![](_page_0_Picture_0.jpeg) # **Career Development Award (CDA) IBD Plexus Guidelines** # **Program Guidelines and Policies** # **Effective Jan 2025** Crohn's & Colitis Foundation National Office Research Department 733 Third Avenue Suite 510 New York, NY 10017 E-mail contact: [ibdplexusrfp@crohnscolitisfoundation.org](mailto:ibdplexusrfp@crohnscolitisfoundation.org) # *MISSION:* *To cure Crohn's disease and ulcerative colitis, and to improve the quality of life of children and adults affected by these diseases.* ![](_page_0_Picture_8.jpeg) ![](_page_1_Picture_0.jpeg) # Contents | 1. | Overview | 3 | |------|---------------------------------------------|----| | 2. | IBD Plexus Access | 3 | | 3. | IBD Plexus Cohorts | 4 | | APPI | ENDIX | 11 | | Арре | ndix 1 – IBD Plexus Data Use Agreement | 11 | | Арре | ndix 2 – Material & Data Transfer Agreement | 18 | ![](_page_1_Picture_3.jpeg) ![](_page_2_Picture_0.jpeg) # **1. Overview** The Crohn's & Colitis Foundation (Foundation) is excited to make IBD Plexus data and biosamples available to Career Development Award Investigators. [IBD Plexus®](http://www.crohnscolitisfoundation.org/science-and-professionals/research/IBDPlexus/) was founded by the Foundation to advance science, accelerate progress towards precision medicine and improve the care of patients living with IBD. The first-ofits kind, national-scale, cloud-based platform integrates clinical, patient-reported, genetic and other molecular data from diverse research study cohorts, real world clinical care settings and patients' experiences. IBD Plexus provides researchers with access to research-ready datasets to more rapidly perform activities that promise to speed treatment development, optimize existing therapies through development of biomarkers and diagnostics, and improve health outcomes. IBD Plexus unites clinicians, scientists, educators, industry partners, and patients to answer questions that are critically important to advance the field of IBD research. The multi-component IBD Plexus includes a biobank, pediatric and adult patient clinical data, patient-reported data, biosamples, central reference labs to generate molecular data (genetic, transcriptomic, microbiomic, etc.), as well an analytical platform to house, organize, aggregate, and provide data for research. The novel technological platform supports the mining of data for insights into IBD causes, mechanisms, biomarkers and potential new treatments. The "exchange" model functions under the guiding principle that researchers who take advantage of the resources will also contribute back the raw data (not the analyses) they derive from patient biosamples. As more stakeholders, including patients, clinicians, and researchers, contribute data, the IBD Plexus platform will evolve into an even more powerful database for future scientific research benefitting the entire IBD community. # **2. IBD Plexus Access** **If you are seeking access to IBD Plexus, the Foundation requires you to contact [ibdplexusrfp@crohnscolitisfoundation.org](mailto:ibdplexusrfp@crohnscolitisfoundation.org) at least 1 month prior to your CDA application submission.** The IBD Plexus team will consult with you to confirm data availability and feasibility for your CDA application. Requests for biosamples **must** also be submitted to the IBD Plexus [Academic Request](https://www.crohnscolitisfoundation.org/research/plexus/academic-request-for-proposal) [for Proposals](https://www.crohnscolitisfoundation.org/research/plexus/academic-request-for-proposal) (RFP). Please consider the IBD Plexus Academic RFP review deadlines in your planning. Successful CDA applicants must execute IBD Plexus Data Use Agreement (Appendix 1) or Material Data Transfer Agreement (Appendix 2) prior to gaining access. ![](_page_2_Picture_10.jpeg) ![](_page_3_Picture_0.jpeg) # **3. IBD Plexus Cohorts** IBD Plexus centralizes and links data across diverse IBD research cohorts to facilitate sharing across the research community. The cohorts are all independent programs that have unique goals but the Foundation encourages clinicians and patients to participate in multiple cohorts, when applicable. IBD Plexus links the data and biosamples across these cohorts to create a robust individual patient dataset, enabling Plexus to achieve a comprehensive collection of holistic information to facilitate research and advance the scientific understanding of IBD. This RFP provides the opportunity to gain access to biosamples and / or data from these study cohorts. Please click on the cohort hyperlink to learn more. - [RISK](https://www.crohnscolitisfoundation.org/research/current-research-initiatives/pediatric-risk-stratification) A pediatric research study of newly diagnosed Crohn's disease patients, designed to identify risk factors associated with developing penetrating and/or stricturing complications within 3 to 5 years of diagnosis *(Data sets and biosamples available – Table 1)* - [SPARC IBD](https://www.crohnscolitisfoundation.org/research/current-research-initiatives/sparc-ibd) A translational research study that enrolls adult patients with Crohn's disease and ulcerative colitis and follows them longitudinally to support the advancement of precision medicine *(Data sets and biosamples available – Table 1)* - [IBD Qorus](https://www.crohnscolitisfoundation.org/research/ibd-qorus) A longitudinally-followed adult quality of care program designed to drive progress towards improved care and health outcomes for patients living with IBD *(Data sets available – Table 1)* - [IBD Partners](http://www.ibdpartners.org/) An internet-based registry, open directly to patients, designed to better understand the patient view of the course of IBD and how patient experiences and unique IBD journeys impact disease course *(Data sets available – Table 1*) - [SHP647 program](https://www.businesswire.com/news/home/20200528005415/en/European-Commission-Releases-Takeda-Commitment-Divest-Shire%E2%80%99s) Discontinued SHP647 program clinical trial data and biosamples will be made available to the scientific community through IBD Plexus. More details to come. Patient-level data and biosamples collected from various cohorts include: ![](_page_3_Picture_10.jpeg) ![](_page_4_Figure_0.jpeg) # Table 1: Cohorts Data and Biosamples Collection Details | Cohort | Clinical Data | Patient Reported Data | Molecular Data | DNA | RNA | Plasma | PMBCs | Stool | Tissue