel can achieve
results comparable to those of a more conventional preoperative regimen for LABC, 
consisting of 5-fluorouracil, doxorubicin and cyclophosphamide 45; and 4) because of its 
generic formulation, paclitaxel has resulted as the most convenient available drug for the 
study. As a result, the current study will be the common clinical platform to treat patients 
at each center. As described below, the same standardization procedures implemented at 
each center to assure homogeneity of methods within the network of participating cancer 
centers. All patients will be concurrently studied by the research matrix described above.

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3.3       Establishment of an International Network of Three Participating Clinical
Institutions
A network of clinical academic centers has been established to provide the unified 
methodology, treatment protocols, specimens and data acquisition that are necessary to 
effectively  study  LABC.  In  addition,  a  multidisciplinary  research  approach  was 
developed to describe and understand behavioral, cultural, genetic, immunological and 
molecular components. Our central hypothesis is that by studying LABC from a 
global perspective and in a multi-dimensional manner, those features that are 
common across cultures and those that differ across cultures can be identified.
LABC  is  possibly  the  most  common  stage  at  presentation  of  breast  cancer
worldwide. In many economically disadvantaged countries where LABC is extremely 
common, an unknown, but likely non-trivial number of breast cancer patients never reach 
a formal ―clinical  diagnosis‖  since they die before ever receiving medical treatment of 
any kind. Thus, the burden of breast cancer incidence and mortality is likely to be 
substantially underestimated. In addition, access to screening, early detection and timely 
medical  care  are  not  options  available  to  the  vast  majority  of  women  worldwide, 
including a sizable subset of minority, often underserved  women  in the U.S. These 
women are much more likely than those living in affluent communities to present to 
medical attention with large, palpable breast tumors, often LABC. We are convinced that 
improvements in our understanding of how to manage, treat and minimize the 
complications of LABC represents an untapped opportunity for investigations aimed at 
reducing  the  burden  of  mortality for  breast  cancer.  To  this  aim,  a  clinical  research 
network of academic institutions in 3 distinct international sites capable of delivering the 
same standardized pre-operative therapy and surgery have been established (Table 2). 
These centers are characterized by broadly different cultural, social and economic 
contexts, diverging incidence of breast cancer and different burden of  LABC (areas 
where breast cancer incidence is high have the smallest frequency of advanced stages at 
presentations and vice versa) (Table 2). This unique global network enables the 
establishment of a common clinical trial in well-characterized distinct populations of 
LABC patients, while conducting prospective tissue acquisition, molecular and genomic 
profiling. Key to the success of this initiative has been the enthusiastic endorsement 
provided by each site, with the proposed commitment to contribute 25 patients over a 
four year accrual period. Each patient’s characteristics are entered into the COE Oracle 
Clinical database linked through a website available to the P.I., regularly updated during 
the five years of follow-up, to enable the exploration of the relationships between 
biological profiles and outcomes.

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Geographic
Location
Main Ethnic 
Groups 
Served
Table 2
Breast Cancer
Incidence per
100,000
Participating Academic
Institution
Local Principal
Investigator
 
(ASR-World) 
South Africa
Black 
Asian 
White
11-70a
Tygerberg Hospital 
(Stellenbosch 
University)
Dr. Justus
Apffelstaedt
New York
Hispanic
Asian
d
NYU Hospitals
Dr. Silvia
State (U.S.A).
Black
White
66-90
(New York University)
Formenti
aOnly age-standardized rates available, 1993-95 (CANSA). Range: 11.3, blacks; 14.7, Malay (―coloured‖);
42.1, Asians; 70.2, whites. bPersonal No available cancer registry data for Mexico. Participation not 
confirmed. dNew York State Cancer Registry, 1993-9746. Range: 66.3, blacks; 90.6, whites.
An important issue related to the feasibility of the current trial is the communication and 
diffusion of standard procedures that will enable the clinical and basic scientists to merge 
the data to perform the proposed clinical and laboratory analyses. The leadership of the 
COE has identified this issue as central and has developed the necessary tools to assure 
international standardization of information, data acquisition, tissue acquisition and 
handling, tissue shipment procedures and treatment data review (Appendix). The process 
included each of the P.I.s from the participating clinical cancer centers. Since August
2003, each Principal Investigator from the other sites have visited United States and met 
with Drs. Formenti and Schneider to discuss the current methods and process at their 
respective institutions and worked together to achieve standardized common guidelines 
that can be realistically implemented internationally.
Specifically:
1.   Standard diagnostic criteria have been developed.
2.   Standard eligibility criteria have been developed.
3.   Informed Consent documents have been provided in English (South Africa and
U.S.) and Spanish (U.S.) (Appendix, Section 16.5).
4.   A standard clinical trial protocol was been agreed upon by all of the centers.
5.   Specific Pathology Guidelines were developed in collaboration with each of the 
clinical  centers.  In  addition,  an  informative  Slide  Show  was  developed  for 
training the clinical teams in tissue acquisition, handling and shipment (Appendix, 
Sections 16.3 and 16.4). Centralized review of diagnostic tissue has been 
established and will be conducted at NYU by Drs. Singh and Cangiarella.
6.   Centralized review of radiation simulation films has been established and will be 
conducted at NYU. The South Africa have digital films available and will send 
the images via the Internet.

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7.   Site visits to the international sites have taken place to assure that standardized 
procedures and methods are fully in place before starting the protocol.
8.  Data Collection Forms (Appendix, Section 16.1) were developed and will be 
available in Spanish (for the U.S) and Afrikaans (for South Africa). The 
instruments were closely reviewed by the P.I.s from each site to ensure that the 
instruments are clear, culturally appropriate and adherent to standardized 
guidelines of data collection.
3.4       Establishment  of  a  Research  Matrix  Composed  of  Investigators   with
Complementary, Synergistic Research Expertise
This clinical protocol is the basis for a standardized, unified approach to a clinical 
presentation of breast cancer, LABC, common among the three participating international 
institutions. From each of the three centers the clinical P.I.s will work together as a 
network of clinical investigators committed to treat consistently, as described in the 
protocol, three parallel, synchronous cohorts of LABC patients.
The NYU Clinical Investigators’ team will lead the effort. The team has extensive 
experience in LABC and funded clinical, translational and epidemiological programs that 
are ongoing at our institution. NYU School of Medicine serves Tisch Hospital, Bellevue 
Hospital, NYU Downtown Hospitals. The latter have historically been the flagship of 
Manhattan’s public hospitals. Bellevue Hospital has a multi-centennial tradition of 
providing medical care to immigrant populations and it is a true microcosm of multi- 
ethnicity in health care. Building on their successful tradition for conducting clinical 
trials  among  underserved,  minority  populations,  the  team  has  converged  a  second 
network, composed of basic and behavioral research scientists interested in collaborating 
to deepen the understanding of LABC. Premier investigators from NYU, Cold Spring 
Harbor  Laboratory  (CSH),  Princeton  University  and  the  University  of  Arkansas  in
collaboration with a team of very active patient-survivor advocates have generated a
Matrix Program based at NYU that has brought together the expertise of multiple 
investigators  and  institutions  to  work  collectively  on  a  single  problem,  the 
description of the presentation of locally advanced breast cancer, the response of 
locally advanced breast cancer to treatment, and disease progression.
The following 6 research studies have been developed. They will be enabled by 
this Clinical Research Protocol (Project 1) which is the platform to enable all scientific 
research projects.
Project 2, Functional genomics of pre-treatment LABC tumors. This research is directed 
to identifying gene expression signatures associated with treatment response, resistance, 
and progression to local recurrence and/or metastatic disease. These studies will be led by 
Dr. Schneider-NYU School of Medicine. This research also involves extensive 
collaboration with the Dr. Goldberg (NYU) for study design and statistical analysis. 
While there are many research efforts underway to identify gene expression signatures 
associated with response and failure of different tumors, including breast cancers, this 
approach is novel in its examination of heterogeneous global cohorts and the focus of the 
data analysis on comparison of results within and among cohorts. This approach, in 
conjunction with molecular biology studies of LABC and genomic mutational studies

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(described below), are expected to expedite identification of gene expression responses 
that will ultimately lead to tailored treatment strategies and new targets for intervention.
Project 3, Molecular and tumor cell biology. This research effort will identify molecular 
and biochemical signatures in LABC tumor cell responses that are linked to tumor 
sensitivity or resistance (progression) to treatment, including hypoxia, angiogenesis, 
apoptosis and protein synthesis. These studies will be directed by Dr. Schneider (NYU). 
These studies are novel in their ability to provide a biological context for interpreting and 
understanding the signatures generated by the functional genomics program at the 
molecular level of gene expression, without which gene expression profiling remains 
largely descriptive.
Project 4, Genomic mutational analysis. This research project will be directed by Drs. 
Wigler and Lucito (co-leaders, CSH). Using a state-of-the-art gene chip analytical 
approach developed by these two investigators, this research focuses on identification of 
tumor suppressor and tumor promoting mutations associated with LABC incidence and 
metastatic progression of disease. This is a powerful and unique research project which 
has never been applied to LABC and promises to develop a new genetic understanding of 
this disease which can be used to identify new targets for future therapeutic intervention 
and characterization of this heterogeneous patient population for tailored treatment 
approaches.
Project 5, Association of endogenous reproductive hormones in LABC progression. This 
project, directed by Dr. Toniolo (NYU), will continue efforts to elucidate the role of 
endogenous  reproductive  hormones  in  breast  cancer  by  investigating  the  role  of 
estrogenic and genotoxic estrogen metabolites in breast cancer prognosis.
Project 6, Common and distinct cultural and social barriers to treatment. This project 
will be directed by Dr. Bright (NYU) and Dr. Erwin (University of Arkansas) and will 
aim to develop multicultural and multilingual psychological scales related to traditional 
barriers to screening. This work is unique and important as it seeks to produce narratives 
that describe the experiences of each group in the multi-cultural, multi-national sample. 
Also, the study will develop qualitative approaches and data that have the potential to 
greatly improve models for cross-cultural behavior, and to aid in the development of 
culturally appropriate educational and behavioral interventions.
Project 7, Role of single nucleotide polymorphisms (SNPs) in the p53 signaling pathway 
in LABC. This project is directed by Dr. A. Levine (Princeton University and the Rutgers 
University Cancer Research Program). SNPs have been identified in the p53 signal 
transduction pathway, one of which (SNP 309) is localized in the promoter of the MDM-
2 gene and reduces the p53 response to DNA damage. At the clinical level, individuals 
with  this  SNP  (12%  of  people  tested)  are  diagnosed  with  cancers  (including  breast 
cancers in Li-Fraumeni patients) at much earlier ages than those with the wild type 
sequence. Using LABC tumor core biopsy DNA extracted by Dr. Schneider’s group in 
project 2, the SNP 309 profile will be determined in precisely the same cohorts under 
analysis  for  the  other  projects.  These  data  will  examine  whether  age  of  onset  and

