This challenge is no longer accepting new submissions.
Up For A Challenge (U4C) – Stimulating Innovation in Breast Cancer Genetic Epidemiology
Innovation in Breast Cancer Genetics Epidemiology
Department of Health and Human Services - National Institutes of Health
Type of Challenge: Scientific
Partner Agencies | Non-federal: Sage Bionetworks
Submission Start: 06/05/2015 09:00 AM ET
Submission End: 01/15/2016 08:00 PM ET
This challenge is externally hosted.
You can view the challenge details here: https://www.synapse.org/upforachallenge
The National Institutes of Health, National Cancer Institute’s (NCI) Division of Cancer Control and Population Sciences (DCCPS) announces that they are partnering with Sage Bionetworks to launch “Up For A Challenge (U4C) – Stimulating Innovation in Breast Cancer Genetic Epidemiology” (the “Challenge”) to encourage unique approaches to more fully decipher the genomic basis of breast cancer. Utilizing innovative approaches, the goal of this Challenge is to identify new genes or combinations of genes, genetic variants, or sets of genomic features involved in breast cancer susceptibility. In addition, the NCI aims to advance innovation in the field of genetic epidemiology by making data more widely available, increasing the amount and diversity of minds approaching a difficult scientific problem, and promoting broader collaborations.
In order to stimulate innovation, the National Cancer Institute’s (NCI) Division of Cancer Control and Population Sciences (DCCPS) is launching a prize competition to inspire novel cross-disciplinary approaches to more fully decipher the genomic basis of breast cancer, called “Up For A Challenge (U4C) – Stimulating Innovation in Breast Cancer Genetic Epidemiology” (the “Challenge”) using the America Creating Opportunities to Meaningfully Promote Excellence in Technology, Education, and Science (COMPETES) Reauthorization Act of 2010.
The goal of this Challenge is to use innovative approaches to identify novel pathways—including new genes or combinations of genes, genetic variants, or sets of genomic features—involved in breast cancer susceptibility in order to generate new biological hypotheses. To that end, several data sets have been gathered and will be made available for use in the Challenge; some of these will be released for the first time. In addition, Challenge participants will be free to use any other publicly available data sets (subject to compliance with applicable terms and conditions) for the purposes of developing and applying methods for identification of the novel pathways.
Breast cancer is the most commonly occurring cancer, and the second most common cause of cancer deaths in women in the United States. An estimated 231,840 new cases of invasive breast cancer are expected to be diagnosed among women (2,350 in men) in the U.S. during 2015 with an estimated 40,730 deaths. Despite advances in breast cancer therapies, breast cancer remains a major public health burden. One approach to reduce overall occurrence and mortality from breast cancer is to develop ways of identifying women who are at increased risk for breast cancer.
Epidemiologic studies suggest that genetic factors play a key role in determining who is at increased risk of developing breast cancer, as well as what type of cancer they develop. To date, genome-wide association studies (GWAS) have helped researchers identify more than 90 common genetic variations. Although GWAS have greatly increased our understanding of the genetic components of breast cancer susceptibility, the results to date explain only a small proportion of the estimated genetic contribution to the risk of breast cancer. However, shifting the focus of analysis from individual genetic variants (also known as single nucleotide polymorphisms or SNPs) to pathways (i.e. combinations of genes, genetic variants, or sets of genomic features), could lead to the identification of novel gene sets involved in breast cancer risk.
This Challenge provides an opportunity to examine the heritable contribution to racial disparities, by facilitating access to GWAS data sets from African American, Asian, European, and Latino women. African American women are known to have a lower incidence of breast cancer, but survival is lower for African American than for non-Hispanic white women at every stage of diagnosis. Meanwhile, Asian women have the lowest rates of breast cancer incidence and mortality compared with non-Hispanic white, African American, and Hispanic/Latino women. Findings from this Challenge may provide insights into some of these observed differences.
As more fully described below, participants are invited to use innovative approaches to identify novel pathways—including new genes or combinations of genes, genetic variants, or sets of genomic features—involved in breast cancer susceptibility. Besides developing a better understanding of cancer risk assessment, the identification of breast cancer susceptibility genes holds promise for providing therapeutic targets for drug development.
PrizesUp For A Challenge
Cash Prize Amount: $50,000
- To be eligible to win a prize under this Challenge, an individual or entity—
- Shall have registered to participate in the Challenge under the rules promulgated by the National Cancer Institute (as published in this notice);
- Shall have complied with all the requirements under this section;
- In the case of a private entity, shall be incorporated in and maintain a primary place of business in the United States, and in the case of an individual, whether participating singly or in a team, shall be a citizen or permanent resident of the United States;
- May not be a Federal entity;
- May not be a Federal employee acting within the scope of his or her employment and further, in the case of HHS employees may not work on their Entries during assigned duty hours. Note: Federal ethical conduct rules may restrict or prohibit Federal employees from engaging in certain outside activities, so any Federal employee not excluded under the prior paragraph seeking to participate in this Challenge outside the scope of employment should consult his/her agency’s ethics official prior to developing an Entry;
- May not be an employee of the NIH, a judge of the Challenge, or any other party involved with the design, production, execution, or distribution of the Challenge or the immediate family member of such a party (i.e., spouse, parent, step-parent, or step-child). Without limiting the generality of the foregoing, members of the Evaluation Panel which will score Entries and the NIH Judges, as well as their students are not eligible to participate in the Challenge.