Biopsies | |--------------|---------------|-----------------------|----------------|---------|---------|--------|---------|---------|-----------------| | SPARC IBD | $\odot$ | $\odot$ | $\odot$ | Ø | $\odot$ | Ø | $\odot$ | $\odot$ | $\odot$ | | RISK | $\odot$ | $\odot$ | $\odot$ | $\odot$ | $\odot$ | Ø | | $\odot$ | $\odot$ | | IBD Qorus | $\odot$ | $\odot$ | | | | | | | | | IBD Partners | | $\odot$ | | | | | | | | Note: More details to come for the SHP647 program data and biosamples. Further details about the data collected in these cohorts can be found in the IBD Plexus Patient Data Specification document. This document is located in proposalCENTRAL within the Download Templates & Instructions section. Table 2: Select clinical and demographic characteristics of IBD Plexus patients ![](_page_4_Picture_6.jpeg) ![](_page_5_Picture_0.jpeg) | Characteristics | RISK | SPARC IBD | IBD Qorus | IBD Partners | |--------------------------------|------|-----------|-----------|--------------| | Gender | | | | | | Female | 42% | 55% | 56% | 72% | | Male | 58% | 45% | 44% | 28% | | Age at enrollment | | | | | | < 21 | 100% | 24% | 24% | 4% | | 21 - 40 | n/a | 37% | 35% | 45% | | 41 - 60 | n/a | 30% | 30% | 38% | | > 60 | n/a | 9% | 11% | 13% | | Diagnosis at enrollment | | | | | | Crohn's Disease | 63% | 66% | 57% | 62% | | Ulcerative Colitis | 8% | 32% | 40% | 35% | | IBD-U | 10% | 2% | 3% | 2% | | Not IBD | 20% | n/a | n/a | n/a | | Medications (at any encounter) | | | | | | 5-ASAs | 43% | 25% | 26% | 48% | | Antibiotics | 35% | 9% | 6% | 12% | | Biologics | 44% | 71% | 75% | 44% | | Immunomodulators | 51% | 32% | 37% | 33% | | Steroid therapies | 61% | 16% | 12% | 30% | | Biologics breakdown | | | | | | Adalimumab | 13% | 27% | 12% | 20% | | Certolizumab | 1% | 3% | 2% | 5% | | Golimumab | n/a | 0.8% | 1% | 0.6% | | Infliximab | 40% | 35% | 48% | 21% | | Natalizumab | 0.2% | 0.1% | 0.5% | 0.9% | | Ustekinumab | n/a | 16% | 8% | 2% | | Vedolizumab | n/a | 19% | 28% | 5% | Table 3: IBD Plexus Molecular data ![](_page_5_Picture_3.jpeg) ![](_page_6_Picture_0.jpeg) | Service | SPARC IBD | | | | | |-----------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------|-----------------------------------------------------------|--|--| | | Samples | Patients | | | | | Global screening array
(genotyping) | 2,863 blood DNA | Collection Time F
CD: 1
UC: 1
IBD-U | ,906
908 | | | | Whole exome sequencing
(genomics) | 2,860 blood DNA | Collection Time Period: Anytime
CD: 1,902
UC: 909
IBD-U: 49 | | | | | Immuno-sequencing
(TCR profiling) | 2,826 blood DNA
(2,834 aliquots) | Collection Time Period: Anytime
CD: 1890
UC: 914
IBD-U: 22 | | | | | Total RNAseg @ 50M reads
(transcriptomics) | 2,661 tissue from 1 ^st collection
643 tissue from longitudinal collection
(2 ^nd to 7 ^th collection) | 1^st Collection
CD: 938
UC: 471
IBD-U: 23 | Longitudinal Collection
CD: 183
UC: 96
IBD-U: 7 | | | | FFPE H& E stained slides digitization | 2,769 tissue from 1 ^st collection
577 tissue from longitudinal collection
(2 ^nd to 4 ^th collection) | 1st Collection
CD: 960
UC: 440
IBD-U:38 | Longitudinal Collection
CD: 170
UC: 82
IBD-U: 7 | | | | WGS - bacteria and fungi
(metagenomics) | 1,434 stool from 1st collection
367 stool from longitudinal collection
(2 ^nd to 8 ^th collection) | 1^st Collection
CD: 917
UC: 493
IBD-U: 24 | Longitudinal Collection
CD: 150
UC: 102
IBD-U: 6 | | | | WGS viruses
(metagenomics) | 247 stool from 1st collection | 1≝ Collection
CD: 104
UC: 141
IBD-U: 2 | | | | | Olink Explore 3072
(proteomics) | 1,338 plasma at enrollment
912 plasma at endoscopy timepoint | 1 ^st Collection
CD: 921
UC: 642 | Longitudinal Collection
CD; 233
UC: 157 | | | | Service | RISK | | |-------------------------------------------------------------------|----------------------------------------------------------------------------------------------|----------------------------------------------------------------| | | Samples | Patients | | Immunochip (genotyping) | 1,456 blood DNA | 1,456 | | Global screening array (genotyping) | 1,000 blood DNA | 982 | | Protein expression (proteomics)
13 Olink Panels, 1196 proteins | 250 plasma | 250 | | RNAseq @ 10 M reads (transcriptomics) | 778 (baseline tissue)
10 (longitudinal tissue) | 565
10 (longitudinal) | | RNAseq @ 30 M reads(transcriptomics) | 850 baseline tissue
44 longitudinal tissue | 567
29 (longitudinal) | | RNAseg from FFPE slides | 188 baseline FFPE slides
281 longitudinal FFPE slides
24 unknown timepoint FFPE slides | 183 (baseline)
169 (longitudinal)
24 (unknown timepoint) | | 16S (rDNA sequencing) | 888 tissue and stool | 625 | | WGS - bacteria and fungi (metagenomics) | 295 baseline stool | 295 | | WGS viruses (metagenomics) | 100 baseline stool | 100 | | Methylation (epigenetics) | 402 baseline and follow-up blood
DNA | 238 | Table 4: IBD Plexus RISK Biosamples ![](_page_6_Picture_7.jpeg) ![](_page_7_Picture_0.jpeg) | RISK Biosamples | | | | | | | |-------------------|------------------------------------|-------------------------------------------------------------|---------------------------|--|--|--| | Source | Sample Type | Time Point | Samples available details | | | | | Peripheral Blood | Enrollment, 1 year, 2 years
DNA | | DNA extracted | | | | | Peripheral Blood | Tempus™ RNA | Enrollment, 1 year, 2 years
RNA extracted
and 3 years | | | | | | Peripheral Blood | Plasma | Enrollement, 1 year, 2
years and 3 years | Stored -80C | | | | | Stool | Unprocessed | Enrollment | Aliquots stored -80C | | | | | Intestinal Tissue | RNAlater | Scope | RNA/DNA extracted | | | | # **Periodicity of RISK Biosample Collection** Baseline blood and stool samples were collected at / or around the time of enrollment. Follow-up blood samples were collected at year 1 and years 2 and 3. Mucosal biopsies are collected during routine colonoscopy as part of patient's clinical care. ## *Peripheral Blood* Collected at the time of baseline, year 1, year 2, and year 3. Blood samples were used to isolate plasma, DNA and RNA, and thus whole blood samples or PBMCs are not available. #### *Stool* Fresh fecal samples were collected within 2 weeks of enrollment and flash frozen. ### *Intestinal tissue biopsies* Pinch biopsies were collected from Crohn's disease patients during routine scheduled colonoscopies. 4 ileal and 4 rectal biopsy samples were collected in triplicate and stored in RNAlater. Table 5: IBD Plexus SPARC IBD Biosamples ![](_page_7_Picture_11.jpeg) ![](_page_8_Picture_0.jpeg) | SPARC Biosamples | | | | | | |--------------------------------------------|------------------------|---------------------------------------------------------------------|-----------------------------------------------------------------------|--|--| | Source