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progression of LABC are associated with this important SNP in a manner related to 
ethnicity and global pattern.
4.         STUDY DESIGN/SUBJECT ELIGIBILITY
4.1       Study Design: Overview
The primary objective of this study is to confirm the pathological response rate of 34% 
(pCR+pPR), reported for patients in the U.S. Phase I-II trial 44. This is a phase II trial 
because it is designed to extend and confirm the smaller U.S. Phase I/II trial reported 
previously. With 100 cohorts at NYU/Bellevue and 25 patients accrued at each of the two 
other funded sites (S. Africa), patients in each cohort, pathological response rates will be 
estimated  in  each  cohort  individually and  for  the  combined  cohort  of  150  patients.
Progression free survival and overall survival will also be estimated for each cohort 
individually and across cohorts. Patients will be randomly selected within cohorts to 
participate in the studies of genomics, genetics, biomarkers, and hormonal markers. The 
approach of the Center will be to use a common stratified random sample for each of the 
research projects that will not be conducted on all of the 150 enrolled patients. This 
approach, which ensures that a random sample of  75 patients are included in all of the 
research studies, will facilitate the identification of characteristics that can be used to 
predict pathological response, progression, and survival from the multi-ethnic cohorts 
under study and to identify hypotheses for the generation of further studies. Further 
details of the design and analysis strategy are included in Statistical Considerations, 
Section 13.
4.2       Projected Accrual
150 patients over 4.5 years at the three centers (100/NYU-Bellevue; 25/site x 2).
4.2.1
Recruitment at the NYU/Bellevue site will involve 20 patients in year 1 
during the phase-in period; 30 patients in years 2 and 3; and 20 patients in 
year 4, while accrual at the other sites will be 5 patients in year 1; 7 to 8 
patients in years 2 and 3; and the remainder in year 4.
4.2.2
Recruitment will continue into the mid-fourth study year to permit each 
enrolled patient to complete at least 12 months of follow-up from time of 
diagnosis to the evaluation of pathologic response, the primary endpoint of 
this study.
4.3       Inclusion Criteria
4.3.1
Biopsy proven locally advanced breast cancer: IIB, IIIA and IIIB.
4.3.2
Metastatic breast cancer: limited to the subset of patients with intact 
breast, locally advanced tumor and involved ipsilateral supraclavicular 
nodes.
4.3.3
Measurable disease required.
4.3.4
Adequate laboratory values: 
Hgb > 10
ANC >1500

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Platelets >150,000
Creatinine < 1.5
Liver function < 3 X normal.
4.3.5    Patient > 18 years of age.
4.3.6    Medically and psychologically able to comply with all study requirements.
4.3.7    ECOG performance score 0-1.
4.3.8    CT chest, abdomen, and pelvis performed.
4.3.9    Mammogram or USG performed.
4.3.10  Signed informed consent.
4.4
Exclusion Criteria
4.4.1    Breast cancer patients with Stage 0, Stage I, Stage IIA.
4.4.2    Previous XRT or chemotherapy.
4.4.3
Presence of distant metastases documented clinically or radiographically 
with the exception of ipsilateral supraclavicular nodes.
4.4.4    Pregnancy.
4.4.5    Inflammatory breast cancer.
4.4.6
Patients under treatment (or who will have recently been treated) with 
anti-neoplastic, immunosuppressive or hormonal medications
4.4.7    Patients who are found to have a cancer positive for the marker HER-
2/neu (Note: this exclusion criterion applies only to patients at the NYU 
Tisch and Bellevue sites where there is currently a protocol open and 
available for patients who are HER-2/neu positive. This exclusion 
criterion does not apply to patients at the South Africa site).
5.
DATA AND TISSUE STANDARDIZATION PROCEDURES
5.1
Epidemiology and Data Collection (EDC) Core
The EDC core, based at NYU, will coordinate the procurement of samples and
data collection forms at each of the centers and will provide on-site quality 
assurance. In addition, the EDC will distribute the samples to the various labs 
according to the pre-specified sampling plan. As part of its distribution plan, the 
EDC core will provide each site with bar-coded adhesive tags bearing a site- 
specific number series for all tissue specimens, slides, bloods, and data forms, etc. 
Two training slide shows were developed to enable uniform procedures among 
the centers (Appendix, Sections 16.3 and 16.4).
5.2
Tissue Acquisition and Handling
Protocol for tissue sampling (Slide Shows in Appendix, Sections 16.3 and 16.4)
5.2.1
Patient with locally advanced breast cancer will be consented for tissue 
acquisition to collect core biopsies before beginning therapy and samples 
from the surgical specimen.
5.2.2
Sampling kits, provided by NYU will be available for each patient. A 
sampling kit will contain core biopsy needles, glass slides and vials 
containing RNAlater. Bar coded labels for de-identification purposes will 
also be included.

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5.2.3
Patient will undergo a core biopsy of the breast using 18 gauge spring 
loaded core biopsy gun (Tenmo). Four core biopsies will be taken from 
the mass.
5.2.4
A  pathologist  will  be  present  at  the  time  of  core  biopsy  to  perform 
concomitant touch preparations to determine the adequate presence of 
malignant cells: viable cores will be considered those with at least 50% 
neoplastic cells.
5.2.5
Touch preparations will be performed by imprints of the core biopsy onto 
glass slides. Each core biopsy specimen will be imprinted on a separate 
corresponding glass slide. Glass slides will be stained by a modified 
Giemsa stain (Diff-quik) stain and assessed for the presence of malignant 
cells.
5.2.6
Once the cores are determined to be adequate, two cores will be fixed in
formalin for paraffin embedding to generate tumor blocks. One 
representative tumor block will be retained by the participating institution 
for records and routine histologic analysis with hematoxylin and eosin 
stains. The remaining tumor blocks will be sent to NYU for research 
studies. The remaining two cores will be placed in vials of RNA later.
5.2.7
All samples will be de-identified and bar coded labels will be affixed to all 
the vials and all the specimens  before shipment to NYU at described 
below under Shipment (also see Appendix Shipment Slide show).
5.2.8
In collaboration with the EDC each regional study manager will catalogue, 
code and ship core biopsies, bloods samples and surgical samples (made 
anonymous) to NYU on a bimonthly basis.
5.2.9
In addition, Amrita Institute of Medical Sciences (AIMS) in Cochin India 
has entered into a data-sharing agreement with NYUSOM to make 
available   the   following   de-identified   LABC   data   for   analysis   at 
NYUSOM.  Please  note  that  AIMS  is  not  taking  part  in  the  DOD 
sponsored treatment trial—rather, it is participating in the sharing of de- 
identified archived LABC specimens and data that will enrich the diversity 
and scientific robustness of the overall international study.
a.   fresh tumor samples collected at biopsy from LABC trial patients and 
again at surgery at AIMS, and preserved in RNAlater for subsequent 
extraction and purification of genetic material at NYUSOM;
b.   a small portion of each fresh tumor sample preserved in paraffin for 
local banking in the Pathology Department at AIMS Cancer Institute;
c.   a slice of paraffin block stored on slides and shipped to NYUSOM;
d.  de-identified clinical forms that contain key baseline, demographic, 
clinical and pathological response information for these patients.
5.3
Protocol upon Receipt of Tissue at NYU
5.3.1
Upon receipt, one core will be paraffin embedded for routine histologic
analysis with hematoxylin and eosin stains. Pathologic diagnoses will 
include nuclear grade, architectural grade, mitotic count, presence and 
extent of intraductal component, lymphatic and vascular invasion.
5.3.2
Immunohistochemical  staining  for  estrogen  and  progesterone  receptor, 
Her-2- neu, p27 and p53 will be performed.

