An Evaluation of a Multi-target Stool DNA (Mt-sDNA) Test, Cologuard, for CRC Screening in Individuals Aged 45-49 and at Average Risk for Development of Colorectal Cancer: Act Now
Conditions: Colorectal Cancer
Sponsor: Exact Sciences Corporation

 
 
 
2018-10 Protocol V.1 
 
 
An Evaluation of a Multi-Target Stool DNA (mt-sDNA) Test, Cologuard, for CRC Screening in 
Individuals Aged 45-49 and at Average Risk for Development of Colorectal Cancer: Act Now 
 
 
NCT Number: NCT03728348 
 
 
Document Date: September 21st, 2018 

Document Type: 
Master Clinical Protocol 2018-10 
1 Protocol 2018-10 v1.0 
AN EVALUATION OF A MULTI-TARGET STOOL 
DNA (mt-sDNA) TEST, COLOGUARD, FOR CRC 
SCREENING IN ASYMPTOMATIC INDIVIDUALS 
AGED 45-49 AND AT AVERAGE RISK FOR 
DEVELOPMENT OF COLORECTAL CANCER 
Investigational plan
Study Title: 
An Evaluation of a Multi-target Stool DNA (mt-sDNA) Test, Cologuard, for CRC 
Screening in Asymptomatic Individuals Aged 45-49 and at Average Risk for 
Development of Colorectal Cancer 
Study Number:   
2018-10 
Version and Date: 
Protocol Version 1.0, September 21, 2018 
Study Sponsor:  
Exact Sciences 
441 Charmany Drive 
Madison, WI 53719  
Sponsor Contact: 
: 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
2 Protocol 2018-10 v1.0 
 
INVESTIGATOR SIGNATURE 
Protocol Title: An Evaluation of a Multi-target Stool DNA (mt-sDNA) Test, Cologuard, for CRC Screening 
in Asymptomatic Individuals Aged 45-49 and at Average Risk for Development of Colorectal Cancer 
Protocol Version and Date: Protocol Version 1.0, September 21, 2018 
I have read the protocol and agree to: 
• Conduct the investigation in accordance with this protocol, ICH GCP E6 (R2), applicable national, state 
and local laws and regulations, and conditions of approval imposed by the reviewing IRB/EC; 
• Supervise all activities involved in this study when study responsibilities are delegated; 
• Ensure that the requirements for obtaining informed consent are met; 
• Provide sufficient and accurate financial disclosure information and update information if any relevant 
changes occur during the investigation and for one year following the completion of the study; 
• Maintain the confidentiality of all information received or developed in connection with this protocol; 
• Adhere to the publication policy of Exact Sciences for data collected during this trial; 
• Not initiate this study without approval from the appropriate Institutional Review Board (IRB)/Ethics 
Committee (EC) and understand that any changes to the protocol must be approved in writing by the 
Sponsor and the IRB/EC before they can be implemented, except where necessary to eliminate 
immediate risks to the subject. 
 
______________________________________                                     ________________________ 
Signature of Principal Investigator 
  
 
 
 
Date 
 
_______________________________________ 
Printed Name of Principal Investigator 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
3 Protocol 2018-10 v1.0 
 
Table of Contents 
1 
LIST OF ABBREVIATIONS ................................................................................................................... 6 
2 
DISCLOSURE STATEMENT ................................................................................................................. 7 
3 
PROTOCOL SYNOPSIS ....................................................................................................................... 7 
4 
BACKGROUND / RATIONALE .............................................................................................................. 8 
4.1 
Background ............................................................................................................................... 8 
4.2 
Rationale ................................................................................................................................... 9 
5 
OBJECTIVES ......................................................................................................................................... 9 
5.1 
Primary Objective ...................................................................................................................... 9 
6 
ENDPOINTS .......................................................................................................................................... 9 
6.1 
Primary Endpoint ....................................................................................................................... 9 
6.2 
Other Outcomes ........................................................................................................................ 9 
7 
STUDY DESIGN .................................................................................................................................. 10 
8 
STUDY DEVICE .................................................................................................................................. 10 
8.1 
Description of the Investigational Device ................................................................................ 10 
8.2 
Regulatory History ................................................................................................................... 10 
9 
SUBJECT SELECTION AND WITHDRAWAL ..................................................................................... 11 
9.1 
Inclusion Criteria...................................................................................................................... 11 
9.2 
Exclusion Criteria .................................................................................................................... 11 
9.3 
Subject Withdrawal.................................................................................................................. 12 
9.4 
Subject Replacement .............................................................................................................. 12 
10 
STUDY PROCEDURES .................................................................................................................. 12 
10.1 
Overview ................................................................................................................................. 12 
10.2 
Enrollment ............................................................................................................................... 12 
10.3 
Blood Sample Collection ......................................................................................................... 12 
10.4 
Stool Sample Collection .......................................................................................................... 12 
10.5 
Sample Assays ........................................................................................................................ 13 
10.6 
Colonoscopy and Histopathology ............................................................................................ 13 
10.6.1 
Colonoscopy Procedure ...................................................................................................... 13 
10.6.2 
Colonoscopy and Histopathology Reports .......................................................................... 14 
10.7 
Data Collection ........................................................................................................................ 15 
10.8 
End of Study ............................................................................................................................ 15 
10.9 
Sample Retention .................................................................................................................... 15 
10.10 
Unusable Samples .................................................................................................................. 15 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
4 Protocol 2018-10 v1.0 
 
11 
ADVERSE EVENT REPORTING.................................................................................................... 15 
11.1 
Definition of Adverse Events ................................................................................................... 15 
11.2 
Reporting Period ..................................................................................................................... 16 
11.3 
Serious Adverse Events .......................................................................................................... 16 
11.4 
Unanticipated Adverse Events ................................................................................................ 16 
11.5 
Reporting Requirements ......................................................................................................... 16 
11.5.1 
SAE Reporting Requirements ............................................................................................. 16 
11.5.2 
Non-Serious Adverse Event Reporting Requirements........................................................ 17 
11.5.3 
Reporting Requirements of Unanticipated Adverse Devices Effects (UADEs) .................. 17 
11.5.4 
Sponsor Reporting Requirements to Regulatory Authorities .............................................. 17 
12 
DATA ANALYSIS AND STATISTICAL METHODS ........................................................................ 17 
12.1 
Effectiveness Endpoints .......................................................................................................... 17 
12.1.1 
Definitions ............................................................................................................................ 17 
12.2 
Primary Endpoint ..................................................................................................................... 18 
12.3 
Sample Size and Rule Out Lower Threshold Justification ...................................................... 19 
12.3.1 
Analysis Approach, Primary Effectiveness Analysis ........................................................... 19 
12.4 
Other Prespecified Analyses ................................................................................................... 20 
12.4.1 
Additional Analysis .............................................................................................................. 20 
12.5 
Handling of Missing Data ........................................................................................................ 20 
12.6 
General Statistical Methods .................................................................................................... 20 
12.6.1 
Categorical Variables .......................................................................................................... 20 
12.6.2 
Continuous Variables .......................................................................................................... 20 
12.6.3 
Determination of Diagnostic Accuracy ................................................................................ 21 
13 
QUALITY CONTROL AND QUALITY ASSURANCE ...................................................................... 21 
14 
DATA HANDLING AND RECORD KEEPING ................................................................................. 21 
14.1 
Protocol Deviations ................................................................................................................. 21 
14.2 
Direct Access to Source Data/Documents .............................................................................. 22 
14.3 
Case Report Forms (CRFs) .................................................................................................... 22 
14.4 
Records Retention................................................................................................................... 22 
15 
ETHICS ........................................................................................................................................... 23 
15.1 
Risk Analysis ........................................................................................................................... 23 
15.1.1 
Risk to the subject ............................................................................................................... 23 
15.1.2 
Benefit to Subject ................................................................................................................ 23 
15.2 
Institutional Review Board (IRB) / Ethics Committee (EC) ..................................................... 23 
15.3 
Ethical Conduct of the Study ................................................................................................... 23 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
5 Protocol 2018-10 v1.0 
 
15.4 
Subject Information and Consent ............................................................................................ 23 
15.5 
Reporting of Safety Issues and Serious Breaches of the Protocol or GCP ............................ 24 
16 
A DEFINITION OF END TRIAL ....................................................................................................... 24 
17 
SPONSOR DISCONTINUATION CRITERIA .................................................................................. 24 
18 
AUDITING PROCEDURES ............................................................................................................. 24 
19 
REFERENCES ................................................................................................................................ 25 
APPENDIX 1.0 – STUDY SCHEMA ........................................................................................................... 26 
APPENDIX 2.0 – STUDY SCHEDULE ....................................................................................................... 27 
APPENDIX 3.0 – GUIDELINES FOR COLONOSCOPY ............................................................................ 28 
APPENDIX 4.0 – GUIDELINES FOR PATHOLOGY REVIEW AND DOCUMENTATION ......................... 29 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
6 Protocol 2018-10 v1.0 
 