Sample Type | | Time Point | Samples available details | | | | Peripheral Blood | DNA | Baseline | DNA extracted | | | | Peripheral Blood | Paxgene RNA | Baseline, Scope and 3 months after scope
if change in therapies | Stored -80C | | | | Peripheral Blood | PBMC's | Baseline, Scope and 3 months after scope
if change in therapies | Aliquots of 5 million cells stored -80C | | | | Peripheral Blood | Plasma | Baseline, Scope and 3 months after scope
if change in therapies | Stored -80C | | | | Stool | Nucleic Acid Archiving | Baseline, Scope and 3 months after scope
if change in therapies | Stool in ethanol stored frozen | | | | Stool | Unprocessed | Baseline, Scope, and 3 months after
scope if change in therapies | faecal calprotectin generated + 6 aliquots
unprocessed stored -80C | | | | Intestinal Tissue
(CD or UC or
IBDU) | RNAlater | Scope | Stored -80C | | | | Intestinal Tissue
(CD or UC or
IBDU) | Formalin | Scope | Paraffin embedded block | | | | Intestinal Tissue
(CD or UC or
IBDU) | Flash Freeze (LN2) | Scope | Stored -80C | | | # **Periodicity of SPARC IBD Biosample Collection** Biosamples are collected around the time of consent (blood and stool) and when the patient undergoes a sigmoidoscopy or colonoscopy as part of his or her clinical care. Blood and stool samples are also obtained approximately 3 months after a change in therapy that follows a colonoscopy or sigmoidoscopy if the patient has a follow-up office visit during that time. ## *Peripheral Blood* Collected at the time of enrollment, and used to isolate plasma, RNA and DNA. Additional samples are collected at the time of colonoscopy and 3 months after a colonoscopy if change in therapy where plasma, RNA, and PBMCs are isolated. These samples can be used for a variety of purposes including genotyping, transcriptomics, proteomics and metabolomics. ### *Stool* For baseline stool sample collection participants are provided with a stool kit at their first visit with instructions to collect the stool sample immediately after their visit. Participants collect the sample at home and ship cool whip container of preservative-free stool and an aliquot of stool stored in 95% alcohol to preserve the sample for metabolomics. For the collection of stool at the time of colonoscopy, participants receive the stool kit 2 weeks prior the colonoscopy with instructions to collect ![](_page_8_Picture_8.jpeg) ![](_page_8_Picture_9.jpeg) ![](_page_9_Picture_0.jpeg) samples preceding their bowel preparation. Preservative-free samples are subaliqouted upon arrival to the biobank and stored at -80˚C. Stool samples are suitable for microbiomics, proteomics and metabolomics studies as well as for measurement of routine inflammatory markers such as fecal calprotectin. #### *Intestinal tissue biopsy* For patients with Crohn's disease undergoing colonoscopy up to 5 pinch biopsies are obtained using forceps from the ileum or the most proximal extent of the exam and the rectum (at 20 cm from the anal verge). If both the rectum and the ileum (or cecum) appear normal on insertion of the colonoscope, an additional 5 pinch biopsies are obtained from an area with macroscopically active disease, if present. For those with ulcerative colitis or IBDU, up to 5 pinch biopsies are obtained from the cecum (or most proximal extent of the exam) and the rectum (at 20 cm). When there is not pancolitis, if feasible and safe, biopsies from the normal area just adjacent to the transition area from abnormal to normal appearing mucosa are obtained. If the only evidence of inflamed tissue on colonoscopy is located distal to 20 cm, the biopsies from the rectum are obtained more distally in the area of active inflammation. For each anatomical region, biopsies are collected in RNAlater, snapped frozen at sites equipped with LN2, and collected in formalin and embedded into paraffin blocks at the biobank within 24hrs of collection. ![](_page_9_Picture_6.jpeg) ![](_page_10_Picture_0.jpeg) # **APPENDIX** ### **Appendix 1 – IBD Plexus Data Use Agreement** This Data Use Agreement ("Agreement") is by and between the Crohn's & Colitis Foundation ("Foundation"), a non-profit tax-exempt organization pursuant to Section 501(c)(3) of the Internal Revenue Code, with an address at 733 Third Avenue, Suite 510, New York, NY 10017 and XXX ("Site"), with offices at XXX. Foundation and Site each may be referred to herein as a "Party" or collectively as the "Parties" to this Agreement. ### **Recitals** Foundation administers IBD Plexus, a resource for scientific researchers which includes patient data and information, that was created to accelerate research, drive progress toward precision medicine, and transform the care of patients living with Inflammatory Bowel Diseases ("IBD"). Site employs XXX (the "Principal Investigator" or "PI"), an IBD researcher approved by the IBD Plexus Project Selection Committee ("PSC") to receive IBD Plexus data. Foundation and Site agree that PI shall receive access to certain IBD Plexus data on the terms and conditions of this Agreement. #### **Agreements** For good and valuable consideration, the sufficiency of which is acknowledged, the Parties agree as follows: **1. Data**. PI shall receive the data ("Data") identified for the sole purpose of conducting the project set forth in the PSC approved research proposal attached as Exhibit A (the "Approved Project"). PI may request additional use of the Data but no such additional use shall occur without prior written permission of Foundation and, upon such written permission such additional use shall be an Approved Project. (a) Transfer/Disclosure of Data. The Data shall not be transferred to anyone not working on the Project without the prior written permission of Foundation, provided that nothing herein shall prevent Site from meeting its obligations pursuant to any applicable law, or PI from meeting any obligation requiring the Data to be made available in connection with publication of the results of the Approved Project. EFFECTIVE DATE: JAN 2025 (b) Subject PHI. PI shall receive a deidentified data set. Neither Site nor PI shall be permitted