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5.3.3.   One of the 2 cores in RNAlater will be banked and frozen in a –80 degree 
locked freezer owned by the COE and backed-up with a liquid carbon 
dioxide sentinel system. Of the two core biopsies obtained for research 
purposes, one will be banked as whole tissue and the other micro-dissected 
and used for Trizol extraction and separation of DNA, protein and RNA. 
Extraction is described under project 2 in the COE grant proposal and will 
be carried out by Dr. Schneider’s group, distributed to the other research 
groups and banked.
5.3.4
The second core biopsy preserved in RNAlater will be utilized for gene 
expression profiling.
5.3.5
Paraffin  embedded  LABC  blocks  collected  by  the  EDC  core  will 
ultimately be used to produce tissue microarrays at NYU. Initial 
hematoxylin and eosin stained slides will be examined and marked to 
determine the best area for punch biopsy of the core. A 4 mm punch 
biopsy will be performed on each paraffin block and multiples cores from 
different patients will be re-embedded in paraffin to produce a tissue 
microarray.
5.3.6
Dr.  Hiran,  Assistant  Professor  of  Pathology  at  AIMS,  will  travel  to 
NYUSOM with a collection of archived paraffin LABC specimens, and 
under the supervision of Drs. Robert Schneider (Microbiology) and Baljit 
Singh (Pathology) develop expertise in and a common practice approach 
to the analysis of the specimens consisting of: (1.) micro-dissection of 
tumor specimens, (2.) use of non-conventional immunohistochemical 
techniques and antibodies vital to the LABC study; (3.) specific 
biochemical purification techniques for preparation and purification of 
RNA and DNA from specimens; and (4.) production of tissue microarrays.
5.4
Protocol for Assessment of Pathologic Response
5.4.1
The primary study outcome will be pathological response to therapy.
Pathologic samples (mastectomies or segmental mastectomy) will be 
serially sectioned and evaluated macroscopically. Approximately 30 
sections of the post-treatment tumor bed should be taken for histologic 
analysis.
5.4.2
Important pathologic information from local pathologists will include:
1. measurement of the greatest diameter of invasive carcinoma
2. size of the residual tumor bed in three dimensions
3. assessed proportion (%) of tumor bed that contains invasive carcinoma
4. location of the tumor bed in the breast specimen (quadrant, o’clock
position)
5. number of axillary lymph nodes and presence of tumor within the nodes
5.4.3
Banking of tumor and normal tissue from the mastectomy or segmental 
mastectomy specimens will be performed. In each patient both paraffin 
embedded and RNAlater preserved samples will be obtained, similar to 
that described in 5.3.3 and 5.3.4.
5.5
Pathologic complete response: no residual invasive carcinoma in breast or 
axillary lymph nodes.
5.5.2
Pathologic partial response: presence of less than 10 microscopic (X40

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magnification) foci of invasive tumor cells in either the breast or axillary 
lymph nodes.
5.5.3    All other cases will be classified as no pathological response.
5.6
Peripheral Blood Sampling and Handling
5.6.1  For each patient 30 cc of peripheral blood (from which we will extract 5
cc of serum and plasma) will be obtained, in three occasions;
1. when the core biopsies are performed at baseline before the start of 
treatment; 2. at the end of second week of radiation therapy and 3. at the 
time of surgery, after chemo-radiation.
5.6.2  Peripheral  Mononuclear  Blood  Cells  (PBMC)  and  polymorphonuclear 
cells will be isolated after gradient separation, cryo-preserved in DMSO 
and stored at -80°C at each of the centers.
5.7
Standardization of Pathology Procedures
5.7.1    All   head   pathologists   at   each   site   will   visit   NYU   early   in   the
developmental phase to review cases and discuss/agree on procedures;
these pathologists will form the standardization committee.
5.7.2
100% of diagnoses and path reports in year 1 will be reviewed by all head 
clinicians and pathologists at each site (the committee): disagreements are 
discussed in periodic teleconferences and resolved by consensus.
5.7.3
In subsequent years, a random sample of all diagnoses and pathologies 
will be reviewed by all committee members and disagreements discussed 
in monthly teleconferences for consensus resolution.
5.7.4. All controversial cases will be reviewed at NYU and unresolved 
divergences, if any, are discussed at the full committee level, in 
teleconferences.
5.8
Shipment and Storage of Tissue Samples
Details on international shipment procedures are included in Appendix 16.4.
At NYU, all samples will be stored in a –80 degree locked freezer owned by the 
COE and backed-up with a liquid carbon dioxide sentinel system. Of the two core 
biopsies obtained for research purposes, one will be banked as whole tissue and 
the other micro-dissected and used for Trizol extraction and separation of DNA, 
protein and RNA. Extraction methods are described under project 2 and will be 
carried out by Dr. Schneider’s group, distributed to the other groups and banked. 
Samples collected for this study will be stored at NYU for 10 years or until the 
completion of the study whichever is later. Only investigators on the trial will 
have access to the tissue.
6.
TREATMENT
6.1
Radiation Therapy
6.1.0    Quality assurance measures.
Central review of all simulation films will occur at NYU. Simulation films 
images will be sent from S. Africa via the Internet and approved 
electronically.

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6.1.1
Breast Irradiation
6.1.1.1 Treatment planning on a simulator is required in all patients and for each 
field treated with photon radiation. The whole breast and underlying chest 
wall will be treated through opposed medial and lateral tangential fields. 
Non-divergence of the deep margins will be assured by half-beam block or 
multi-leaf collimator (MLC) blocking.
6.1.1.2 Patient Position: The patient will be supine, +/- table (breast) wedge, with 
the ipsilateral arm abducted approximately > 90∞ and supported 
appropriately in the horizontal position (with or without elbow flexion).
6.1.1.3 Field Margins: As clinically determined, these will be 1.5-2 cm around 
palpable breast tissue in the medial, lateral and inferior dimensions. The 
superior field margin will be at the matchline with the inferior margin of 
the  regional  lymphatic  field  and  will  generally  be  at  the  level  of the 
inferior aspect of the sternoclavicular joint.
6.1.1.4 Blocks: Blocking material with > 5 HVL will be utilized in the half beam 
block technique to comply with field margin and normal tissue dose 
requirements. In addition, blocking at the superior border of the tangential 
fields will be necessary to obtain a precise matchline with the nodal field. 
MLC is accepted.
6.1.1.5 Normal  Tissues:  No  more  than  3  cm  (demagnified)  of  lung  will  be 
included within the tangential  fields  as measured along the transverse 
plane of the central axis. For left-sided primary tumors, care will be taken 
to exclude as much of the heart as possible from the tangential fields. If it 
is impossible to avoid including part of the heart in the tangent field, the 
heart will be blocked after the first 36 Gy.
6.1.1.6 Treatment Equipment: Megavoltage units with peak photon energies of <
6 MV will be used. An occasional (large breasted) patient may be treated 
with a > 6 MV linear accelerator if necessary to comply with dose 
homogeneity requirements. A source-axis distance or source-skin distance 
of > 80 cm is used.
6.1.1.7 Beam Verification (Port) Films: Beam verification films on the radiation 
treatment machine will be obtained of each treatment field until 
satisfactory. Thereafter, beam verification films of each treatment field 
will be obtained each 5 treatments and at the time of any field 
modification(s).
6.1.1.8 Dosimetry: Transverse contours at the central axis, 2 cm inferior to the 
superior field border and 2 cm superior to the inferior field border will be 
obtained. 
Employing 
computerized 
dosimetry, 
without 
tissue 
inhomogeneity  correction,  for  the  above-mentioned  contours,  the 
maximum dose inhomogeneity allowed will be + 10% (measured by an
isodose area > 2 cm2 rather than ―hot spots‖) and –5%. It is expected that 
compensating blocking and wedge filters or tissue compensating devices 
will be used to maximize dose homogeneity.

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6.1.2
Regional Lymphatic
6.1.2.1 Supraclavicular  +  full  axillary  lymph  node  irradiation  will  be  given 
concurrent with whole breast or chest wall irradiation. No attempt will be 
made to include the internal mammary lymph nodes within a separate 
treatment field, within the supraclavicular + full axillary nodal fields (i.e., 
the ―hockey stick‖) or within the breast tangential treatment fields. 
Treatment planning on a simulator is required in all patients and for each 
field treated with photon radiation.
6.1.2.2 Patient Position: The patient will be supine +/- table (breast) wedge, with 
the ipsilateral arm abducted approximately > 90∞ and supported 
appropriately in the horizontal position (with or without elbow flexion). 
Patients with large, pendulous breasts will be treated prone to limit the 
extent of infra-mammary wet desquamation.
6.1.2.3 Technique: Treatment will be administered through a photon beam field 
angled into the ipsilateral side at approximately 10∞-15∞ so as to avoid 
irradiation of the entire trachea, esophagus, and spinal cord (e.g., for 
treatment of the right side, the field direction would be left anterior 
oblique).
6.1.2.4 Field Margins: supraclav ± full axillary field: The field margins will be 
defined as follows
Superior: level of the thyro-cryoid membrane. If necessary, a trapezial 
ridge ―splash‖ block to avoid fall off over the skin surface may be used. 
Inferior:  to  coincide with  the superior  border  of the breast/chest  wall 
tangential field. Commonly, this will be at the level of the inferior aspect 
of the sternoclavicular joint. A half-beam block technique, so as to avoid 
field divergence, is required.
Medial: 1 cm to the contralateral side of the anterior mid-line. A superior- 
medial block to shield portions of the spinal cord will, if necessary, be 
used.
Lateral: to the level of the humeral head or, when so treated, to include the 
full axillary contents. Blocking will, if necessary, be used to shield the 
humeral head.
6.1.2.5 Field Margins axillary field: posterior axillary boost In order to administer 
the target dose at the axillary midplane, a PA field will be used to 
supplement dose ―fall-off‖ from the anterior-oblique field, and will have 
field margins defined as follows:
Superior: coracoid process; blocking bisects clavicle in craniocaudad 
dimension.
Inferior: to coincide with the inferior margin of the supraclav/axillary 
field.
Medial: junction of 1st rib and clavicle, medially.
Lateral: to coincide with the lateral margin of the supraclav/axillary field;
if necessary, blocking will be used to shield the humeral head.
6.1.2.6 Treatment equipment.
Megavoltage units with peak photon energies < 6 MV will be used. A
source-skin distance of > 80 cm will be used.