1 
LIST OF ABBREVIATIONS 
Abbreviation 
Definition 
AA 
Advanced Adenoma 
AE 
Adverse Event 
CRC 
Colorectal Cancer 
CRF 
Case Report Form 
CUC 
Chronic Ulcerative Colitis 
DNA 
Deoxyribonucleic Acid 
EC 
Ethics Committee 
FAP 
Familial Adenomatous Polyposis 
FDA 
Food and Drug Administration 
FIT 
Fecal Immunochemical Test 
FoBT 
Fecal Occult Blood Test 
GCP 
Good Clinical Practice 
IBD 
Inflammatory Bowel Disease 
ICH 
International Council for Harmonization  
IRB 
Institutional Review Board 
IVD 
In Vitro Diagnostic 
HNPCC 
Hereditary Non-Polyposis Colorectal Carcinoma (Lynch Syndrome) 
MSTF 
Multi Society Task Force 
mt-sDNA 
Multi-target stool DNA 
SAE 
Serious Adverse Event 
UADE 
Unanticipated Adverse Device Effect 
USPSTF 
United States Preventive Services Task Force 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
7 Protocol 2018-10 v1.0 
 
2 
DISCLOSURE STATEMENT 
This document contains information that is confidential and proprietary to Exact Sciences. This 
information is being provided to you solely for the purpose of evaluating and/or conducting a clinical study 
for the Sponsor.  You may disclose the contents of this document only to study personnel under your 
supervision, institutional review boards (IRBs)/ ethics committees (ECs), or duly authorized 
representatives of regulatory agencies for this purpose under the condition that they maintain 
confidentiality. The contents of this document may not be used in any other clinical study, disclosed to 
any other person or entity, or published without the prior written permission of the Sponsor.  The 
foregoing shall not apply to disclosure required by any regulations; however, you will give prompt notice 
to the Sponsor of any such disclosure.  All other nonpublic information provided by the Sponsor, as well 
as any information that may be added to this document, also is confidential and proprietary to the 
Sponsor and must be kept in confidence in the same manner as the contents of this document. 
3 
PROTOCOL SYNOPSIS 
Primary Objective: 
The primary objective is to confirm the specificity of the 
multi-target stool DNA test (mt-sDNA), Cologuard, in an 
average risk population, ages 45-49.    
Study Design: 
Prospective, cross-sectional, multi-center study 
Investigational Device 
Multi-target stool DNA test (mt-sDNA), Cologuard, 
(Exact Sciences, Madison, WI)  
Population: 
Subjects 45-49 years of age who are at average risk for 
development of CRC. 914 subjects are targeted to 
enroll. 
Primary Endpoint: 
The primary endpoint of this study is specificity of the 
mt-sDNA test (Cologuard) in the 45-49 age group in an 
average risk population, using colonoscopy with 
histopathology (when required) as the reference 
method.  The primary analysis requires the one-sided 
97.5% lower bound of the specificity of Cologuard to 
exceed 85.0%. 
Study Duration: 
Duration of study participation for each subject will be 
approximately 60 days from enrollment into the study. 
Study Procedures: 
Subjects providing written informed consent to 
participate in the study will complete the mt-sDNA test 
(Cologuard) followed by a screening colonoscopy which 
should be completed within approximately 60 days of 
enrollment. Subjects may also choose to consent to 
2018-10B and provide a blood sample at the time of 
enrollment. 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
8 Protocol 2018-10 v1.0 
 
4 
BACKGROUND / RATIONALE 
4.1 Background 
The 2018 American Cancer Society colorectal cancer (CRC) screening guideline [1] now recommends 
initiating colorectal cancer (CRC) screening at age 45 in asymptomatic, average risk individuals. This 
change in a prominent national guideline was based on recent data [2] showing that the incidence of CRC 
in the 40-49 age group has increased with that of the 45-49-year-old group similar to that of 50-54-year-
olds. There has been a 51% increase in the incidence of CRC from 1994 to 2014 and an 11% increase in 
mortality from 2005 to 2015 among individuals 55 years old and younger. Importantly, this change 
appears to be a birth cohort effect, likely starting for those born in the early 1950s who will carry this 
increased risk forward for their lifetimes. Compared to birth cohorts between 1890-1950 where the rate of 
CRC has been steadily declining, the rate in those generations born after 1950 has been steadily 
increasing. The ACS estimates that in 2014, over 7,073 cases of CRC were diagnosed in individuals 
aged 45 to 49 years with over 16,450 cases diagnosed in patients under 50.   
 Rising incidence of CRC in 40-49-year-olds compared to decreasing incidence in those 50 years 
of age and older (from Siegel R et al JNCI 2017 [2]). 
 
Previously, a recommendation for starting at age 45 in average risk individuals was proposed by the 2009 
American College of Gastroenterology guideline in African Americans [3] and reiterated in the 2017 U.S. 
Multi-Society Task Force CRC screening guideline [4]. The USMSTF includes members of the American 
Gastroenterological Association, the American College of Gastroenterology, and the American Society of 
Gastrointestinal Endoscopy. While the 2016 United States Preventive Services Task Force guideline did 
not recommend starting screening at age 45 [5] and continued to give its “A” rating to screening 
asymptomatic average risk individuals from ages 50-75, the data supporting a cohort effect generally 
showing increased risk in younger individuals were not available when the USPSTF reviewed the CRC 
screening evidence base prior to the 2016 guideline update.  
According to Dr. Thomas Weber, former Chair of the National Colorectal Cancer Roundtable and director 
of surgical oncology for the northwest region of Northwell Health, as quoted in the N.Y Times [6], “Solid 
epidemiological data from our national cancer registries documents a dramatic increase in the incidence 
of colon and especially rectal cancer among individuals under the age of 50, and the vast majority of 
those cases are in the 40- to 49-year-old age bracket.”  
Importantly, the ACS guideline includes the multi-target stool DNA test as one of the recommended 
methods for CRC screening, including for the expanded age range of 45-49 years of age. The ACS 
Guideline development group states, “The GDG concluded that mt-sDNA warrants inclusion among test 
options based on its sensitivity for detecting CRC, its improved advanced adenoma and serrated sessile 
polyp detection compared with FIT, and evidence indicating that some adults would choose screening 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
9 Protocol 2018-10 v1.0 
 
with mt-sDNA over other CRC screening tests.”[7] Currently the labeled indication for mt-sDNA includes 
average risk asymptomatic individuals 50 years of age and older.  In order to accommodate this change 
in medical practice, Exact Sciences wishes to expand the labeled indication for mt-sDNA into this 45-49 
age group. 
4.2 Rationale 
Given its high sensitivity for CRC and advanced pre-cancers demonstrated in the mt-sDNA pivotal study 
[8],and given the safety of mt-sDNA as a non-invasive stool-based test, mt-sDNA could be an important 
option for patients and providers in this younger age group. 
 
 
 
 
 
. 
The study is designed to provide additional evidence of test performance in this age group to support an 
application for FDA label expansion. Biologically, there is little reason to believe there is a significant 
difference in the underlying mechanism of CRC in average risk individuals age 45-49 vs. 50-59, which is 
included in the current label.  
5 
OBJECTIVES 
5.1 Primary Objective 
The primary objective is to confirm the specificity of the mt-sDNA test (Cologuard) in an average risk 
population, ages 45-49.     
6 
ENDPOINTS 
6.1 Primary Endpoint 
The primary endpoint of this study is specificity of the mt-sDNA test (Cologuard) in the 45-49 age group in 
an average risk population, using colonoscopy with histopathology (when required) as the reference 
method.  The primary analysis requires the one-sided 97.5% lower bound of the specificity of Cologuard 
to exceed 85.0%. 
6.2 Other Outcomes  
Other outcomes to be assessed include the following 
• 
Sensitivity for CRC + advanced adenoma  
• 
The positive and negative predictive values 
• 
The positive and negative likelihood ratios (PLR and NLR, respectively) 
• 
The distribution of colorectal epithelial lesions (by Category) among positive mt-sDNA test 
(Cologuard) subjects  
• 
The rate of no mt-sDNA (Cologuard) result  
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
10 Protocol 2018-10 v1.0 
 