to use such information to re-identify the individuals nor to contact them under any circumstances. In the event PI receives protected health information or information that is otherwise protected by any applicable law (any of the foregoing, "Subject PHI"), then PI shall not use such information to identify any individual nor ![](_page_10_Picture_13.jpeg) ![](_page_11_Picture_0.jpeg) contact them under any circumstances, shall only use such Subject PHI in accordance with applicable law, and PI shall return or destroy upon Foundation's written request and option, or, if PI requests in writing and Foundation agrees that return or destruction is not feasible under the circumstances, then Site shall retain such information under these terms and conditions. **2. Storage and Access to/Use of Data**. Site shall safeguard storage of the Data and prevent its use or disclosure in violation of this Agreement. Only the PI, and individuals under the PI's supervision, will have access to and use the Data. **3. Compliance; Notice of Withdrawal**. PI shall use the Data in compliance with all applicable laws. Site and PI are responsible for obtaining and adhering to any Institutional Review Board ("IRB") approvals necessary to perform the Approved Project. If Site receives written notice from Foundation that a patient, as identified using the unique coded identifier, whose Data has been provided, wishes to withdraw permission for use of such Data (a "Notice of Withdrawal"), then PI only shall use such Data to the extent necessary to protect the integrity of the Project. **4. Notifications of Breaches and Security Incidents**. Site shall notify Foundation in writing as soon as possible, but in no event more than three (3) calendar days, after becoming aware of any breach or, or security incident involving, Subject PHI. Site shall be deemed to be aware of any breach or security incident as of the first day on which such breach or security incident is known to any of its officers or employees. Site shall identify as soon as practicable each individual whose Subject PHI has been, or is reasonably believed to have been accessed, acquired, or disclosed during such breach or security incident. Site shall cooperate in good faith, at its own cost and expense, in the investigation by Foundation of any breach or security incident. (a) Prompt Corrective Actions. Site shall: (i) take prompt corrective action to remedy any breach or security incident, and (ii) mitigate, to the extent practicable, any harmful effect of a use or disclosure of Subject PHI in violation of this Agreement. (b) Notification of Corrective Action and Provision of Policies. Site will provide written notice as soon as possible but no later than ten (10) calendar days from the date that Site provided notice to Foundation, of: (i) the actions taken by Site to mitigate any harmful effect of such breach or security incident; and (ii) the corrective action Site has taken or shall take to prevent future similar breaches or security incidents. Upon Foundation's request, Site will also provide to Foundation a copy of Site'spolicies and procedures for handling patient information or information security. **5. Intellectual Property Rights ("IPRs"); New data/information; New Resources**. ![](_page_11_Picture_8.jpeg) ![](_page_12_Picture_0.jpeg) (a) Claim of IPRs. Site and/or PI may claim IPRs on inventions or discoveries involving use of the Data provided that Site and PI shall not claim any IPRs or any ownership rights, or permit any claim or assertion of IPRs or ownership rights, in any of or any part of, the Data. (b) Non-Targeted Data. If the Approved Project generates analyzed or interpreted Approved Project data ("Project Results") not directed at a particular hypothesis, but rather is a preliminary exploration of the data ("Non Targeted Data"), then, with respect to such Non-Targeted Data, upon the earlier of: (a) one hundred eighty (180) days after the last grant of Data to PI; (b) acceptance of an Approved Project manuscript for publication; or, (c) filing of a patent application, Site shall provide to Foundation in writing: (i) information about the status of the Approved Project, including identification of any New Resource (defined in Subsection (d)); and (ii) new raw Approved Project data in a manner that retains linkage of such data to the Data, which new raw Approved Project data may be released to third party researchers in connection with new research projects. (c) Targeted Data. If the Approved Project generates Project Results directed at one or more particular hypotheses ("Targeted Data"), then, with respect to such Targeted Data, upon the earlier of: (a) five hundred forty (540) days after the last grant of Data to PI; (b) acceptance of an Approved Project manuscript for publication; or, (c) filing of a patent application, Site shall provide to Foundation in writing: (i) information about the status of the Approved Project, including any New Resource; and, (ii) new raw Approved Project data in a manner that retains linkage of such data to the Data, which new raw Approved Project data may be released in connection with new research projects. (d) New Resources. If PI and/or Site creates any novel resources (which shall include new data, bioinformatic tools, information and results) useful to scientific researchers that arise from use of the Data, including without limitation that may be protectible as an IPR ("New Resources"), then Site shall notify Foundation and, if requested by Foundation, provide a copy of all such New Resources to Foundation at cost and without markup, for at cost distribution to scientists performing research into the causes of and cures for IBD, and provided that (i) any New Resource that is not new raw Approved Project data that may be commercializable by Site only shall be made available by Foundation to non-commercial organizations, (ii) this sublicensable license shall be subject to Sections 5(b) and (c), (iii) such distribution will not grant to any third party any other right to such New Resources; and (iv) any recipient of such New Resources shall agree to substantially similar terms and conditions as the ones set forth in this Agreement, including without limitation release and indemnification of Site and PI as contributor for receipt, storage and use of any New Resource. ![](_page_12_Picture_5.jpeg) ![](_page_13_Picture_0.jpeg) **6. Reporting Requirements**. PI and/or Site is required to submit an annual progress report for the Approved Project, which will be reviewed by the members of the National Scientific Advisory Committee or Foundation staff. **7. Term.