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6.1.2.7 Beam Verification (Port) Films Beam verification films on the radiation 
treatment machine will be obtained of each treatment field until 
satisfactory. Thereafter, beam verification films of each treatment field 
will be obtained following each five treatments.
6.1.2.8 Total dose to the breast, axilla and supraclavicular area will be 45 Gy
@1.8 Gy/fraction, + 14 Gy to the area of original palpable tumor @ 2
Gy/fraction (total 32 fractions).
6.1.3
Expected toxicities
6.1.3.1 Acute reactions: Common acute side effects of radiation treatment include 
skin desquamation, with possible blistering and tumor ulceration. The skin 
reaction is more brisk due to the sensitizing effect of systemic therapy. 
Tiredness is commonly reported and it subsides at the completion of 
radiotherapy.
6.1.3.2 Intermediate Reactions: After treatment it is common to find darkening of 
the skin within the field. Wound closure delay also tends to occur more 
often, when compared to non-irradiated patients.
6.1.3.3 Late  Reactions:  Rare  late  reactions  are  rib  fractures  and  radiation 
pneumonitis (less than 3% of treated patients). If radiation pneumonitis is 
not treated with low dose steroids for 2-3 months complications may occur 
and (if mismanaged) can evolve in death.
6.1.4
Treatment Modifications
Radiation therapy will be interrupted for any Grade III toxicity, except for
Grade III skin toxicity.
6.2
Chemotherapy
6.2.1
Paclitaxel (including Abraxane), 30 mg/m2 twice per week. Paclitaxel will 
be given IV over 1 hour, Abraxane® will be administered over 30 min, and 
administered on a Monday/Thursday or Tuesday/Friday schedule.
6.2.2
Pre-medication for paclitaxel should be based on institutional standards; it 
is suggested that decadron, 20 mg IV, be given with the first paclitaxel 
dose. If the patient tolerates the treatment, the decadron may be tapered 
and/or discontinued for subsequent doses. While reactions can occur to 
any medication, severe allergic reactions to ABRAXANE are uncommon 
and premedication is not required.
6.2.3
Duration of pre-operative systemic therapy.
Systemic therapy will  be  given  for 12  weeks  total.  Radiation  therapy 
should commence within the first week of chemotherapy so that patient is 
receiving  6  weeks  of  concurrent  chemotherapy  and  radiation  therapy. 
Chemotherapy should be continued for 5 weeks after radiation. During 
pre-operative therapy, tumor assessments will be performed every two 
weeks; patients with progressive disease will be taken off study treatment. 
Other reasons for removal of patients from treatment are:
(a)
patient choice or failure to keep appointments, follow directions or 
take medications as instructed
(b)
a serious adverse reaction to drug therapy

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(c)
the need for treatment that is not allowed in the study
(d)
termination or cancellation of the study by study sponsor.
6.2.4
Dose Modifications Guidelines for Paclitaxel
Paclitaxel doses should be adjusted according to the following table for all 
toxicities, except for radiation dermatitis, anemia, lymphopenia and any 
not significant laboratory abnormality.
Toxicity Grade
(NCI CTC)
Continue/Hold therapy
Dose Modification
1 and 2
Continue treatment
None
3
Hold until resolution to grade 1 or 0
For absolute neutrophil count (ANC) <
1,000 or Platelets < 75,000, hold 
chemotherapy and monitor counts 
weekly. Resume therapy after counts 
have recovered to ANC > 1,000 or 
platelets > 75,000. If a patient is delayed 
more than one week, reduce 
chemotherapy dose by 25%. Other 
Hematological toxicities (i.e., 
lymphopenia) will not require dose 
modification.
1st event: Decrease dose by 25%.
2nd event: Decrease dose by 50%
4
For CTC grade 4 hematologic toxicity,
reduce chemotherapy dose by 25%.
6.2.5
Patients  who  experience  recurrent  toxicity  that  would  lead  to  a  dose 
reduction below 50% of the starting dose should be withdrawn from study 
treatment.
6.2.6
Dose Modifications Guidelines for Abraxane.
Patients who experience severe neutropenia (neutrophil <500 cells/mm3 
for a week or longer) or severe sensory neuropathy during Abraxane 
therapy should have dosage reduced to 220 mg/m2 for subsequent courses 
of Abraxane. For recurrence of severe neutropenia or severe sensory 
neuropathy, additional dose reduction should be made to 180 mg/m2. For 
grade 3 sensory neuropathy hold treatment until resolution to grade 1 or 2, 
followed by a dose reduction for all subsequent courses of Abraxane. 
Patients  should  not receive  Abraxane  if  AST  > 10 x ULN or bilirubin
> 5.0 x ULN.
6.3
Surgery
6.3.1
Patients will undergo lumpectomy and axillary node dissection or 
modified radical mastectomy within two months from the end of chemo- 
radiation, contingent upon recovery of skin toxicity.
6.3.2
For patients achieving clinical CR or PR, the decision regarding the type 
of surgery will be based on the preferences of the patient and the

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surgeon’s recommendation based on the clinical assessment of the residual
tumor47.
6.3.3
In the absence of clinical response, if operable, patients will undergo 
modified radical mastectomy.
7.
STUDY PARAMETERS
The research procedures will be conducted as indicated in the following table:
Parameter
Baseline
During Preoperative
Treatment
During Long-term Follow-up
Tumor tissue
Core Biopsy
Required
None
At the time of surgery
Blood for Serum
and Plasma
Banking
Required at time of
core biopsy.
Required at the end of
second week of 
radiation therapy and 
after completion of 
pre-op therapy
None
History and
Physical
Complete H & P
required at 
baseline.
Complete physical q 2
weeks
Complete physical every 3
months during the first 2 years 
post therapy; every 6 months 
during years 3, 4 and 5 post 
therapy; thereafter once a year 
(up to 10 years)
ECOG PS
Required
q 2 weeks
At each F/U visit
Tumor
Measurement
Bi-dimensional
measurements.
q 2 weeks
N/A
Lymphedema
Measurement
Required
q 2 weeks
Required at each F/U
Mammogram
Required pre-
therapy.
None
For the involved breast, q 6 mos
(lumpectomy pts.); standard 
annual mammogram of the 
uninvolved breast.
PET/CT (or CT
Chest, Abdomen, 
Pelvis with Bone 
scan)
Required.
None
As medically indicated.
Serum Pregnancy
Test
Required for
patients of child- 
bearing potential.
None
None
CBC,diff
Required.
weekly
As medically indicated.
Electrolytes, BUN,
Cr, LFT’S
Required.
q 2 weeks
As medically indicated.
8.
CRITERIA FOR EVALUATION AND ENDPOINT DEFINITIONS 
Clinical Measurement
Clinical response will be measured by the following criteria:
Complete Response (CR): complete disappearance of all known tumor masses 
and the appearance of no new lesions.

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Partial Response (PR): greater than 50% reduction in the product of 
perpendicular measures of all measurable tumor masses and the appearance of no 
new lesions.
Stable Disease (SD): less than a 50% decrease or less than 25% increase in the 
product of perpendicular measures of tumor masses and the appearance of no new 
lesions.
Progressive Disease (PD): greater than a 25% increase in the product of 
perpendicular measures of tumor masses or the appearance of new lesions.
Pathologic Measurement
Mastectomy  specimens  will  be  processed  and  sectioned  to  identify  residual  tumor.
Accurate measurements  will  be performed for  quantification  of pathologic response. 
Residual tumor measurements will be carried on at pathology and will be classified as:
Complete Pathological Response (pCR): absence of residual invasive tumor 
cells both in the removed breast and axillary contents specimens (persistent DCIS 
is accepted).
Partial  pathological  response  (pPR):  <10  persistent  microscopic  foci  of 
invasive cancer cells in either the breast or nodal specimens;
No pathological response (pNR): microscopic confirmation of persistence of 
invasive tumor (in more than 10 microscopic foci).
9.
PRODUCT INFORMATION
9.1
PACLITAXEL22, 48-52
OTHER NAMES Taxol, NSC 673089
CLASSIFICATION: Antimicrotubule agent.
MODE OF ACTION: Promotes microtubule assembly and stabilizes tubulin polymers by 
preventing their depolarization, resulting in the formation of extremely stable and nonfunctional
microtubules, and consequently inhibition of many cell functions.
STORAGE AND STABILITY: The intact ampules are stored at controlled room temperature, 2-
25C. Freezing does not adversely affect the product. Solutions diluted to a concentration of 0.3 to
1.2 mg/ml in normal saline or 5% dextrose are stable for up to 27 hours when stored at room 
temperature and normal room light. Analyses of solutions filtered through IVEX-2 and IVEX-HP
(Abbott) 0.2 micron filters showed no appreciable loss of potency.
PREPARATION: The concentrated solution must be diluted prior to use in normal saline, 5%
dextrose, 5%dextrose and normal saline, or 5% dextrose in Ringer's solution to a concentration of
0.3 to 1.2 mg/ml. Solutions exhibit a slight haze, common to all products containing nonionic 
surfactants. Glass, polypropylene, or polyolefin containers and non-PVC-containing
(nitroglycerin) infusion sets should be used. A small number of fibers (within acceptable limits 
established by the USP) have been observed after dilution. Solutions exhibiting excessive
particulate formation should not be used.
ADMINISTRATION: Usually administered as an intravenous infusion with a hydrophilic in-line
0.22 micron filter.
INCOMPATIBILITIES: Avoid the use of PVC bags and infusion sets, due to leaching of DEHP 
(plasticizer). Prior administration of cisplatin may increase myelosuppression because of reduced
clearance of taxol. Ketoconazole may inhibit taxol metabolism, based on in vitro data. 
AVAILABILITY: A concentrated solution of 6mg/ml in polyoxyethylated castor oil (Cremophor
EL) 50% and dehydrated alcohol 50% is commercially available in 5 ml ampules.