7 
STUDY DESIGN 
This is a prospective, cross-sectional, multi-center study to confirm the specificity of the mt-sDNA test 
(Cologuard) in average risk individuals ages 45 to 49.   
All subjects enrolled into the study will be provided a stool collection kit for the mt-sDNA test (Cologuard) 
and scheduled for a screening colonoscopy.  Stool sample collection must occur prior to subjects initiating 
bowel preparation for the colonoscopy procedure. All subjects will undergo a screening colonoscopy 
within approximately 60 days of enrollment. 
The results of the mt-sDNA test (Cologuard) will be compared with the results of the colonoscopy and 
with any corresponding diagnostic histopathology results from biopsies or excised tissues obtained for 
clinical purposes to confirm the performance estimates. 
Stool samples collected by the subject for the mt-sDNA test (Cologuard) will be sent to Exact Sciences 
Laboratories and tested. Individuals conducting the mt-sDNA tests will be blinded to all subject clinical 
information, including colonoscopy results.  Investigators, subjects, and endoscopists will be blinded to 
the mt-sDNA test (Cologuard) results, and the results of the tests will not be used for clinical management 
of study subjects.  
All subjects enrolled in the study will also be offered the opportunity to provide a blood sample for 
biomarker evaluation and assay optimization (Protocol 2018-10B). Blood samples will be used for 
research on biomarkers from plasma and serum. 
8 
STUDY DEVICE 
8.1 Description of the Investigational Device 
The mt-sDNA-based test (Cologuard) is a colorectal cancer screening option that consists of a stool 
collection kit and proprietary assay methodologies for the detection of fecal hemoglobin and fecal DNA 
markers known to be associated with CRC 
 
. Cologuard is approved by the FDA for use in average risk adults 
ages 50 years or older.  Cologuard has not been evaluated in average risk individuals under the age of 
50. 
The Stool Collection Kit includes: Sample Collection Instructions, a stool collection container and support 
bracket, a bottle of liquid sDNA preservative, a fecal hemoglobin sample tube, return shipping box, and 
return shipping label. The stool collection kits will be labeled as investigational use only. The stool 
collection kits will be provided by the Sponsor. The sites are responsible for management of the stool 
collection kits. The investigator must maintain complete and current accountability records (including kit 
receipt, dispensation, and return) for all kits supplied by the Sponsor.  All unused kits and their original 
packaging should be kept on-site for reconciliation by a site monitor. The site must return all unused kits 
and packaging after accountability has been performed at the end of the study. Stool collection kit return 
must be documented in the accountability records.  
8.2 Regulatory History 
Cologuard received Pre-Market Approval from the U.S. Food & Drug Administration on August 11, 2014 
(P130017) (as well as approval for subsequent PMA supplements) with the following Indication for use: 
Cologuard is intended for the qualitative detection of colorectal neoplasia associated DNA markers and 
for the presence of occult hemoglobin in human stool. A positive result may indicate the presence of CRC 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
11 Protocol 2018-10 v1.0 
 
or AA and should be followed by diagnostic colonoscopy. Cologuard is indicated to screen adults of either 
sex, 50 years or older, who are at typical average-risk for CRC. Cologuard is not a replacement for 
diagnostic colonoscopy or surveillance colonoscopy in high risk individuals.  
9 
SUBJECT SELECTION AND WITHDRAWAL 
914 subjects are targeted to enroll. The following eligibility criteria are designed to select subjects who are 
at average risk for development of CRC.  All relevant medical and non-medical conditions should be 
taken into consideration when deciding whether this protocol is suitable for a particular subject.  No 
waivers to these criteria will be permitted. 
9.1 Inclusion Criteria  
Subjects must meet the following criteria to be eligible for the study: 
1. Subject is at average risk for development of CRC.  
2. Subject is asymptomatic with respect to those symptoms that would ordinarily result in a 
colonoscopy to rule out CRC or clinical work-up for gastrointestinal pathology or disease. 
3. Subject is 45-49 years of age at the time of enrollment through expected study completion, 
approximately 60 days after enrollment.  
4. Subject is willing and able to sign informed consent. 
 
9.2 Exclusion Criteria 
Subjects presenting with any of the following will not be included in the study: 
1. Subject has a personal history of CRC. 
2. Subject has ≥2 first-degree relatives who have been diagnosed with colon cancer.  
3. Subject has a first degree relative with CRC diagnosed before the age of 60. 
4. Subject has any of the following: 
• 
Overt rectal bleeding, e.g., hematochezia or melena (blood on toilet paper, after wiping, does 
not constitute rectal bleeding). 
• 
Unexplained iron deficiency anemia with a severity that would indicate a workup for 
gastrointestinal bleeding within the previous six (6) months.  
• 
Positive fecal occult blood test or FIT within the previous six (6) months.  
• 
Subject has had a previous colonoscopy.  
5. Subject has a known syndromic hereditary condition (FAP, HNPC, etc.) or has a documented first 
degree relative with a known heritable cancer syndrome, including: 
• 
Familial adenomatous polyposis (also referred to as "FAP", including attenuated FAP and 
Gardner’s syndrome). Hereditary non-polyposis CRC syndrome (also referred to as 
"HNPCC" or "Lynch Syndrome"). 
• 
Other hereditary cancer syndromes including but are not limited to Peutz–Jeghers 
Syndrome, MYH-Associated Polyposis (MAP), Turcot's (or Crail’s) Syndrome, Cowden's 
Syndrome, Juvenile Polyposis, Neurofibromatosis and Familial Hyperplastic Polyposis. 
6. Subjects with Cronkhite-Canada Syndrome. 
7. Subject has a diagnosis or personal history of inflammatory bowel disease (IBD) including chronic 
ulcerative colitis (CUC) and Crohn's disease. 
8. Subject has a history of non-colorectal aerodigestive tract cancer. 
9. Subject has had a prior colorectal resection for any reason other than sigmoid diverticular 
disease. 
10. Subject has any condition that in the opinion of the investigator should preclude participation in 
the study. 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
12 Protocol 2018-10 v1.0 
 
9.3 Subject Withdrawal 
Subjects may be withdrawn from the study by any of the following mechanisms: 
1. Voluntary withdrawal of consent to participate by the subject at any time during the study. 
2. Determination by the clinical investigator that it is in the best interest of the subject. 
3. Determination by the Sponsor it is in the best interest of the subject or study. 
4. Stool sample not provided within 30 days of enrollment. 
5. Colonoscopy procedure is not done.  
All data available from enrollment to subject withdrawal will be collected unless the subject withdraws 
consent from the study.  Data for all study visits will be collected for subjects who discontinue participation 
but who do not withdraw consent.  Withdrawal of consent must be documented by site personnel in the 
subject source record. 
9.4 Subject Replacement 
Enrolled subjects may be replaced for any of the following reasons: 
1. No stool sample provided and/or no completed colonoscopy procedure.  
2. A valid stool sample result cannot be obtained for a subject after two (2) attempts (Section 10.4). 
10 STUDY PROCEDURES 
10.1 Overview 
Individuals ages 45 to 49 who are at average risk for development of CRC will be invited to participate in 
the study. 914 subjects are targeted to enroll. Subjects providing written informed consent to participate in 
the study will complete the mt-sDNA test (Cologuard) followed by a screening colonoscopy which should 
be completed within approximately 60 days of enrollment. Subjects may also choose to consent to 2018-
10B and provide a blood sample at the time of enrollment. 
Refer to Appendix 1.0 – Study Schema and Appendix 2.0 – Schedule of Activities  
10.2 Enrollment 
Subjects are considered enrolled once written informed consent is obtained and subject eligibility 
confirmed.  
10.3 Blood Sample Collection 
If the subject also consents to 2018-10B, approximately 40 mL of peripheral blood will be collected from 
the subject. Blood sample collection should occur on the same day as enrollment. The Sponsor will 
provide the site with blood sample collection, processing, and shipping procedures.  
10.4 Stool Sample Collection 
Enrolled subjects will complete the mt-sDNA test (Cologuard) prior to bowel preparation for the 
colonoscopy procedure. Subjects enrolled into the study will be provided with a Stool Collection Kit.  Stool 
samples must be collected prior to initiation of bowel preparation for the colonoscopy procedure.  Stool 
samples will be collected by following the instructions provided. Instructions for kit return are provided to 
the subject with the Stool Collection Kit. 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
13 Protocol 2018-10 v1.0 
 
The shipment and arrival of the Stool Collection Kit at Exact Sciences Laboratories will be tracked. Once 
the sample arrives at Exact Sciences Laboratories, it will be inspected for acceptability per the 
specifications outlined in the Cologuard Instructions for Use. If the stool sample is not collected according 
to the instructions for use or damaged in a way that compromises the specimen, a repeat sample 
collection may be requested if the collection can occur prior to the initiation of bowel preparation for the 
scheduled colonoscopy. The site will be asked to contact the subject to request another stool specimen.  
At that time, another stool collection kit will be dispensed to the subject by the site.   
10.5 Sample Assays 
Assay results will be recorded as 'Positive', 'Negative', ’Sample Could Not Be Processed’, or ‘No 
Result Obtained.’ If there are no valid results, a repeat test may be requested. Repeat stool sample 
requests will be sent to the site. Repeat stool sample collection must occur prior to bowel 
preparation for the colonoscopy procedure. If a valid stool sample result cannot be obtained for a 
subject after two (2) attempts, the subject will be withdrawn and may be replaced.   
 