** This Agreement shall be effective upon date of first receipt of Data and shall remain in effect for two (2) years thereafter, unless otherwise extended or terminated by the parties. Upon the expiration or earlier termination of this Agreement, Site shall return or delete, in the sole discretion of the Foundation, all Data (which shall include any data synthetically derived from IBD Plexus Data) and confirm deletion of the same with Foundation. **8. Notice**. Any notice required or permitted by this Agreement shall be made by one Party to the other Party as follows: to Foundation: to Site: # **9. Press and Publication.** (b) The Parties shall agree on any press release or other public announcement concerning this Agreement, other than an academic, scholarly, or scientific publication, prior to its public release, except to the extent any such release or announcement is required by law, rule, or regulation or the rules of any securities exchange. Notwithstanding the foregoing, each Party may, without prior approval from the other Party, make public announcement of the content of the abstracts submitted by Site in support of its Approved Project and the identity of research collaborators, including without limitation on Foundation's website. (c) Within thirty (30) days after creation of the final draft of any abstract, poster or paper analyzing or otherwise utilizing Data and prior to its submission for publication (each manuscript, a "Project Paper"), PI shall provide the IBD Plexus Publication Review Committee with a copy. PI shall use best efforts to seek publication of any Project Paper in accordance with generally accepted scientific standards. (d) Project Papers will be reviewed by a subset of the Publication Review Committee on an ad hoc basis, provided that such review shall not exceed thirty (30) days from receipt of the Project Paper by such Committee. If there are no concerns with publication, then PI may move forward with publication efforts; however, if review of the manuscript indicates that issues need to be addressed, then the Project Paper will be reviewed by the entire Publication Review Committee, provided that such review shall not exceed sixty (60) days from receipt of the Project Paper by such Committee. Reasons for additional review include, but are not limited to, the following: ![](_page_13_Picture_10.jpeg) ![](_page_13_Picture_11.jpeg) ![](_page_14_Picture_0.jpeg) - Manuscript contains one or more egregious methodological errors - Manuscript generates major reviewer concerns regarding methodology, findings and/or conclusions that are found to misinterpret the data and/or cohorts - Manuscript is market research analysis - Manuscript falls outside the scope of the approved Project (e) In the event that the Committee provides comments to the PI, PI shall consider such comments. (f) Foundation may make any Project Paper available through IBD Plexus after its publication, provided that it is permissible by the publishing journal and doing so does not compromise the publishability of any Project Paper. (g) Any Project Paper shall include written acknowledgement of the Foundation: e.g., "The results published here are in whole or part based on data obtained from the IBD Plexus program of the Crohn's & Colitis Foundation." (h) The Foundation acknowledges that researchers with access to IBD Plexus resources may be required by third parties to provide copies of data they use in research projects for the purposes of validating or reproducing research results, for example, in order to publish their results in a journal, or because they are subject to other data sharing requirements, for example, because they receive funding from the U.S. government. This Policy sets forth the Foundation's commitment to support these researchers in fulfilling their commitments to third parties by allowing for the use of IBD Plexus data resources for validation, reproducibility, data sharing or other legitimate purposes. The Foundation will use the following procedures to allow for access to IBD Plexus data as discussed in this Policy: a. A researcher with access to IBD Plexus resources will notify the Foundation in writing promptly upon becoming aware that the researcher is subject to a requirement described in this Policy, including identification of the IBD Plexus data that is subject to this requirement, a description of the requirement, and the third party that imposes this requirement, as follows: [name and email address]. If the circumstances are such that the researcher cannot provide this notice, then the entity requiring access to the IBD Plexus data may provide this information to the Foundation. b. The Foundation will cooperate in good faith to make available, through the IBD Plexus data repository, the IBD Plexus data that must ![](_page_14_Picture_14.jpeg) ![](_page_15_Picture_0.jpeg) be accessed for a purpose set forth in this Policy. Ordinarily, this will mean that a particular third party researcher or research team will be given access to IBD Plexus data through execution of a data use agreement with a researcher or research team for access to the IBD Plexus data only for the purpose of validating or reproducing the results as required by a journal policy, data sharing requirement, or other legitimate purpose. The Foundation may require other reasonable terms and conditions in return for providing access to IBD Plexus data, such as: that the third party researcher or research team not use the data for any purpose other than validation or reproduction of the research results, and that the data and all copies be securely stored so that the data is not used for any other purpose, and/or returned or destroyed. c. With respect to all of the foregoing in this Policy, the Foundation reserves its rights to, at its discretion, manage IBD Plexus so that the Foundation's obligations to third parties are not violated or otherwise compromised in its efforts to support researchers in fulfilling their responsibilities with respect to journal publication requirements, receipt of U.S. government funding and other requirements. **10. No Representations or Warranties.