NYU 06-209
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SIDE EFFECTS:
1. Hematologic: Myelosuppression (neutropenia, leukopenia, thrombocytopenia, anemia).
2. Hypersensitivity: Thought to be caused by the Cremophor vehicle. Minor symptoms include 
hypotension, flushing, chest pain, abdominal or extremity pain, skin reactions, pruritus, dyspnea, 
and tachycardia. More severe reactions include hypotension requiring treatment, dyspnea with 
bronchospasm, generalized urticaria, and angioedema. The majority (53%) of the reported 
reactions occurred within 2-3 minutes of initiation of treatment and 78% occurred within the first
10 minutes. Reactions usually occurred with the first and second doses.
3. Cardiovascular: Atrial arrhythmia (sinus bradycardia [usually transient and asymptomatic], 
sinus tachycardia, and premature beats); significant events include syncope, hypotension, other
rhythm abnormalities (including ventricular tachycardia, bigeminy, and complete heart block
requiring pacemaker placement), and myocardial infarction. Hypertension, possibly related to 
concomitant administration of dexamethasone, may also occur.
4. Neurologic: Sensory changes (taste changes); peripheral neuropathy; arthralgia and myalgia
(dose-related, more common when colony-stimulating factors are also administered); seizures; 
mood alterations; neuroencephalopathy; hepatic encephalopathy; motor neuropathy; and 
autonomic neuropathy (paralytic ileus and symptomatic hypotension).
5. Dermatologic: Alopecia, universal, complete, and often sudden, between days 14-21; injection 
site reactions (erythema, induration, tenderness, skin discoloration); infiltration (phlebitis,
cellulitis, ulceration, and necrosis, rare); radiation recall; and rash.
6. Gastrointestinal: Nausea, vomiting, diarrhea, mucositis, pharyngitis, typhlitis
(neutropenicenterocolitis), ischemic colitis, and pancreatitis.
7. Hepatic: Increased SGOT (SAST), SGPT (ALT), bilirubin, alkaline phosphatase; hepatic 
failure, and hepatic necrosis.
8. Other: Fatigue, headaches, light-headedness, myopathy, elevated serum creatinine, elevated 
serum triglycerides, and visual abnormalities (sensation of flashing lights, blurred vision).
NURSING IMPLICATIONS
1. Monitor CBC and platelet count prior to drug administration.
2. Symptom management of expected nausea, vomiting, and stomatitis.
3. Monitor for and evaluate abdominal pain occurring after paclitaxel administration (especially 
in severely neutropenic patients and in those receiving G-CSF) due to the risk
of ischemic and neutropenic enterocolitis.
4. Advise patients of possible hair loss.
5. Cardiac monitoring for assessment of arrhythmias in patients with serious conduction 
abnormalities.
6. Monitor liver function tests.
7. Advise patient of possible arthralgias and myalgias which may occur several days after 
treatment. Monitor for symptoms of peripheral neuropathy.
8. Monitor for signs and symptoms of hypersensitivity reactions. Insure that the recommended 
premedications have been given. Premedications (diphenhydramine, steroids, and H2 blocker)
appear to reduce the incidence and severity of hypersensitivity reactions but do not provide 
complete protection. Emergency agents (diphenhydramine and epinephrine) should be available.
9. Evaluate IV site regularly for signs of infiltration. It is not known if taxol is a vesicant;
however, the Cremophor vehicle for this drug can cause tissue damage.
10. In-line filtration with a 0.22 micron filter should be used.
9.2
ABRAXANE® OTHER NAMES: 
paclitaxel CLASSIFICATION: 
Antimicrotubule agent.

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MODE OF ACTION: Promotes microtubule assembly and stabilizes tubulin polymers by 
preventing their depolarization, resulting in the formation of extremely stable and nonfunctional 
microtubules, and consequently inhibition of many cell functions.
STORAGE AND STABILITY: Retain in the original package to protect from bright light. 
Unopened vials of Abraxane® are stable until the date indicated on the package when stored 
between 20°C to 25°C (68°F to 77°F), in the original package. Neither freezing nor refrigeration 
adversely affects the stability of the product. Reconstituted Abraxane® should be used 
immediately, but may be refrigerated at 2°C to 8°C (36°F to 46°F) for a maximum of 8 hours if 
necessary. If not used immediately, each vial of reconstituted suspension should be replaced in 
the original carton to protect it from bright light. Discard any unused portion. The suspension for 
infusion prepared as recommended in an infusion bag should be used immediately, but may be 
stored at ambient temperature (approximately 25° C) and lighting conditions for up to 8 hours. 
PREPARATION: Abraxane® is supplied as a sterile lyophilized powder for reconstitution before 
use. AVOID ERRORS, READ ENTIRE PREPARATION INSTRUCTIONS PRIOR TO 
RECONSTITUTION.
1.   Aseptically, reconstitute each vial by injecting 20 mL of 0.9% Sodium Chloride
Injection, USP.
2.   Slowly inject the 20 mL of 0.9% Sodium Chloride Injection, USP, over a minimum of 1 
minute, using the sterile syringe to direct the solution flow onto the INSIDE WALL OF
THE VIAL.
3.   DO NOT INJECT the 0.9% Sodium Chloride Injection, USP, directly onto the 
lyophilized cake as this will result in foaming.
4.   Once the injection is complete, allow the vial to sit for a minimum of 5 minutes to ensure
proper wetting of the lyophilized cake/powder.
5.   Gently swirl and/or invert the vial slowly for at least 2 minutes until complete dissolution 
of any cake/powder occurs. Avoid generation of foam.
6.   If foaming or clumping occurs, stand solution for at least 15 minutes until foam subsides. 
Each mL of the reconstituted formulation will contain 5 mg/mL paclitaxel.
Calculate the exact total dosing volume of 5 mg/mL suspension required for the patient: Dosing
volume (mL) = Total dose (mg)/5 (mg/mL)
The reconstituted suspension should be milky and homogenous without visible particulates. If 
particulates or settling are visible, the vial should be gently inverted again to ensure complete
resuspension prior to use. Discard the reconstituted suspension if precipitates are observed. 
Discard any unused portion. Inject the appropriate amount of reconstituted Abraxane® into an 
empty, sterile IV bag.
ADMINISTRATION: Intravenous infusion in sterile IV bag (plasticized polyvinyl chloride 
(PVC) containers, PVC or non-PVC type IV bag). The use of specialized DEHP-free solution 
containers or administration sets is not necessary to prepare or administer Abraxane® infusions. 
The use of an in-line filter is not recommended. Infusion rate: administer intravenously over 30 
minutes.
INCOMPATIBILITIES: Abraxane® should not be used in patients who have baseline neutrophil 
counts of < 1,500 cells/mm3. The metabolism of paclitaxel is catalyzed by CYP2C8 and
CYP3A4. In the absence of formal clinical drug interaction studies, caution should be exercised 
when administering Abraxane® concomitantly with medicines known to inhibit (e.g. ketoconazole 
and other imidazole antifungals, erythromycin, fluoxetine, gemfibrozil, cimetidine, ritonavir, 
saquinavir, indinavir, and nelfinavir) or induce (e.g. rifampicin, carbamazepine, phenytoin, 
efavirenz, nevirapine) either CYP2C8 or CYP3A4.
SIDE EFFECTS:
1. Hematologic: Myelosuppression (neutropenia, leukopenia, thrombocytopenia, anemia).