The mt-sDNA test (Cologuard) result will not be provided to investigators for clinical management of 
study subjects. All mt-sDNA test results will remain blinded to investigators and study subjects.   
 
10.6 Colonoscopy and Histopathology 
Every subject will undergo a screening colonoscopy after completing a mt-sDNA test (Cologuard) test.  
Colonoscopies should occur as soon as possible following informed consent and stool collection.  
Subjects who have poor bowel preparation and will not repeat the procedure or subjects who do not 
complete a colonoscopy should be withdrawn and may be replaced. Bowel preparation procedures and 
colonoscopy will be performed following the usual practice at each clinical site. Personnel performing the 
colonoscopy and producing the resulting report and the personnel performing the histopathological 
review of tissue will remain blinded to the results of the mt-sDNA test (Cologuard) result.  
10.6.1 Colonoscopy Procedure 
Bowel preparation procedures and colonoscopy will be performed following standard of care at each 
clinical site.  The colonoscopist will record the quality of the bowel preparation (after washing/suctioning) 
as follows:  
• Excellent: minimal fecal residue and liquid, small volume of liquid easily aspirated, <5% of 
colonic surface covered;  
• Good: small amounts of fecal residue, volume of clear liquid covering 5-25% of surface, easily 
aspirated;  
• Fair: moderate amounts of fecal residue; stool limited examination but >90% could be 
examined; or  
• Poor: large amounts of stool, <90% of surface could be examined.  
Cecal intubation will be documented with photographic evidence and/or documentation of cecal 
intubation; and colonoscope withdrawal time will be recorded. Withdrawal time is defined as the time from 
cecal identification to the time when the colonoscope is withdrawn across the anus (Barclay, Vicari, 
Doughty, et al, 2006.).  

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
14 Protocol 2018-10 v1.0 
 
A bowel preparation considered excellent, good, or fair will be acceptable. Subjects with no findings on 
the colonoscopy, and no photographic evidence of cecal intubation or no documentation of cecal 
intubation in the report, will be deemed to have a failed colonoscopy. These subjects will be deemed to 
be unevaluable and therefore will be excluded from analysis of the primary and secondary endpoints.  
Those subjects determined to have had a poor bowel preparation (after washing/suctioning) may repeat 
the colonoscopy again if the Investigator feels this is in the best interest for the subject. The subject may 
repeat the colonoscopy procedure. A repeat stool specimen is not required.  
A completed colonoscopy procedure will be considered and defined as: reaching the cecum (or) reaching 
the junction between the small and large intestine (in the event the cecum has been resected). 
A colonoscopy wherein a CRC or AA was identified will be included in the analyses regardless of any 
limiting factors experienced during the colonoscopy. 
10.6.2 Colonoscopy and Histopathology Reports 
Colonoscopy findings will be recorded on the colonoscopy reports per site-specific standard of practice. 
Histopathology interpretation of tissue samples will be conducted according to each of the clinical site’s 
local histopathology practice provider(s) as used for daily patient management.  
Subjects who have lesions identified by colonoscopy that are neither biopsied initially nor excised 
subsequently or that are lost during lesion retrieval and, therefore, not submitted for histopathologic 
analysis, will be identified by the sites, and the colonoscopy report will be sent to the study central 
pathologist(s) for review. Because of the absence of confirmatory histopathologic diagnosis, these 
subjects will be excluded from the study based on the fact that they cannot be categorized for the study 
analysis.  
The sites will grant independent central pathologist(s) access to colonoscopy, surgical, and 
histopathological reports by providing them a copy of those reports. All protected health information on 
the documents will be removed before release to the central pathologist(s). The study-specific subject 
identification number will be used to identify colonoscopy reports and applicable histopathology reports 
submitted to the central pathologist(s). 
Histopathological results will be categorized as defined in Appendix 4. For subjects that undergo surgical 
removal of CRC and/or non-CRC lesions, an excisional surgical pathology report should be available. To 
ensure diagnostic accuracy, investigative sites with subjects diagnosed with CRCs or AAs may be 
required to provide representative histology slides for review by a central pathologist. When the central 
pathologist histopathology result differs from the local histopathology result, the results will be adjudicated 
with a review and interpretation by a second central pathologist.  
Patient management will be conducted locally at each investigative site based upon colonoscopy 
outcomes and the histopathology results reported by the local pathology lab. In the event that the 
centralized histopathology laboratory assigns a higher-grade histology result than the local histopathology 
laboratory, the Investigator will be notified. The Investigator should maintain the central pathology results 
with the subject’s source records. The central pathology laboratory results may not be available prior to 
the subsequent treatment of the subject. 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
15 Protocol 2018-10 v1.0 
 
10.7 Data Collection 
Subject data will be collected on CRFs and provided to the Sponsor. After subjects have provided 
informed consent, demographics, medical history, social history, and family history will be obtained. The 
clinical site will send a copy of available colonoscopy reports and applicable histopathology reports and/or 
other diagnostic information to the Sponsor. All reports that are provided to the Sponsor will be de-
identified of all protected health information, prior to submission to the Sponsor.  
10.8 End of Study 
Subjects will be considered completed from the study when they have provided a stool sample and have 
completed their colonoscopy procedure, OR at the point of subject withdrawal per Section 9.3. 
 
Ensure all data is assessed, entered into the CRF and reporting on AEs/SAEs, UADEs, and/or Protocol 
Deviations has occurred, if necessary. 
 
10.9 Sample Retention 
Retained samples comprise of residual stool samples. Retained subject samples will not be used other 
than to develop and evaluate the performance of biomarker assays to detect cancers. Retained samples 
will be de-identified of all protected health information, and clinical study data will only be associated by a 
subject identification number. Samples will be stored for no more than 20 years in Exact Sciences’ or 
designee’s on-site biorepository and will be used for developing and evaluating the performance of 
biomarker assays for cancer detection. Specimens de-accessioned from the biorepository will be 
destroyed under standard biohazardous material protocol and record of the removal and destruction will 
be maintained for 7 years by the Sponsor. Retained subject samples will not be used for any other 
purposes.   
10.10 Unusable Samples 
Subjects who provide stool samples which are insufficient for testing may be asked to provide another 
stool sample if the subject has not yet begun bowel preparation for colonoscopy.  
11 ADVERSE EVENT REPORTING 
11.1 Definition of Adverse Events 
An adverse event (AE) is any unfavorable or unintended sign, symptom, or disease temporally associated 
with the use of an investigational product or protocol-imposed intervention, regardless of attribution. 
 
 
 
 The liquid buffer/liquid preservative in the quantities provided is non-toxic. 
An AE may be investigated as an Unanticipated Adverse Device Effect (UADE), if applicable. 
 
Adverse events commonly associated with colonoscopy will not be collected. Such events 
include: Abdominal discomfort, bowel irregularity, bleeding, intestinal perforation, and adverse 
reaction to the sedation.   
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
16 Protocol 2018-10 v1.0 
 
Surgical intervention, such as, but not limited to, colectomy and sub-mucosal resection are part 
of routine patient care for subjects with CRC or AA; therefore, adverse events commonly 
associated with surgeries will not be collected. Such events include: Bleeding, blood clots in the 
legs (deep vein thrombosis) and lungs (pulmonary embolism); infection; injury to organs near the 
colon, such as the bladder and small intestines; and tears in the sutures that reconnect the 
remaining parts of the digestive system.  
 