** EACH PARTY MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, WITH RESPECT TO THE DATA OR OTHER SUPPLIED MATERIALS, INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR THAT THE DATA OR OTHER SUPPLIED MATERIALS WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS. ALL DATA AND OTHER SUPPLIED MATERIALS ARE PROVIDED ON AN "AS IS" BASIS. **11. Risk of Liability/Indemnification**. Each Party shall assume all risk of and hereby does release the other Party, including without limitation, Foundation, IBD Plexus, its members, contributors, and their directors, officers, employees and agents (collectively, the "Releasees"), from all liability related to access to, storage and use of any data and other materials supplied to it by the other Party (the "Activities") and, only if Site is permitted by law to do so, each Party shall and hereby does indemnify, defend and hold Releasees harmless from and against all liability relating to the Activities, except to the extent that any such liability is caused by the gross negligence or willful misconduct of any of the Releasees. **12. Remedies for Violation**. Any material violation of these terms and conditions shall constitute good cause for Foundation to immediately revoke permission granted for use of the Data and, upon such written notice from Foundation, Site and PI shall promptly cease all such use and at the election of Foundation return or destroy all such Data. Site agrees that any ![](_page_15_Picture_6.jpeg) ![](_page_16_Picture_0.jpeg) material violation of these terms and conditions may cause Foundation to pursue any and all available legal remedies. ![](_page_16_Picture_2.jpeg) ![](_page_17_Picture_0.jpeg) #### **Appendix 2 – Material & Data Transfer Agreement** This Materials and Data Use Agreement ("Agreement") is by and between the Crohn's & Colitis Foundation ("Foundation"), a non-profit tax-exempt organization pursuant to Section 501(c)(3) of the Internal Revenue Code, with an address at 733 Third Avenue, Suite 510, New York, NY 10017 and XXX ("Site"), with offices at [XXX]. Foundation and Site each may be referred to herein as a "Party" or collectively as the "Parties" to this Agreement. #### **Recitals** Foundation administers IBD Plexus, a resource for scientific researchers which includes patient biosamples, data and information, that was created to accelerate research, drive progress toward precision medicine, and transform the care of patients living with Inflammatory Bowel Diseases ("IBD"). Site employs [XXX] (the "Principal Investigator" or "PI"), an IBD researcher approved by the IBD Plexus Project Selection Committee ("PSC") to receive IBD Plexus biosamples and data ("Materials") pursuant to an approved research proposal. Foundation and Site agree that Site shall receive access to certain Materials on the terms and conditions of this Agreement. #### **Agreements** For good and valuable consideration, the sufficiency of which is acknowledged, the Parties agree as follows: **1. Materials**. Site shall receive the Materials identified at Exhibit A ("Provided Items") for the purpose of conducting the project set forth in the PSC approved research proposal attached as Exhibit B (the "Approved Project"). Foundation agrees that the Provided Items shall not include any Protected Health Information, as that term is defined in the Health Insurance Portability and Accountability Act of 1996, as well as the implementing privacy and security regulations (collectively, "HIPAA"). Any data or information related to human tissue or sera samples shall be de-identified in accordance with the requirements set forth in 45 C.F.R. § 164.514(a) and (b) prior to disclosure to Site. Site shall maintain the Materials and other Provided Items in a secure environment and prevent their unauthorized use or disclosure and shall be solely responsible to remediate any breach or any unauthorized use or disclosure of Materials or Provided Items in its possession in accordance with all applicable laws and to the extent practicable. Site, upon knowledge, shall promptly report to Foundation any use or disclosure of Materials or Provided Items that are in material violation of any applicable law or this Agreement. (a) Transfer/Disclosure of Materials. The Provided Items shall not be transferred to anyone not working on the Approved Project without the prior written permission of Foundation, provided that nothing herein shall prevent Site from meeting its obligations pursuant to any applicable law, or from meeting any obligation requiring the Materials to be made available in connection with publication of the results of the Approved Project. ![](_page_17_Picture_12.jpeg) ![](_page_18_Picture_0.jpeg) Site may request additional use of the Provided Items but no such additional use shall occur without prior written permission of Foundation and, upon such written permission such additional use shall be an Approved Project. (b) Subject PHI. Neither Site nor PI shall be permitted to use data to reidentify the individuals nor to contact them under any circumstances. In the event PI mistakenly receives protected health information or information that is otherwise protected by any applicable law (any of the foregoing, "Subject PHI"), then PI shall not use such information to identify any individual nor contact them under any circumstances, shall only use such Subject PHI in accordance with applicable law, and PI shall return or destroy upon Foundation's written request and option, or, if PI requests in writing and Foundation agrees that return or destruction is not feasible under the circumstances, then Site shall retain such information under these terms and conditions. **2. Storage and Access to/Use of Materials**. Site shall safeguard storage of the Provided Items and prevent its use or disclosure in violation of this Agreement. Only the PI, and individuals appropriately trained in the handling of sensitive Materials under the PI's supervision, will have access to and use the Provided Items. **3. Compliance; Notice of Withdrawal**. PI shall use the Provided Items in compliance with all applicable laws. If Site receives written notice from Foundation that a patient, as identified using the unique coded identifier, whose Materials has been provided, wishes to withdraw permission for use of such Materials (a "Notice of Withdrawal"), then PI only shall use such Materials to the extent necessary to protect the integrity of the Approved