NYU 06-209
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2. Hypersensitivity: In the randomized controlled metastatic breast cancer study, Grade 1 or 2
Hypersensitivity Reactions occurred on the day of Abraxane® administration and consisted of 
dyspnea (1%) and flushing, hypotension, chest pain, and arrhythmia (all <1%).
3. Cardiovascular: Hypotension, sinus bradycardia (in <1% of patients) - these vital sign changes
most often caused no symptoms and required neither specific therapy nor treatment 
discontinuation; severe cardiovascular events possibly related to single-agent Abraxane® 
occurred. These events included chest pain, cardiac arrest, supraventricular tachycardia, edema, 
thrombosis, pulmonary thromboembolism, pulmonary emboli, and hypertension. Cases of 
cerebrovascular attacks (strokes) and transient ischemic attacks have been reported rarely. ECG 
abnormalities on study did not usually result in symptoms, were not dose-limiting, and required 
no intervention. The most frequently reported ECG modifications were non-specific 
repolarization abnormalities, sinus bradycardia, and sinus tachycardia.
4. Respiratory: Dyspnea and cough were reported after treatment with Abraxane®. Rare cases of
(<1%) of pneumothorax were reported. Rare reports of interstitial pneumonia, lung fibrosis, and 
pulmonary embolism have been received as part of the continuing surveillance of paclitaxel 
injection safety and may occur following Abraxane® treatment. Rare reports of radiation 
pneumonitis have been received in paclitaxel injection patients receiving concurrent radiotherapy. 
There is no experience with the use of Abraxane® with concurrent radiotherapy.
5. Neurologic: The frequency and severity of neurologic manifestations were influenced by prior 
and/or concomitant therapy with neurotoxic agents.
In general, the frequency and severity of neurologic manifestations were dose-dependent in 
patients receiving single-agent Abraxane®. The frequency of sensory neuropathy increased with 
cumulative dose. No incidences of grade 4 sensory neuropathies were reported. Only one incident 
of motor neuropathy (grade 2) was observed.
Cranial nerve palsies and vocal cord paresis have been reported during postmarketing 
surveillance of Abraxane®. Because these events have been reported during clinical practice, true 
estimates of frequency cannot be made and a causal relationship to the events has not been 
established.
Reports of autonomic neuropathy resulting in paralytic ileus have been received as part of the 
continuing surveillance of paclitaxel injection safety.
Ocular/visual disturbances occurred in patients treated with Abraxane® in single arm and
randomized trials and 1% were severe. The severe cases (keratitis and blurred vision) were 
reported in patients in a single arm study who received higher doses than those recommended 
(300 or 375 mg/m2). These effects generally have been reversible. However, rare reports in the 
literature of abnormal visual evoked potentials in patients treated with paclitaxel injection have 
suggested persistent optic nerve damage.
6. Arthralgia/Myalgia: Patients experienced arthralgia/myalgia; 8% experienced severe 
symptoms. The symptoms were usually transient, occurred two or three days after Abraxane® 
administration, and resolved within a few days.
7. Hepatic :Among patients with normal baseline liver function treated with Abraxane®, 7%,
36%, and 39% had elevations in bilirubin, alkaline phosphatase, and AST (SGOT), respectively. 
Grade 3 or 4 elevations in GGT were reported for 14% of patients treated with Abraxane®.
Rare reports of hepatic necrosis and hepatic encephalopathy leading to death have been received
as part of the continuing surveillance of paclitaxel injection safety and may occur following
Abraxane® treatment.
8. Renal: Overall 11% of patients experienced creatinine elevation, 1% severe. No 
discontinuations, dose reductions, or dose delays were caused by renal toxicities.
9. Gastrointestinal (GI): Nausea/vomiting, diarrhea, and mucositis were reported.
Rare reports of intestinal obstruction, intestinal perforation, pancreatitis, and ischemic colitis have 
been received as part of the continuing surveillance of paclitaxel injection safety and may occur 
following Abraxane® treatment. Rare reports of neutropenic enterocolitis (typhlitis), despite the

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coadministration of G-CSF, were observed in patients treated with paclitaxel injection alone and 
in combination with other chemotherapeutic agents.
10. Injection Site Reaction: Injection site reactions have occurred infrequently with Abraxane®
and were mild in the randomized clinical trial. Recurrence of skin reactions at a site of previous 
extravasation following administration of paclitaxel injection at a different site, i.e., "recall", has
been reported rarely.
Rare reports of more severe events such as phlebitis, cellulitis, induration, skin exfoliation, 
necrosis, and fibrosis have been received as part of the continuing surveillance of paclitaxel
injection safety. In some cases the onset of the injection site reaction in paclitaxel injection
patients either occurred during a prolonged infusion or was delayed by a week to ten days. 
Given the possibility of extravasation, it is advisable to closely monitor the infusion site for 
possible infiltration during drug administration.
Asthenia: Asthenia was reported. Asthenia included reports of asthenia, fatigue, weakness, 
lethargy and malaise.
11. Other Clinical Events
Rare cases of cardiac ischemia/infarction and thrombosis/embolism possibly related to Abraxane®
treatment have been reported. Alopecia was observed in almost all of the patients. Nail changes 
(changes in pigmentation or discoloration of nail bed) were uncommon. Edema (fluid retention) 
was infrequent; no patients had severe edema. In clinical trials and during postmarketing 
surveillance of Abraxane®, dehydration was common and pyrexia was very common.
The following rare adverse events have been reported as part of the continuing surveillance of 
paclitaxel injection safety and may occur following Abraxane® treatment: skin abnormalities 
related to radiation recall as well as reports of Stevens-Johnson syndrome, toxic epidermal 
necrolysis, conjunctivitis, and increased lacrimation. As part of the continuing surveillance of 
Abraxane®, skin reactions including generalized or maculo-papular rash, erythema, and pruritis 
have been observed. Additionally, there have been case reports of photosensitivity reactions, 
radiation recall phenomenon, and in some patients previously exposed to capecitabine, reports of 
palmar-plantar erythrodysaesthesiae. Because these events have been reported during clinical 
practice, true estimates of frequency cannot be made and a causal relationship to the events has 
not been established.
NURSING IMPLICATIONS
1. Monitor CBC and platelet count prior to drug administration.
2. Symptom management of expected nausea, vomiting, and stomatitis.
3. Monitor for and evaluate abdominal pain occurring after Abraxane® administration (especially 
in severely neutropenic patients and in those receiving G-CSF) due to the risk
of ischemic and neutropenic enterocolitis.
4. Advise patients of possible hair loss.
5. Cardiac monitoring for assessment of arrhythmias in patients with serious conduction 
abnormalities.
6. Monitor liver function tests.
7. Advise patient of possible arthralgias and myalgias which may occur several days after 
treatment. Monitor for symptoms of peripheral neuropathy.
8. Monitor for signs and symptoms of hypersensitivity reactions..
9. Evaluate IV site regularly for signs of infiltration.

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10.
PATIENT RECRUITMENT AND REGISTRATION
10.1
Recruitment and Registration in New York City
10.1.1  Recruitment
Potential patients in New York City will be recruited through several outreach
programs in addition to walk-ins to the Bellevue Hospital Clinic (see Figure 1). 
Bellevue Hospital Center (BHC) is an NYU School of Medicine teaching 
institution with a diverse patient population of which 74% are ethnic minorities. 
Approximately 60% of BHC’s patients are Latino (predominantly Puerto Rican, 
Dominican, and Mexican), 20% are Chinese and the remainder comprises a 
mixture of South Asians, Africans, African-Americans (approximately 14%) and 
non-Hispanic whites. Many women with breast cancer are identified as walk-ins 
to the BHC clinic and will be recruited into this study if eligible by informed 
house staff. In addition, potential patients will be recruited to the BHC Breast 
Cancer clinic through Patient Navigation Assistance and Health Education 
programs supported by BHC and the Center for Immigrant Health (CIH) at New 
York University School of Medicine. The CIH has a highly regarded history of 
working  with  immigrant  communities,  bridging  some  of  the  City’s  most 
medically underserved populations with the health care system for the past 15 
years. The CIH has established a large series of community based breast cancer 
education and referral services for women to the BHC. The CIH arranges for 
health care coverage for all women regardless of citizenship and ability to pay, 
and  coordinates  scheduling  of  mammograms  with  the  BHC  Patient  Care 
Resources and the Rita Kaplan Breast Cancer Imaging Center. All women with 
suspected breast cancer are then guided to the BHC Breast Clinic, where in triage 
by consultation with a surgical and medical oncologist women are informed of the 
COE LABC protocol.
10.1.2  Registration at New York University and Bellevue Hospitals
Eligible patients will be identified by clinical staff at each site. Once eligibility is
confirmed (see Patient Eligibility Sections 4.3 and 4.4) and Informed Consent is 
documented, the patient will be registered with the NYUCI Clinical Trials Office 
(CTO) registry which is available Monday through Friday from 8:00 AM to 5:00
PM, EST at (212)263-4210, Fax (212)263-4111. All patients will be consented 
(see Section 12, below) and the last page of the Informed Consent form will be 
faxed to the CTO registry.

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10.2     Recruitment and Registration at South Africa Sites
Patients will be identified by clinical staff at each site for possible recruitment into the 
study.  Registration  for  each  patient  will  take  place  at  the  local  clinical  center.  To 
complete  registration  of  a  patient  accrued  to  trial  from  Tygerberg  Hospital  (South 
Africa), the study coordinator at each site will fax to the NYUCI Clinical Trials Office 
(CTO) the completed Eligibility form and Informed Consent (signed) and supporting 
source documentation according to the same registration process described above in 
Section 10.1.2.
Further details regarding these clinical centers (including Standard of Care and Patient
Safety Assurances; as well as IRB committees and criteria) are included in Appendix 6.8.
11.       PROTECTION OF HUMAN SUBJECTS
11.1     Benefits/Risks
11.1.1  Clinical procedures: specific benefits/risks associated with each clinical 
procedure were outlined in the TREATMENT Section 6. Potential toxicities 
associated with treatment were listed there as well.
11.1.2   Research procedures: each patient will be asked to donate a small part of 
the biopsy tissue that was collected to confirm her cancer diagnosis. In addition, 
she will be asked to donate a small amount of blood (2-3 tablespoons). The study 
biopsy is usually a well-tolerated procedure that involves only minor discomfort. 
Occasionally, biopsy sites may bleed or become infected. The study blood will be 
drawn in three occasions during a routine blood test so no additional needle stick 
is required. Occasionally, the site of the blood draw may bleed, become sore for a 
few days or become infected. The potential risks and discomforts associated with 
tissue sample, blood sample are explained in the Informed Consent document 
(Appendix, Section 16.5).
11.2     Privacy/Confidentiality
11.2.1 The medical, hospital and research records associated with this study are
considered confidential. Members of the treating team and designated study 
assistants will have access to the records as required to administer treatment and 
comply with the protocol. Neither the name nor any other identifying information 
for an individual will be used for reporting or publication regarding this study. All 
laboratory  and   baseline   data   including   Baseline   Case   Report   forms   and 
Qualitative Interviews will be de-identified and transferred via secure links to the 
BDM core at NYU School of Medicine. Patient records will be made available for 
inspection to auditing agencies to satisfy regulatory requirements. 
11.3     Non-Health Related Risks
Participation in this research study could potentially expose the research subject
to  non-health  related  risks.  These  include  the  potential  breach  of  medical