11.2 Reporting Period 
Adverse events will only be recorded for events that occur during or otherwise associated with the subject 
use of the mt-sDNA test (Cologuard), specifically the stool sample collection procedure. AEs are collected 
from the time of enrollment to return of the Stool Collection Kit.  All AEs will be reported on the adverse 
event page(s) of the CRF. 
11.3 Serious Adverse Events 
Serious adverse events are not expected for this study but will be reported to the Sponsor if they occur. 
A serious adverse event (SAE) is any AE that results in one or more of the following outcomes. 
• 
Death; Note: “Death” should not be reported as an SAE.  The cause of death should be reported 
as the SAE.  The only exception is “Sudden Death” when the cause is unknown. 
• 
A life-threatening illness or injury; 
• 
A permanent impairment of a body structure or a body function; 
• 
Required in-patient hospitalization or prolongation of existing hospitalization; 
• 
Necessitates medical or surgical intervention to prevent permanent impairment of a body 
structure or a body function; or 
• 
Fetal distress, fetal death or a congenital abnormality or birth defect. 
11.4 Unanticipated Adverse Events 
An unanticipated adverse device effect (UADE) is “any serious adverse effect on health or safety or any 
life-threatening problem or death caused by, or associated with, a device, if that effect, problem, or death 
was not previously identified in nature, severity, or degree of incidence in the investigational plan or 
application (including a supplementary plan or application), or any other unanticipated serious problem 
associated with a device that relates to the rights, safety, or welfare of subjects” (21 CFR 812.3(s)). 
11.5 Reporting Requirements 
11.5.1 SAE Reporting Requirements 
If a SAE occurs, Exact Sciences or its designee is to be notified within 24 hours of awareness of the event 
by the Investigator. In particular, if the SAE is fatal or life-threatening, notification to Exact Sciences or its 
designee must be made immediately, irrespective of the extent of available adverse event information. 
This timeframe also applies to additional new information (follow-up) on previously forwarded SAE 
reports. 
In the rare event that the Investigator does not become aware of the occurrence of a SAE immediately 
(e.g., if an outpatient study subject initially seeks treatment elsewhere), the Investigator is to report the 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
17 Protocol 2018-10 v1.0 
 
event within 24 hours after learning of it and document the time of his/her first awareness of the adverse 
event. 
For all SAEs, the Investigator is obligated to pursue and provide information to Exact Sciences or its 
designee in accordance with the timeframes for reporting specified above. In addition, the Investigator 
may be requested by Exact Sciences or its designee to obtain specific additional follow-up information in 
an expedited fashion. This information may be more detailed than that captured on the adverse event 
case report form. In general, this will include a description of the adverse event in sufficient detail to allow 
for a complete medical assessment of the case and independent determination of possible causality. 
Information on other possible causes of the event, such as concomitant medications and illnesses must 
be provided. In the case of a subject death, a summary of available autopsy findings must be submitted 
as soon as possible to Exact Sciences or its designee. SAEs may be reported to the local IRB/EC per 
institutional requirements. 
11.5.2 Non-Serious Adverse Event Reporting Requirements 
All AEs will be reported on the adverse event page(s) of the CRF.  It should be noted that the form for 
collection of SAE information is not the same as the adverse event CRF. 
11.5.3 Reporting Requirements of Unanticipated Adverse Devices Effects (UADEs) 
All UADEs must be reported by the Investigator to the Sponsor within 3 days from identification or 
awareness of the event.  Investigators are responsible for preparing and submitting complete, accurate, 
and timely reports to the reviewing IRB/EC of any UADE occurring during an investigation as soon as 
possible, but in no event later than 10 working days after they first learn of the effect. 
11.5.4 Sponsor Reporting Requirements to Regulatory Authorities 
Exact Sciences will immediately conduct an evaluation of any UADE.  If Exact Sciences determines that 
an UADE presents an unreasonable risk to subjects Exact Sciences shall terminate all investigations or 
parts of investigations presenting that risk as soon as possible. Termination shall occur no later than 5 
working days after the Sponsor makes this determination and not later than 15 working days after the 
Sponsor first received notice of the effect. 
12 DATA ANALYSIS AND STATISTICAL METHODS 
Detailed methodology for summary and statistical analyses of the data collected in this study will 
be documented in a Statistical Analysis Plan.  This document may modify the plans outlined in the 
protocol; however, any major modifications of the primary endpoint definition and/or its analysis 
will also be reflected in a protocol amendment. 
 
12.1 Effectiveness Endpoints 
12.1.1 Definitions 
 
 
Advanced Neoplasia 
(AN) 
Colonoscopic findings that include colorectal cancer (CRC) (category 1) 
and advanced adenoma (AA) (category 2). 
Non-advanced neoplasia 
(NAN) 
Colonoscopic findings ≤ 1.0 cm that exclude colorectal cancer (CRC) 
and advanced adenoma (AA) and include categories 3 – 5. 
Sensitivity (Se) 
The sensitivity (Se)  or true positive fraction of the test is defined as 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
18 Protocol 2018-10 v1.0 
 
TP/(TP + FN) 
Specificity (Sp) 
The specificity (Sp) or true negative fraction of the test is defined as 
TN/(TN+FP) 
False positive fraction 
(FPF) 
The false positive fraction (FPF) is defined as FP/(TN+FP) 
Odds ratio 
The odds ratio (OR) is defined as (TP/FP)/(FN/TN) 
Negative likelihood ratio 
The negative likelihood ratio (NLR) is defined as (1-Se)/(Sp) 
Positive likelihood ratio 
The positive likelihood ratio (PLR) is defined as Se/(1-Sp) 
Negative Predictive 
Value 
The Negative Predictive Value (NPV) is defined as: TN/(FN+TN) and/or 
[Sp*(1-Prevalence)]/[(1-Se)*(Prevalence+Sp*(1-Prevalence)].  
Positive Predictive Value 
The Positive Predictive Value (PPV) is defined as: TP/(TP+FP) and/or 
(Se*Prevalence)/[Se*Prevalence+(1-Sp)*(1-Prevalence)] 
 
12.2 Primary Endpoint 
The primary endpoint of this study is the specificity of the mt-sDNA test (Cologuard) in the 45-49 
age group in an average risk population, using colonoscopy with histopathology (when required) 
as the reference method.  The primary analysis requires the one-sided 97.5% lower bound of the 
specificity of Cologuard to exceed 85.0%. 
 
The primary endpoint of this study is to confirm the specificity of the mt-sDNA test (Cologuard) in 
the 45-49 age group in an average risk population. Specificity will be determined by comparing the 
mt-sDNA test result to the results of optical colonoscopic examination and confirmation of the 
colonoscopic findings by histopathology, if appropriate.  
 
Possible categories of colonoscopic findings are as follows: 
 1. 
CRC, all stages (I-IV); 
 2. 
Advanced adenoma, including the following subcategories: 
2.1 Adenoma with carcinoma in situ or high-grade dysplasia, any size 
2.2 Adenoma, villous growth pattern (> 25%), any size 
2.3 Adenoma > 1.0 cm in size, or 
2.4 serrated lesion, > 1.0 cm in size; 
 3. 
1 or 2 adenoma(s), > 5 mm in size, or < 10 mm/1.0 cm size, non-advanced; 
 4. 
> 3 adenomas, < 10 mm in size, non-advanced; 
 5. 
1 or 2 adenoma(s), < 5 mm in size, non-advanced; 
 6. 
Negative – no neoplastic findings, including the following subcategories: 
6.1 Negative, no colorectal neoplasia upon histopathological review 
6.2 No findings on colonoscopy, no biopsy(s) taken  
 
Subjects with colonoscopic findings in categories 3-6 above will be included in the specificity analysis as 
negative outcomes for the primary endpoint calculation.  Thus, specificity to advanced neoplasia (AN) will 
be calculated for the primary endpoint evaluation. The colonoscopically 'negative' population (category 6) 
will include those subjects with a colonoscopy showing no findings of colorectal neoplasia, non-neoplastic 
disease, and/or hyperplastic polyps < 1 cm in diameter.   
Subjects with no findings on the colonoscopy, no photographic evidence of cecal intubation and no 
documentation of cecal intubation in the report, will be deemed to be unevaluable and therefore will be 
excluded from all analyses.  Subjects found to have occult inflammatory bowel disease (IBD) on 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
19 Protocol 2018-10 v1.0 
 
colonoscopy will be excluded from all analyses.  Subjects with unevaluable Exact CRC screening test 
results will be excluded from the primary endpoint analyses. All excluded cases will be assessed for bias. 
Subjects with colonoscopic/histopathologic findings in category 1 (confirmed colorectal cancer cases) will 
be considered to have a positive outcome and will be included in the CRC sensitivity calculations. Note: 
Due to the low prevalence of CRC in the Age 45-49 group, there will likely be no CRC prospectively 
enrolled in the study, so no endpoints will be designed around CRC sensitivity. Similarly, due to the low 
prevalence of AA in the Age 45-49 group there may only be approximately 29 subjects* with 
colonoscopic/histopathologic findings in category 2 (advanced adenomas) prospectively enrolled in the 
study, so no endpoints will be designed around AA sensitivity.  
*Advanced adenoma prevalence among never-screened individuals aged 45-49 years may be derived, 
based on simulation results, to be 3.92%. 731*3.92%= 29 [9]. 
 
12.3 Sample Size and Rule Out Lower Threshold Justification 
The minimum number of non-advanced neoplasia and negative instances (categories 3-6.2) needed to 
rule out an 85.0% lower bound on the specificity with 90% power for a one-sided test with 2.5% Type 1 
error according to an exact binomial distribution is 225, as outlined in Table 1. Furthermore, the minimum 
sample size needed such that the confidence interval width for the alternative proportion (92.2%) is within 
+/-2.2% (i.e. 92.2%+/-2.2% = 90.0%/94.4%) is 731. Using this sample size, the power of the study is 
>99.99%. 
 