Project. **4. Notifications of Breaches and Security Incidents**. Site shall notify Foundation in writing as soon as possible, but in no event more than three (3) calendar days, after becoming aware of any breach or, or security incident involving Provided Items. Site shall be deemed to be aware of any breach or security incident as of the first day on which such breach or security incident is known to any of its officers or employees. Site shall cooperate in good faith, at its own cost and expense, in the investigation by Foundation of any breach or security incident. (a) Prompt Corrective Actions. Site shall: (i) take prompt corrective action to remedy any breach or security incident, and (ii) mitigate, to the extent practicable, any harmful effect of a use or disclosure of Provided Items in violation of this Agreement. (b) Notification of Corrective Action and Provision of Policies. Site will provide written notice as soon as possible but no later than ten (10) calendar days from the date that Site provided notice to Foundation, of: (i) the actions taken by Site to mitigate any harmful effect of such breach or security incident; and (ii) the corrective action Site ![](_page_18_Picture_8.jpeg) ![](_page_18_Picture_9.jpeg) ![](_page_19_Picture_0.jpeg) has taken or shall take to prevent future similar breaches or security incidents. # **5. Intellectual Property Rights ("IPRs"); New Materials/information; New Resources**. (a) Claim of IPRs. Site and/or PI may claim IPRs on inventions or discoveries involving use of the Provided Items provided that Site and PI shall not claim any IPRs or any ownership rights, or permit any claim or assertion of IPRs or ownership rights, in any of or any part of, the Materials. (b) Non Targeted Materials. If the Project is not directed at a particular hypothesis, but rather is a preliminary exploration of the IBD Plexus Data **("Non-Targeted Project")**, and such Project generates Biosample-Derived data from use of IBD Plexus Materials, then Recipient shall, promptly upon generation thereof, provide to Foundation such new raw Biosample-Derived Data in a manner that retains linkage of such Biosample-Derived data to the Materials, which shall be kept confidential by Foundation until the earlier of: (a) one hundred and eighty (180) days after the last receipt of Materials by Recipient for such Non-Targeted Project or (b) acceptance of a manuscript for publication on the Non-Targeted Project or (c) Recipient's filing of a patent application covering or claiming such Biosamplederived Data **("Non-Targeted Exclusivity Period"),** at which point such Biosample-Derived Data may be released to third party researchers in connection with new research projects. (c) Targeted Materials. If a Project directed at one or more particular hypotheses (**"Targeted Project"**) generates Biosample-Derived Data from use of IBD Plexus Materials, Recipient shall, promptly upon generation thereof, provide to Foundation such new raw Biosample-Derived Data in a manner that retains linkage of such Biosample-Derived Data to the Materials, which shall be kept confidential by Foundation until the earlier of: (a) five hundred forty (540) days after the last grant of Materials to PI; (b) acceptance of an Approved Project manuscript for publication; or (c) filing of a patent application, at which point such Biosamplederived Data may be released to third party researchers in connection with new research projects. (d) New Resources. If PI and/or Site creates any novel resources (which shall include new Materials, bioinformatic tools, information and results) useful to scientific researchers that arise from use of the Materials, including without limitation that may be protectible as an IPR ("New Resources"), then Site shall notify Foundation and, if requested by Foundation, provide a copy of all such New Resources to Foundation at cost and without markup, for at cost distribution to scientists performing research into the causes of and cures for IBD, and provided that (i) any New Resource that is not new raw Approved Project Materials that may be commercializable by Site only shall be made available by Foundation to noncommercial organizations, (ii) this sublicensable license shall be subject to Sections 5(b) and (c), (iii) such distribution will not grant to any third party any other right to such ![](_page_19_Picture_8.jpeg) ![](_page_20_Picture_0.jpeg) New Resources; and (iv) any recipient of such New Resources shall agree to substantially similar terms and conditions as the ones set forth in this Agreement, including without limitation release and indemnification of Site and PI as contributor for receipt, storage and use of any New Resource. **6. Reporting Requirements**. Site is required to submit an annual progress report for the Approved Project, which will be reviewed by the members of the National Scientific Advisory Committee or Foundation staff. **7. Term.** This Agreement shall be effective upon date of first receipt of Materials and shall remain in effect for two (2) years thereafter, unless otherwise extended or terminated by the parties. Upon the expiration or earlier termination of this Agreement, Site shall return or delete, in the sole discretion of the Foundation, all Provided Items (which shall include any data synthetically derived from IBD Plexus Data) and confirm deletion of the same with Foundation. **8. Notice**. Any notice required or permitted by this Agreement shall be made by one Party to the other Party as follows: to Foundation: to: Site # **9. Press and Publication.