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confidentiality  and  release  of  personal  medical  information  to  an  insurer, 
employer, family members, or other persons outside the research study staff. The 
release of this information could result in denial of medical coverage, termination 
of existing medical insurance coverage, or loss of employment. The actual risk of 
these events is extremely low.
11.4     Serious Adverse Events (SAE) Reporting
SAEs that occur in this study must be promptly reported to the study P.I. (Dr. Nelly 
Huppert) as well as to the NYU IRB (1 Park Avenue, 6th Floor  New York, NY 10016) 
and to the NYU Clinical Trials Office (462 First Avenue, New York, NY 10016) for 
reporting to the NYUCI Data Safety Monitoring Committee.
The IRB Serious Adverse Event Report Form (Appendix, Section 16.6) available 
electronically at  http://www.med.nyu.edu/IRB/ should be used for all adverse events with
an attached copy of information provided to the Sponsor. The requirements for the 
reporting of adverse events are delineated in the Adverse Event policy that is appended to 
document 16.6. Investigators should also be aware of local facility requirements for 
reporting adverse events associated with patients seen at the local facility. The NYU 
Clinical Trial Office will submit all summaries of safety data and the standardized SAE 
reports to the NYUCI Data and Safety Monitoring Committee for the regularly scheduled 
semi-annual review. Dr. Huppert will attend the DSMC meeting to present the trial and 
discuss the safety issues. DSMC will review the SAEs and the accuracy of the reporting 
to appropriate review committees annually from the date the first patient is enrolled and 
at pre-specified interim  analysis time points defined in the protocol (Appendix  16.7
DSMC Procedures). Details of the interim safety monitoring rule for each site are 
provided below in Section 13.0. 
The Medical Monitor is required to review all unanticipated problems involving 
risk to volunteers or others, serious adverse events and all volunteer deaths associated 
with the protocol and provide an unbiased written report of the event. At a minimum, the 
medical monitor should comments on the outcomes of the event or problem, and in the 
case of a serious adverse event or death, comment on the relationship to participation in 
the study. The medical monitor should also indicate whether he/she concurs with the 
details of the report provided by the study investigator. Expedited SAE reporting will 
utilize for this study the descriptions and grading scales as presented in  Expected 
Toxicities and Treatment Modifications sections for Breast Irradiation (Sections 6.1.3-
1.1.4) and Chemotherapy (Sections 6.2.4-6.2.5).

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11.5     Medical Care for Research Related Injury
Consent Forms (Appendix 16.5) contain the following language to inform volunteers
regarding medical care for research related injuries: ―If you experience any research- 
related injury or side effect during the course of this study, please contact the Principal 
Investigator, Nelly Huppert, MD, at the following telephone number: 212-731-5003. In 
the event that you experience a side effect or injury as a result of the drugs or procedures 
related to this study, the study doctor will assist you in obtaining appropriate medical 
treatment but this study does not provide financial assistance for medical or other injury- 
related costs. You do not give up any rights to seek payment for personal injury by 
signing this form. All forms of medical (or mental health) diagnosis and treatment— 
whether routine or experimental—involve some risk of injury. In addition, there may be 
risks associated with this study that we do not know about. In spite of all precautions, you 
might develop medical complications from being in this study. If you have questions 
about this medical care, talk to the principal investigator for this study, Nelly 
Huppert, MD, at the following telephone number 212-731-5003. If you pay out-of-pocket 
for medical care elsewhere for injuries  caused by this  research  study, contact the 
principal investigator. 
12.       INFORMED CONSENT
12.1     Procedure for obtaining Informed Consent
Patients or their legal guardians will be provided a comprehensive explanation of the
proposed treatment including the type of therapy, the rationale for treatment on the 
protocol, alternative treatments that are available, any known adverse events, the 
investigational nature of the study and the potential risks and benefits of the treatment. 
The Informed Consent document will meet all requirements of Federal  Regulations, as 
well as the Institutional Review Boards of the treating centers. An English and Spanish 
version of the Informed Consent form is included in the Appendix, Section 16.5. The 
physicians who may obtain informed consent are listed on the title page of this protocol 
for each participating site. The Informed Consent form will be  signed  by  the  participant  
and  the  registering  physician  in  triplicate.  One  signed original will be given to the 
patient, one will be maintained with the patient’s medical record and one will be kept 
on file at the CTO. A copy will be kept on file by the EDC Core.
12.2     Procedure for Obtaining Research Authorization
Before any protocol specific procedures can be carried out, investigators/staff will fully
explain the details of the protocol, the study procedures and the aspects of patient privacy 
regarding research information. In addition to signing the IRB Informed Consent, all 
patients must sign the Research Authorization component of the Informed Consent form.

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The original signed documents will be a part of the patient’s medical records as described
above.
12.3     Minimization of Coercion and Undue Influence
All  subjects/patients  are  informed  in  the  Consent  that  participation  or  refusal  to
participate in the research study will not affect any of the clinical treatment or services to 
which they would otherwise be entitled.
13.       DATA ANALYSIS/STATISTICAL CONSIDERATIONS
13.1     Study Objectives
The primary objective of the study is to confirm the pathological response rate of 34% 
(pCR+pPR), reported for patients in the US Phase I-II trial44.
The anticipated power to interpret the results of the international clinical trial versus the 
US trial: An overall difference in pathologic response rates between and South Aftrica 
combined of +/- 24% compared to the overall NYU cohort will be detectable with power
80% (150 total, 100 at NYU) and significance level ≤5%, 2-sided binomial comparison. 
(The inclusion of 20 additional patients from India will yield a detectable difference of
+/- 22%.). For the comparison of South Africa individually to the NYU cohort, with 25 
patients/site, a difference of +/-34% is detectable. Each of the cohorts will be analyzed 
separately.
The classical chi-square test will be used to compare the three pathological response 
rates. If the test finds the rates differ as expected, we will identify the cohorts with 
different rates using multiple comparison tests and report confidence intervals for the 
response rates within and across the cohorts, and for the magnitude of related differences 
and odds ratios. If there are no differences between the cohorts with respect to overall 
response rates, with a total of 150 patients, we can estimate the pathologic response rate 
with 95% confidence limits of +/-8%, if the expected overall rate is 34% in this 
confirmatory study.
Across all cohorts, logistic regression models will be used to identify predictors of 
pathologic response. If the proportion of patients with LABC with the predictor ranges 
from 0.05 to 0.1 to 0.25 to 0.5, the detectable odds ratio at 0.05 level (2-sided) and 80% 
power ranges from 8.7 to 4.6 to 2.8 to 2.5 for the overall cohort of 150 patients (assuming 
path response rate of 34%).
If the cohorts are similar with respect to pathologic response rates, then they can be 
combined for further analysis of predictors of progression and survival. Progression free 
survival  and  survival  will  also  be  estimated  in  each  cohort  individually  and  across 
cohorts. All patients will have completed at least one year of follow-up on study after 
diagnosis  and  be  evaluable  for  the  analysis  of  the  primary  endpoint  of  pathologic 
response to treatment in year 5 of the study. Follow-up of all patients for recurrence, 
metastases, and death will continue beyond the 5 years of the study. Methods of censored 
data analysis that incorporate all patients taking into account variable lengths of follow- 
up will be used for the analysis of these other endpoints in study year 5 and again when 
more complete long term follow-up data are available.

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Interim  monitoring for safety will  be conducted  at  the NYU/Bellevue  site  when  25 
patients have completed the evaluation for pathologic response and when 50 patients 
have completed the evaluation for pathologic response. Toxicity/failure is defined as 
having at least one of the following during the chemoradiation phase of this study: grade 
3-4 non skin positively (possibly, probably, definitely) related toxicity (excluding 
Lymphopenia)), disease progression requiring  change  in  treatment,  or  recurrent  
toxicity  requiring  greater  than  a  50% reduction in chemotherapy dose. The study will 
discontinue enrollment at an individual site if the observed toxicity/failure rate is greater 
than the upper edge of the 95% confidence interval (assuming a true underlying 
toxicity/failure rate of 20%)  as  in the table below at each of the two early looks. If the 
NYU/Bellevue site continues past the 50 patient enrollment, enrollment will continue to 
the end of the planned 100 patients. For the other two sites combined, interim monitoring 
will occur when 15 patients and when 25 patients have completed the evaluation for 
pathologic response. The criteria for discontinuation of enrollment are provided in Table
A.  Stopping rule for interim monitoring NYU/Bellevue
Interim Look
Number of Patients
Upper
Edge
of
Exact*
95%
Confidence   Interval   for   Failure
Rate
1
25
41%
2
50
34%
B.  Stopping rule for interim monitoring (S. Africa. combined)
Interim Look
Number of Patients
Upper
Edge
of
Exact*
95%
Confidence   Interval   for   Failure
Rate
1
15
48%
2
25
41%
* Clopper  Pearson  exact  95%  confidence  interval;  calculations
from PASS 2008, NCSS, Hintze, J., Kaysville, Ut.
This  project  is  part  of the  LABC  Center  of  Excellence and  patients  will  be 
included in the various projects to study genomics, biomarkers and hormonal markers. A 
common random sample of 75 patients, stratified by site, will be selected from the 
complete cohort of 150 patients enrolled in the treatment protocol in Project 1 for study 
in Projects 2 (functional genomic), 3 (molecular and biochemical alterations), 4 (mutation 
analysis), 7 (p53 polymorphisms) to allow a complete set of data to be generated for the 
same subset of patients. Similarly, the study of cultural norms (Project 6) will be based 
on a stratified random sample. The approach to using a common sample of patients for 
each of the research projects that will not be conducted on all 300 patients will facilitate 
the identification of characteristics that can be used to predict pathological response and 
progression and survival from the multi-ethnic cohorts under study and the identification 
of hypotheses for the generation of further studies.
The general strategy for these statistical analyses follows here. In the first stage of 
these analyses, we will use descriptive (numerical and graphical) statistics to summarize 
the  baseline  clinical  and  disease  variables  for  each  cohort,  including  pathological