Table 1: One-sided Exact Test Power: Single Proportion 
 
Sample Size Scenarios 
1 
2 
Test significance level, α 
0.025 
0.025 
One or 2-sided test 
1 
1 
Null hypothesis proportion  
85.0% 
85.0% 
Alternative Proportion  
92.2% 
92.2% 
Power (%) 
90% 
>99.99% 
# Non-CRC/AA Cases 
225 
731 
 
The alternative proportion of 92.2% is the observed specificity in the DeeP-C study [SSED P130017, 
Source: fda.gov] for the age group 50-59.   It is anticipated that the specificity of Cologuard in individuals 
age 45-49 is not different than the specificity of the next closest age category. The null hypothesis 
proportion of 85.0% is identical to specificity null hypothesis used in the DeeP-C study (NCT). 
 
A minimum sample size of 193 evaluable subjects (age 45-49 inclusive) is required to adequately power 
the primary analysis. This minimum sample size requirement will be adjusted to 731 to more accurately 
estimate the specificity by narrowing the CI.  Since the expected drop-out rate is 20%, the total enrollment 
target is 914 (i.e. 731/ (0.8) = 914). 
12.3.1 Analysis Approach, Primary Effectiveness Analysis   
Primary Effectiveness Analysis:   

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
20 Protocol 2018-10 v1.0 
 
The primary analysis for mt-sDNA test (Cologuard) specificity will be performed using an exact binomial 
(Clopper-Pearson) test to compute the one-sided 97.5% lower bound; the lower bound must exceed 
85.0%. Specificity will be assessed for a random sample of 731 colonoscopy negatives.   
Rejecting the null hypothesis will demonstrate the Specificity in the Age 45-49 group is no worse than the 
pre-specified lower bound limit established in the DeeP-C protocol.  
 
12.4 Other Prespecified Analyses 
• 
Analysis of distribution of test performance by race/ethnicity using chi-square tests. 
• 
Analysis of distribution of test performance by age (yearly interval, 45-49) using chi-square tests. 
• 
Analysis of test performance by gender using chi-square tests. 
• 
Analysis of test performance by polyp size and location (including those with no polyps). This 
model will be repeated to include gender, race, and age. Modeling will be regression-based. 
• 
Analysis of Sensitivity to Advance Adenoma (Clopper-Pearson Exact confidence interval). Due to 
the expected low frequency of Advanced Adenoma, subgroup (Category 2.1, 2.2, 2.3, 2.4) 
analysis will not be performed, but observed rates will be reported.  
• 
Analysis of Specificity inclusive and exclusive of non-advanced neoplasia (Categories 3.0-5.0) 
(Clopper-Pearson Exact confidence interval). 
12.4.1 Additional Analysis 
• 
NPV, PPV, Odds Ratio, NLR, PLR and diagnostic yield for the 45-49 age group will be estimated 
using the observed study specificity and different assumptions regarding prevalence of CRC/AA 
and assumptions regarding sensitivity to CRC/AA. 
12.5 Handling of Missing Data 
The primary analysis will be based on all available data without imputation for missing data.  Missing data 
on mt-sDNA test (Cologuard) outcome and CRC/AA occurrence will be imputed using other available 
observed study data.  Based on exclusion patterns, demographic data such as age, gender, race, and 
ethnicity will be considered for imputing missing data.  Detailed imputation methods to be used will be 
documented in the SAP.  The method of Campbell, Pennello, and Yue will be used to assess the impact 
of missing cases [10]. 
12.6 General Statistical Methods 
All tables, listings and figures will be produced using SAS version 9.2 (or higher).  Data analysis will be 
performed using SAS:  Statistical Analysis Software (SAS 9.2 and JMP Version 9.0.3 or higher, both from 
SAS Institute, Cary, and NC).  The testing results from all sites will be compiled and data analysis will be 
performed on the compiled results as described in this protocol.  
12.6.1 Categorical Variables 
Categorical variables will be summarized by presenting the number and percent of observations in each 
category and the two-sided 95% confidence interval (CI), unless otherwise noted.  When calculating 
percentages, the denominator will be the number of participants in the entire study population, unless 
otherwise specified in the output. Comparisons across Categorical Subgroups will be performed using 
Chi-Square tests. 
12.6.2 Continuous Variables 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
21 Protocol 2018-10 v1.0 
 
Continuous variables will be summarized using n (sample size), mean, SD, minimum and maximum 
values, and 95% confidence interval unless otherwise noted. Continuous variable data distributions will 
be evaluated for Normality using Shapiro-Wilk method using 99% confidence level method.  Distribution-
free descriptive statistics (e.g. median value) would be documented if the Normality test fails. 
12.6.3 Determination of Diagnostic Accuracy 
These data will be presented in the form of 2 x 2 tables, which will be presented separately for colorectal 
cancer (CRC), Advanced adenoma (AA), and advanced colorectal neoplasia (CRC+AA).  Point estimates 
of sensitivity and specificity, along with Clopper-Pearson confidence intervals will be used to assess 
performance against study endpoint. 
Results of study will be displayed in 2x2 tables (for CRC, AA, and combined) as shown below: 
Table 2:  Outcome for all CRC (AA, or combined) subjects 
EXACT 
Test 
Reference Test (Colonoscopy) 
CRC+ 
CRC- 
sDNA + 
A (TP) 
B (FP) 
sDNA - 
C (FN) 
D (TN) 
 
The table includes the number of true positives (TP: those that have the disease and test positive), false 
positives (FP: those that do not have the disease and test positive), false negatives (FN: those that do 
have the disease and test negative) and true negatives (TN: those that do not have the disease and test 
negative). 
 
13 QUALITY CONTROL AND QUALITY ASSURANCE 
During study conduct, Exact Sciences or its agent will conduct periodic monitoring visits to ensure that the 
protocol and GCPs are being followed.  The site monitors may review source documents to confirm that 
the data recorded on CRFs is accurate.  The Investigator and institution will allow site monitors and 
appropriate regulatory authorities direct access to source documents to perform this verification. 
The study site may be subject to review by the (IRB)/Ethics Committee (EC), and/or to quality assurance 
audits performed by Exact Sciences, or companies working with or on behalf of Exact Sciences, and/or to 
inspection by appropriate regulatory authorities. 
It is important that the Investigator(s) and their relevant personnel are available during the monitoring 
visits and possible audits or inspections and that sufficient time is devoted to the process. 
14 DATA HANDLING AND RECORD KEEPING 
All references to the Sponsor in this section include all designees e.g., Contract Research Organizations 
or Consultants acting on behalf of the Sponsor.  
14.1 Protocol Deviations 
The site should make all efforts not to deviate from any of the study procedures or requirements as 
described in this protocol, except where necessary to eliminate immediate risks to the subject(s).  

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
22 Protocol 2018-10 v1.0 
 
Any deviations from this protocol must be reported to the Sponsor and documented properly. Protocol 
deviations must also be reported to the IRB/EC per IRB/EC policy.  
14.2 Direct Access to Source Data/Documents 
The Investigator’s institutions must permit trial-related monitoring, audits, IRB/IEC review, and regulatory 
inspection(s) by providing direct access to source data/documents. This can include Electronic Medical 
Records (EMR) systems and/or original paper records.  
14.3 Case Report Forms (CRFs) 
As used in this protocol, the term Case Report Form (CRF) should be understood to refer to either a 
paper form or an electronic data record or both, depending on the data collection method used in this 
study. 
A CRF is required and should be completed for each enrolled subject.  The completed original CRFs are 
the sole property of Exact Sciences and should not be made available in any form to third parties, except 
for authorized representatives of Exact Sciences or appropriate regulatory authorities, without written 
permission from Exact Sciences. 
The Investigator has ultimate responsibility for the collection and reporting of all clinical, safety and 
laboratory data entered on the CRFs, any other data collection forms and source documents, ensuring 
that they are accurate, authentic/original, attributable, complete, consistent, legible, timely 
(contemporaneous), enduring and available when required.  The CRFs must be signed by the 
Investigator to attest that the data contained on the CRFs is true.  Any corrections to entries made in the 
CRFs or source documents must be dated, initialed and explained (if necessary) and should not obscure 
the original entry.  
14.4 Records Retention 
The ICH E6(R2) Good Clinical Practice: Consolidated Guidance defines source documents as, "Original 
documents, data, and records (e.g., hospital records, clinical and office charts, laboratory notes, 
memoranda, subjects' diaries or evaluation checklists, pharmacy dispensing records, recorded data from 
automated instruments, copies or transcriptions certified after verification as being accurate copies, 
microfiches, photographic negatives, microfilm or magnetic media, x-rays, subject files, and records kept 
at the pharmacy, at the laboratories and at medico-technical departments involved in the clinical trial)." 
To enable evaluations and/or audits by regulatory authorities or Exact Sciences, the Investigator agrees 
to keep records, including the identity of all participating subjects (sufficient information to link records, 
e.g., CRFs and hospital records), all original signed informed consent forms, copies of all CRFs, serious 
adverse event forms, source documents, and detailed records of treatment disposition, and adequate 
documentation of relevant correspondence (e.g., letters, meeting minutes, telephone calls reports).  The 
Investigator or Sponsor shall maintain study records for a period of 2 years after the latter of the following 
three dates: the date on which the investigation is terminated or completed, the date that the records are 
no longer required for purposes of supporting a premarket approval application or a notice of completion 
of a product development protocol, or date provided in applicable national law. 
If the Investigator becomes unable for any reason to continue to retain study records for the required 
period (e.g., retired, relocation), Exact Sciences should be prospectively notified.  The study records must 
be transferred to an appropriately qualified designee acceptable to Exact Sciences, such as another 
Investigator, another institution, or to an independent third party arranged by Exact Sciences.  The 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
23 Protocol 2018-10 v1.0 
 