** (i) The Parties shall agree on any press release or other public announcement concerning this Agreement other than an academic, scholarly, or scientific publication, prior to its public release, except to the extent any such release or announcement is required by law, rule, or regulation or the rules of any securities exchange. Notwithstanding the foregoing, each Party may, without prior approval from the other Party, make public announcements regarding the content of the abstracts submitted by Site in support of its Approved Project and the identity of research collaborators, including without limitation on Foundation's website. (j) Within thirty (30) days after creation of the final draft of any abstract, poster or paper analyzing or otherwise utilizing Data and prior to its submission for publication (each manuscript, a "Project Paper"), PI shall provide the IBD Plexus Publication Review Committee with a copy. PI shall use best efforts to seek publication of any Project Paper in accordance with generally accepted scientific standards. (k) Project Papers will be reviewed by a subset of the Publication Review Committee on an ad hoc basis, provided that such review shall not exceed thirty (30) days from receipt of the Project Paper by such Committee. If there are no concerns with publication, then PI may move forward with publication efforts; however, if review of the manuscript indicates that issues need to be addressed, then the Project Paper will be reviewed by the entire Publication Review Committee, provided that such review shall not ![](_page_20_Picture_11.jpeg) ![](_page_21_Picture_0.jpeg) exceed sixty (60) days from receipt of the Project Paper by such Committee. Reasons for additional review include, but are not limited to, the following: - Manuscript contains one or more egregious methodological errors - Manuscript generates major reviewer concerns regarding methodology, findings and/or conclusions that are found to misinterpret the data and/or cohorts - Manuscript is market research analysis - Manuscript falls outside the scope of the approved Project (l) In the event that the Committee provides comments to the PI, PI shall consider such comments. (m) Foundation may make any Project Paper available through IBD Plexus after its publication, provided that it is permissible by the publishing journal and doing so does not compromise the publishability of any Project Paper. (n) Any Project Paper shall include written acknowledgement of the Foundation: e.g., "The results published here are in whole or part based on data obtained from the IBD Plexus program of the Crohn's & Colitis Foundation." (o) The Foundation acknowledges that researchers with access to IBD Plexus resources may be required by third parties to allow access to copies of data they use in research projects for the purposes of validating or reproducing research results, for example, in order to publish their results in a journal, or because they are subject to other data sharing requirements, for example, because they receive funding from the U.S. government. This Policy sets forth the Foundation's commitment to support these researchers in fulfilling their commitments to third parties by allowing for the use of IBD Plexus data resources for validation, reproducibility, data sharing or other legitimate purposes. The Foundation will use the following procedures to allow for access to IBD Plexus data as discussed in this Policy: 1) A researcher with access to IBD Plexus resources will notify the Foundation in writing promptly upon becoming aware that the researcher is subject to a requirement described in this Policy, including identification of the IBD Plexus data that is subject to this requirement, a description of the requirement, and the third party that imposes this requirement, as follows: [name and email address]. If the circumstances are such that the researcher cannot provide this notice, then the entity requiring access to the IBD Plexus data may provide this information to the Foundation. ![](_page_21_Picture_13.jpeg) ![](_page_22_Picture_0.jpeg) 2) The Foundation will cooperate in good faith to make available, through the IBD Plexus data repository, the IBD Plexus data that must be accessed for a purpose set forth in this Policy. Ordinarily, this will mean that a particular third party researcher or research team will be given access to IBD Plexus data through execution of a data use agreement with a researcher or research team for access to the IBD Plexus data only for the purpose of validating or reproducing the results as required by a journal policy, data sharing requirement, or other legitimate purpose. The Foundation may require other reasonable terms and conditions in return for providing access to IBD Plexus data, such as: that the third party researcher or research team not use the data for any purpose other than validation or reproduction of the research results, and that the data and all copies be securely stored so that the data is not used for any other purpose, and/or returned or destroyed. 3) With respect to all of the foregoing in this Policy, the Foundation reserves its rights to, at its discretion, manage IBD Plexus so that the Foundation's obligations to third parties are not violated or otherwise compromised in its efforts to support researchers in fulfilling their responsibilities with respect to journal publication requirements, receipt of U.S. government funding and other requirements. - **10. No Representations or Warranties.** EACH PARTY MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, WITH RESPECT TO THE MATERIALS OR OTHER SUPPLIED MATERIALS, INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR THAT THE MATERIALS OR OTHER SUPPLIED MATERIALS WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS. ALL MATERIALS AND OTHER SUPPLIED MATERIALS ARE PROVIDED ON AN "AS IS" BASIS. - **11. Risk of Liability/Indemnification**. Each Party shall assume all risk of and hereby does release the other Party, including without limitation, Foundation, IBD Plexus, its members, contributors, and their directors, officers, employees and agents (collectively, the "Releasees"), from all liability related to access to, storage and use of any Materials and other materials supplied to it by the other Party (the "Activities") and, only if Site is permitted by law to do so, each Party shall and hereby does indemnify, defend and hold Releasees harmless from and against all liability relating to the Activities, except to the extent that any such liability is caused by the gross negligence or willful misconduct of any of the Releasees. - **12. Remedies for Violation**. Any material violation of these terms and conditions shall constitute good cause for Foundation to immediately revoke permission granted for use of the Materials and, upon such written notice from Foundation, Site and PI shall promptly cease all such use and at the election of Foundation return ![](_page_22_Picture_6.jpeg) ![](_page_23_Picture_0.jpeg) or destroy all such Materials. Site agrees that any material violation of these terms and conditions may cause Foundation to pursue any and all available legal remedies. ![](_page_23_Picture_2.jpeg)

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