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response, disease progression and survival of patients enrolled on the clinical protocol. 
We will also use similar descriptive statistics to compare the data on the incomplete 
sample of 75 patients to the entire cohort. Next, we provide nonparametric analyses 
including confidence intervals for various proportions (e.g. response rates) within each 
cohort  and  differences  in  proportions  between  cohorts.  For  each  project,  variable 
selection strategies will be used. Once the variable selection within the project is 
completed, we will fit logistic regression models to study the relationships between the 
predictors (gene profiles, etc) and pathologic response to treatment (complete vs not) 
using variable selection tools. For time to progression and survival, we will develop 
proportional hazard models. Finally, we will describe approaches to analysis of data with 
partially observed covariates. The 3 steps in these analyses include: 1. Use all data 
available in each individual project to select variables predictive of the outcomes 
(pathologic response to treatment, etc) in that project. For projects 1, 3-6 this will be 
accomplished using logistic regression with a variable selection tool such as Lasso. For 
project  2,  we  will  use  a  classification  method  specific  to  microarray  data  to  select
variables (i.e. genes) predictive of the outcome 53. We will then pool the sets of variables 
together to include the complete data model in step 2. Use the variables identified as 
predictive of pathologic response from each individual project as explanatory variables. 
Use complete data (75 patient sample) to fit a logistic regression model with variable 
selection procedure such as Lasso to identify the variables predictive of pathologic 
response. 3. Use all available data on 150 patients with variables selected in Step 2 (some 
of which are only partially observed) and use maximum likelihood methods and the EM 
algorithm to fit the final model.
Some specific methods to be used are described here:
Logistic  Regression:  Multiple  logistic  regression  models 54   will  be  used  to  select 
predictive variables for the binary outcome variables such as pathologic response (e.g., 1
for response and 0 for non-response) to the treatment of LABC characterized in Project 1. 
Other variables from the studied subjects will be used as explanatory variables, including 
gene signatures described in Project 2, molecular and biochemical markers from Project
3, immunological factors of Project 4, mutational factors from the selected patients of 
Project 5, estrogen metabolites from Project 6, genotypes from Project 7 and other 
demographic factors (age, behavioral-cultural, socioeconomic status, etc).
Variable   Selection   Methods:   Multiple   logistic   regression   with   variable   selection 
procedure such as Lasso 55 and Least Angle Regression 56 will be used to identify a subset 
of the predictors among the many factors to pathologic response, progression to local 
recurrence or metastatic disease, and survival, respectively. With the large amount of data 
obtained   from   this   study   concerning   multi-ethnic   cohorts   and   multi-disciplinary
collaborative research projects, we can attempt to characterize sets of predictors that are 
common across cohorts as well as those specific to each individual cohort, ranging from 
genetic, molecular to immunological factors. To assess the performance of these models, 
we will use cross-validation methods.
Interactions: It is natural to expect that there might be interactions among the outcomes
(pathologic  response,  progression,  and  survival),  and  biological  factors  (e.g.  gene

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profiles, Project 2, and genomic mutations, Project 5) or genotypes, Project 7) and other 
groups of variables (e.g. behavioral and cultural). We will employ statistical models to 
investigate these potential predictors concurrently, and the interpretation of these 
predictors  and  findings  will  be  done  in  collaboration  with  COE  investigators.  For 
example, ethnic differences are documented in outcomes of LABC patients 3-5, 57  and,
therefore, it is of interest to see whether the ethnicity remains important in the logistic 
regression model after adjustment for other factors in the model.
Treatment of Data with Partially Observed Covariates: Since several of the projects (2,
4, 5, 8) will be performed using a randomly selected subset of the subjects, we will have 
complete data available for these 75 selected subjects; data on the remaining 150 patients 
will have partially observed covariates. One approach for the analysis of pathologic 
response is to treat the covariates with incomplete observations as categorical and to fit a 
logistic regression model using maximum likelihood methods and the EM algorithm 58-59.
We will use 75 observations with complete data to fit proportional hazards models for 
progression  free  survival  and  survival.  We  will  use  Lasso  penalty  for  variable 
selection 55. The model will then be calibrated using the remaining data with incomplete 
observations on some covariates. While we expect that the models built on 75 patients 
with complete data and the model built on the full dataset of 150 patients with incomplete 
observations will be equivalent, we will compare the survival curves for patients included 
in the complete and incomplete data sets to verify this assumption.
13.2     Disposition of Data - Data Management and Monitoring
13.2.1  Data-Sharing Agreement with Amrita Institute of Medical Sciences (Cochin
India)
Investigators at the Amrita Institute of Medical Sciences (AIMS) in Cochin India and 
NYUSOM agree to participate in a data-sharing arrangement for the investigation of 
outcomes  yielded  from  this  study.  Specifically,  patient  demographic  and  clinical 
treatment data, toxicity data, and pathological outcomes are to be collected and stored 
locally at AIMS, and subsequently de-identified and shared with investigators at 
NYUSOM for the purpose of joint analysis and reporting in co-authored presentations 
and scientific papers.
13.2.2  Database Properties
Data  will  be  entered  into  the  Oracle  Clinical  database  and  maintained  at 
NYUSOM under the direction of staff in the BDM core. De-identified data to be 
shared from the AIMS site will be kept in a distinct, parallel Oracle Clinical 
database maintained at NYUSOM, separate from the NYUSOM generated data. 
This will allow for comparison.
The Oracle system provides audit trails that track creation and modification of 
records that include userid and timestamp. Once entered, the data is subjected to 
validation procedures that are executed either immediately or upon saving the 
eCRF page or during the batch validation process. Validation failures that are 
identified before the page is saved can be corrected immediately. Validation 
failures during saving of the eCRF page and during batch validation processes 
will generate a discrepancy. Depending on the database account privileges, the 
data managers may be able to correct a discrepancy or if not, route it to the project

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data manager at NYU who can take appropriate action to correct the problem. 
Data clarification forms can also be printed out when necessary to be sent to the 
project  data  manager  at  NYU.  Once  the  discrepancy  is  closed,  by  marking
―resolved‖  or  ―irresolvable‖,  the  data  is  marked  clean  and  an  audit  trail  is
generated by the system.
All key end points will be source verified by a second person at each site and 
errors will be corrected. Once the data is verified and all discrepancies are closed, 
the data can be locked/frozen. Locking and freezing can be done at different 
granular levels and will follow institutional SOPs and any specific requirements 
for the project.
Security measures that will be taken in order to protect patient data will include 
firewall technology and database level security which will be achieved by 
assigning roles and privileges to different levels of users and by requiring that the 
users authenticate themselves using userid and password. Additional security for 
data transfer between remote clients and servers will be achieved by using digital 
certificates/SSL. All data will be backed-up to tape periodically according to the 
Institutional SOPs. All data will be stored for at least 5 years following the 
termination of this study.
13.3     Microarray data
The data generated from microarray experiments will be stored using GeneTraffic, a
client-server relational database currently in use by NYU Bioinformatics Group. 
GeneTraffic can also store all microarray files generated by the Affymetrix system and 
by two-color microarray systems. It can store TIFF images as well as output from all of 
the common image analysis programs. The data can be stored as raw images and tables of 
signal  intensities  for  each  probe  and  gene.  GeneTraffic  also  provides  advanced 
algorithms for data normalization and analysis at the level of individual probes. 
Additionally, GeneTraffic software incorporates MIAME guidelines during data 
annotation and has project tracking features, data searching algorithms, data exploration 
and visualization.
The database is accessible over the Internet from other institutions, making it 
simple for members of the COE to collaborate on microarray projects. Data can be 
uploaded and analyzed from any workstation via a web interface, onto a server that is 
maintained in a secure data center and backed up automatically to tape. With the 
appropriate  permissions  (userid  and  password),  users  can  directly upload  data  for  a 
project, or view data that has been loaded and analyzed at NYU. Data will be stored for 
no less than 5 years following completion of this study.
14.       DEVIATION FROM THE PROTOCOL
No modifications to the protocol should be made without the approval of the PI, the 
NYUCI IRB.. Changes that affect the study design including numbers of patients, safety 
of patients, the scope of the investigation, or the scientific quality or efficacy of the study 
will require IRB notification prior to implementation, except where the modification is 
necessary to eliminate an immediate and apparent hazard to patients. If an immediate 
departure from the protocol is necessary, the Investigator will contact the

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PI to discuss the planned  course of action.  If possible,  contact  should  be made prior to the 
implementation of any changes.  Any departures from  protocol  must  be fully documented 
in the Case Report  Form and source  documentation. .

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