Investigator must obtain Exact Sciences’ written permission before disposing of any records, even if 
retention requirements have been met. 
15 ETHICS 
15.1 Risk Analysis 
15.1.1 Risk to the subject 
The risks of using the mt-sDNA test (Cologuard) are similar to the risks associated with any in vitro 
diagnostic (IVD) assay performed on stool samples. Stool sample collection is performed by the subject in 
his/her home. It is not anticipated that this collection process will present any significant risk to the 
subject. The mt-sDNA test (Cologuard) results will not be provided to the investigator or the subject. 
However, minor risks may be associated with use of the collection kit, as detailed in Section 11. 
15.1.2 Benefit to Subject 
There are no benefits to the subjects enrolled in this study.  The results of the mt-sDNA test (Cologuard) 
will not be used in the subject’s clinical management and both the subject and the Investigator will remain 
blinded to the results. Only the colonoscopy procedure results will be used for diagnosis and treatment as 
per the standard of care for the average risk study population.   
15.2 Institutional Review Board (IRB) / Ethics Committee (EC) 
It is the responsibility of the Investigator to have prospective approval of the study protocol, protocol 
amendments, informed consent forms, and other relevant documents, e.g., recruitment advertisements, if 
applicable, from the IRB/EC. All correspondence with the IRB/EC should be retained in the Investigator 
File. Copies of IRB/EC approvals should be forwarded to Exact Sciences or designee. 
15.3 Ethical Conduct of the Study 
The study will be conducted in accordance with legal and regulatory requirements, as well as the general 
principles set forth in the International Ethical Guidelines for Biomedical Research Involving Human 
Subjects (Council for International Organizations of Medical Sciences 2002), the Declaration of Helsinki 
(World Medical Association), and applicable local regulatory requirements and laws. 
15.4 Subject Information and Consent 
All parties will ensure protection of subject personal data and will not include subject names on any 
Sponsor forms, reports, publications, or in any other disclosures, except where required by laws.  In case 
of data transfer, Exact Sciences will maintain high standards of confidentiality and protection of subject 
personal data. 
The informed consent form must be in compliance with ICH GCP, local regulatory requirements, and legal 
requirements. 
The informed consent form used in this study, and any changes made during the course of the study, 
must be prospectively approved by both the IRB/EC and Exact Sciences before use. 
The Investigator must ensure that each study subject, or his/her legally acceptable representative, is fully 
informed about the nature and objectives of the study and possible risks associated with participation.  
The Investigator, or a person designated by the Investigator, will obtain written informed consent from 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
24 Protocol 2018-10 v1.0 
 
each subject or the subject's legally acceptable representative before any study-specific activity is 
performed.  The Investigator will retain the original of each subject's signed consent form. 
15.5 Reporting of Safety Issues and Serious Breaches of the Protocol or GCP 
In the event of any prohibition or restriction imposed (i.e., clinical hold) by an applicable National Authority 
in any area of the world, or if the Investigator is aware of any new information which might influence the 
evaluation of the benefits and risks of the investigational product, Exact Sciences should be informed 
immediately. 
16 A DEFINITION OF END TRIAL  
End of Trial is defined when 731 subjects have completed required study procedures with complete data 
receipt or on the date of early termination notice.   
 
17 SPONSOR DISCONTINUATION CRITERIA 
Premature termination of this study may occur because of a regulatory authority decision, change in 
opinion of the IRB/EC, or at the discretion of Exact Sciences.  In addition, Exact Sciences retains the right 
to discontinue development of the mt-sDNA test (Cologuard) for an average risk population at any time. 
If the study is prematurely terminated or discontinued, Exact Sciences will promptly notify the Investigator.  
After notification, within 30 days, the Investigator must contact all participating subjects who have been 
enrolled but have not yet been completed or withdrawn.  As directed by Exact Sciences, all study 
materials must be collected and all CRFs completed to the greatest extent possible.  
18 AUDITING PROCEDURES 
Investigational sites may undergo a quality assurance audit. The Sponsor, an authorized designee or a 
regulatory agency may conduct the audit. If a regulatory agency requests an audit of the site, the 
Investigator is required to inform the Sponsor immediately.  
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
25 Protocol 2018-10 v1.0 
 
19 REFERENCES 
1. American Cancer Society (ACS). Colorectal cancer prevention and early detection. Atlanta, GA: 
American Cancer Society; [updated May 2018 ]. Available from: 
http://www.cancer.org/cancer/colonandrectumcancer/moreinformation/colonandrectumcancerearlydetecti
on/colorectal-cancer-earlydetection-screening-tests-used. Accessed August 21, 2017. 
2. Siegel R, Fedewa AS, Anderson D et al  et al, Colorectal Cancer Incidence Patterns in the United 
States, 1974–2013 JNCI:  Journal of the National Cancer Institute, Volume 109, Issue 8, 1 August 2017. 
 
3. Rex D, Johnson DA, Anderson JC et al, American College of Gastroenterology Guidelines for 
Colorectal Cancer Screening 2008, Am J Gastroenterol March 2009, 104:739-750. 
 
4. Rex DK, Boland CR, Dominitz JK, Colorectal Cancer Screening: Recommendations fo Physicians and 
Patients from the U.S. Multi-Society, Am J Gastroenterology 2017; 112:1016-1030. 
5. Bibbins-Domingo K, et al., Screening for Colorectal Cancer: US Preventive Services Task Force 
Recommendation Statement. JAMA, 2016. 
6. https://www.nytimes.com/2018/05/30/well/cancer-group-calls-for-colorectal-cancer-screening-starting-
at-age-45.html access 21 Aug 2018. 
7. Wolf et al, 2018, p. 18; citing: Schroy PC 3rd, Lal S, Glick JT, Robinson PA, Zamor P, Heeren TC. 
Patient preferences for colorectal cancer screening: how does stool DNA testing fare? Am J Manag Care. 
2007; 13:393-400. 
 
8. Imperiale TF, Ransohoff DF, Itzkowitz SH, Levin TR, Lavin P, Lidgard GP, Ahlquist DA, Berger BM.  
Multitarget Stool DNA Testing for Colorectal-Cancer Screening, New Engl J Med 2014, 370 (14):1287-
1297 and supplement 
9. Rutter C, Miglioretti D, Savarino J, Bayesian Calibration of Microsimulation Models. J Am Stat 
Association 2009, 104(488): 1338-1350. 
10. Campbell G; Pennello G; Yue L. Missing data in the regulation of medical devices. J Biopharm Stat.  
2011; 21(2):180-95 (ISSN: 1520-5711 
 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
26 Protocol 2018-10 v1.0 
 
APPENDIX 1.0 – STUDY SCHEMA 
 
 
Footnotes for Study Schema 
1. Subjects with an unusable stool sample may be dispensed an additional Stool Collection Kit and 
repeat the stool collection process.  
 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
27 Protocol 2018-10 v1.0 
 
APPENDIX 2.0 – STUDY SCHEDULE  
Activity 
Enrollment  
Stool Sample 
Collection 
Colonoscopy 
Visit 
Colonoscopy and 
Histopathology 
Reports 
End of Study / 
Withdrawal 
Informed Consent [1] 
X 
 
 
 
 
Medical History and 
Demographics 
X 
 
 
 
 
Enrollment 
X 
 
 
 
 
Obtain Stool Sample  
mt-sDNA test (Cologuard) 
 
X 
 
 
 
Colonoscopy Procedure [2] 
 
 
X 
 
 
Submission of all diagnostic 
reports 
 
 
 
X 
 
Adverse Event Reporting [3] 
 
X 
 
 
 
Discontinuation [4] 
 
 
 
 
X 
 
Footnotes for Study Schedule  
1. Informed Consent: Must occur prior to undergoing any study specific procedure 
2. Colonoscopy should occur within approximately 60 days of enrollment. 
3. Adverse Events will only be recorded for events which occur during or are believed to be 
associated with the stool sample collection procedure. 
4. Subjects will have completed the study once the colonoscopy procedure has been completed or 
subject meets the withdrawal criteria in Section 9.3. 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
28 Protocol 2018-10 v1.0 
 
APPENDIX 3.0 – GUIDELINES FOR COLONOSCOPY  
Bowel preparation procedures and post-enrollment colonoscopy will be performed following the 
established standard of practice at each clinical site.  Results of the colonoscopy examination will be 
collected.  
The quality of the colonoscopy bowel prep must be documented after washing/suctioning as follows: 
• 
Excellent - minimal fecal residue and liquid, small volume of liquid easily aspirated, <5% of 
colonic surface covered; 
• 
Good - small amounts of fecal residue, volume of clear liquid covering 5-25% of surface, easily 
aspirated; 
• 
Fair - moderate amounts of fecal residue; stool limited examination but >90% could be examined; 
or 
• 
Poor - large amounts of stool, <90% of surface could be examined. 
Subjects with negative colonoscopy results and a poor bowel preparation will not be included in endpoint 
analyses. 
Cecal intubation must be documented with photographic evidence and/or documentation of cecal 
intubation.  Subjects with a negative colonoscopy will not be included in endpoint analyses if no 
documentation of cecal intubation is present. 
For all subjects with histopathological findings of CRC (Category 1.0) or precursor lesions (Category 2.0), 
neither the quality of bowel preparation nor documentation of cecal intubation need to be present for the 
subject to be included in endpoint analyses. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
29 Protocol 2018-10 v1.0 
 
APPENDIX 4.0 – GUIDELINES FOR PATHOLOGY REVIEW AND DOCUMENTATION 
Sites must acquire and maintain reports of the histopathologic interpretation of endoscopic biopsies, 
polypectomy specimens, and excisional surgical pathology specimens, which should be available on all 
CRCs and precursor lesions (Category 2.0, inclusive). 
Histopathology results will be collected on any excised or biopsied lesion. Lesion location within the colon 
(site), size (cm), will be recorded in the pathology report for all CRC’s and precursor lesions. Table 1 
provides codes for lesion locations. 
Table 1: Index Lesion Location: Use reported location or insertion depth in cm. 
P = Proximal Colon:   cecum, ascending colon, hepatic flexure, transverse colon, splenic flexure, 
right colon NOS, [Insertion Depth >60 cm] 
D = Distal Colon:   descending colon, sigmoid colon, recto-sigmoid colon, left colon NOS, [Insertion 
Depth = 16 – 60 cm (inclusive)] 
R = Rectal:  Rectum, [Insertion Depth = 0-15 cm (inclusive)] 
Lesions are also be categorized for study based on histopathologic diagnosis of the most clinically 
significant lesion (Index Lesion).  Table 2 provides the listing of categories that will be used when 
assessing and determining final categorization of index lesions: 
Table 2: Categorization of Subject for Study based on histopathologic diagnosis of the Index 
Lesion 
Description 
Category 
Adenocarcinoma of colorectum, Stage I-IV 
1.0 
Advanced adenoma, including the following subcategories 
2.0 
Adenoma with HGD/CIS, any size 
2.1 
Adenoma with villous growth pattern (≥ 25%), any size 
2.2 
Adenoma ≥ 1.0 cm in size 
2.3 
Serrated lesion, ≥ 1.0 cm in size (SSA/SSP/HP) 
2.4 
Adenoma, non-advanced, >5.0, <10mm in size, 1 or 2 adenomas 
3.0 
Adenomas, non-advanced, < 10 mm in size, ≥ 3 adenomas 
4.0 
Adenoma, non-advanced, < 5 mm in size, 1 or 2 adenomas 
5.0 
Negative:  No Adenocarcinoma of the colorectum, No 
Adenomas or SSA/SSP or No HP ≥ 10 mm 
6.0 
 
Subjects will be categorized for this study into a single category (1.0 – 6.0) based on the most clinically 
significant lesion present (Index Lesion).  For this study, the hierarchy of clinical significance in 
descending order of significance is 1.0 (highest clinical significance), then 2.1; 2.2; 2.3; 2.4; 3.0; 4.0; 5.0; 
and 6.0 (lowest clinical significance).  Table 3 provides the hierarchy of clinical significance regarding 
Index Lesions. 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
30 Protocol 2018-10 v1.0 
 
Table 3: Hierarchy of Clinical Significance of Index Lesion 
Index Lesion Hierarchy (in Descending order) 
Histopathology Category 
Adenocarcinoma of the colorectum Stage I – IV (CRC, all stages) 
1.0 
Advanced adenoma with HGD/CIS, any size 
2.1 
Advanced adenoma with villous component (≥ 25%), any size 
2.2 
Advanced adenoma ≥ 1.0 cm in size, no HGD/CIS or villous 
component ≥ 25% 
2.3 
Serrated lesion ≥ 1.0 cm in size (includes Sessile serrated 
adenoma/sessile serrated polyp (SSA/SSP) and hyperplastic polyp 
(HP) 
2.4 
Adenoma, non-advanced, >5.0, <10mm 
3.0 
 Adenoma, non-advanced, <10 mm, ≥ 3 adenomas 
4.0 
Adenoma, non- advanced, ≤ 5.0 mm 
5.0 
Hyperplastic polyp < 10 mm 
6.0 
Incidental findings (including malignancies other than colorectal 
adenocarcinoma) 
N/A 
 
A subject with CRC will be classified as CRC category (1.0), regardless of the presence of any other 
dysplastic or neoplastic lesions.  
Subjects with pathologically confirmed non-advanced adenoma(s) but without CRC (1.0) or precursor 
lesions (Category 2.0 inclusive) will be classified into category 3.0, 4.0 or 5.0 based on the size and 
number of lesions. The largest of the non-advanced adenoma will be the index lesion for the case. In the 
case of subjects with both small (<10 mm) non-advanced adenomas and hyperplastic polyps < 10 mm, 
they will be classified based on the non-advanced adenomas only and will be classified into category 3.0, 
4.0 or 5.0. 
All subjects who do not have CRC (1.0), precursor lesions (Category 2.0 inclusive) or non- advanced 
adenomas (Categories 3.0-5.0) will be classified as negative (6.0). Category 6.0 includes subjects with 
any number of hyperplastic polyps <10mm and any non-neoplastic finding including evidence of active or 
chronic IBD, non-colorectal epithelial neoplasia (e.g. carcinoid, lipoma). In cases with hyperplastic 
polyp(s) < 10 mm, the largest hyperplastic polyp is the index lesion.  In the absence of hyperplastic 
polyps, subjects in category 6.0 will either have “no index lesion” or will have had no pathology submitted. 
In addition TNM stage and overall AJCC CRC Stage (I-IV) will be recorded for all CRC’s. Staging System 
to be used for Index Lesions categorized as Category (1) Tumor, Node, Metastasis (TNM) Definitions 
(Adapted from NCCN Guidelines and AJCC Cancer Staging System, 7th edition). Tis (CIS, intramucosal 
carcinoma) categorized as Category 2.  Table 4 defines the TNM staging for cancers. 
 
 
 
 
 

 
 
 
Document Type: 
Master Clinical Protocol 2018-10 
 
32 Protocol 2018-10 v1.0 
 
 
 
Colon Cancer Staging (TNM) AJCC 8th Edition 
(Record as 1, 2, 3, 4, or X, do not record the sub-stage) 
Stage 
T 
N 
M 
0 
Tis 
N0 
M0 
I 
T1 - T2 
N0 
M0 
IIA 
T3 
N0 
M0 
IIB 
T4a 
N0 
M0 
IIC 
T4b 
N0 
M0 
IIIA 
T1 - T2 
N1 / N1c 
M0 
 
T1  
N2a  
M0 
IIIB 
T3 - T4a  
N1 / N1c  
M0  
 
T2 - T3  
N2a  
M0  
 
T1 - T2  
N2b  
M0 
IIIC 
T4a  
N2a  
M0 
 
T3 - T4a  
N2b  
M0  
 
T4b  
N1 - N2  
M0 
IVA 
any T  
any N  
M1
IVB 
any T  
any N  
M1
IVC 
any T  
any N  
M1
 
If stage cannot be assessed, record the AJCC Stage as “X”