- Federal grantees may not use Federal funds to develop Challenge Entries unless consistent with the purpose of their grant award and specifically requested to do so due to the Challenge design, and as announced in the Federal Register.
- Federal contractors may not use Federal funds from a contract to develop Challenge Entries or to fund efforts in support of a Challenge Entry.
- An individual, Team, or entity that is currently on the Excluded Parties List (https://www.epls.gov/) will not be selected as a Finalist or prize winner.
- Whether singly or as part of a team or entity, each individual participating in the Challenge must be 18 years of age or older.
- An individual shall not be deemed ineligible to win because the individual used Federal facilities or consulted with Federal employees during the Challenge provided that such facilities and/or employees, as applicable, are made available on an equitable basis to all individuals and Teams participating in the Challenge.
- Each individual (whether competing singly or in a team) or entity agrees to follow applicable local, State, and Federal laws and regulations.
- Each individual (whether participating singly or in a team) and entity participating in this Challenge must comply with all terms and conditions of these rules, and participation in this Challenge constitutes each such participant’s full and unconditional agreement to abide by these rules, which may also be found on the Challenge website (https://www.synapse.org/upforachallenge). Winning is contingent upon fulfilling all requirements herein.
Entries will be scored by the Challenge Evaluation Panel using the criteria listed below. After the Challenge Evaluation Panel provides final scores, the highest scoring applications will be evaluated for reproducibility by Sage Bionetworks’ data scientists. In order to qualify for a Challenge prize, it must be possible for Sage Bionetworks’ data scientists to reproduce Entry results within 1 month. The NCI Judges will review scores and reproduction by Sage and make recommendations to the NCI Director. The NCI Director will make the final selection of Entries for award.
1. Identification of Novel Findings (25 points) – Using breast cancer GWAS data sets available in dbGaP and/or any other publicly available data sets, Challenge participants must identify new genes or combinations of genes, genetic variants, or sets of genomic features associated with breast cancer susceptibility. a. The National Human Genome Research Institute’s (NHGRI) Catalog of Published Genome Wide Association Studies (http://www.genome.gov/gwastudies/) or variants/loci identified in the following publications can be used to evaluate possible novel findings: i. Mavaddat et al., 2010, http://www.ncbi.nlm.nih.gov/pubmed/?term=20542480; ii. Ghoussani et al., 2013, http://www.ncbi.nlm.nih.gov/pubmed/?term=23973388; iii. Fachal and Dunning, 2015, http://www.ncbi.nlm.nih.gov/pubmed/?term=25727315) b. The scale for novelty for the Challenge Evaluation panel to use as a guide is provided: i. New variants in well-established high or moderate penetrance genes (e.g., BRCA1/BRCA2; ATM; PALB2) (low) ii. New variants in GWAS-identified genes or loci (med) iii. New combinations of variants which were previously identified (i.e., the combination or combined effect is new, but the variants were previously identified) (medium) iv. New genes or loci (high) v. New combinations of variants from genes or loci not identified previously (i.e., the combination and some of the variants are new) (high)
2. Replication of Findings (25 points) – Evidence of the validity of the proposed novel finding will be evaluated through replication. a. There are several different ways replication can be accomplished. These may include using data sets as testing and training data (or discovery in one data set and replication in another data set) or dividing the data into several portions and performing some type of cross-validation. The Challenge Evaluation panel will also be open to other innovative approaches for replication. i. The Challenge participant will need to select criteria for replication and provide a justification for the selected criteria. Using the criteria selected by the Challenge participant, the Challenge participant must demonstrate replication of findings. b. NOTE: Challenge participants should provide their criteria for replication in the narrative portion of their Challenge Entry. c. The adequacy of criteria selected by the Challenge participant and evidence for replication will be scored by the Challenge Evaluation Panel.
3. Innovation of Approach (25 points) – Innovation and creativity of the submitted approach will be evaluated. Innovation will be defined as a new or significantly improved method. The submitted narrative must describe what is innovative about the approach, what this approach is building on, and why the approach is necessary or how it improves upon existing approaches. Some criteria for innovation include the following: a. Does the Entry seek to shift current paradigms by utilizing novel theoretical concepts, approaches, or methodologies? b. Are the concepts, approaches, or methods in the Entry novel to this field of research or novel in a broader sense? c. Does the Entry represent a refinement, improvement, or new application of theoretical concepts, approaches, or methodologies?
4. Evidence of Novel Biological Hypothesis(es) (10 points) – a. Evaluation of this aspect of Challenge Entries will be based on whether findings (i.e., new genes or combinations of genes, genetic variants, or sets of genomic features) lead to novel biological hypotheses. A description of these hypotheses should be provided in the final project Entry. b. Novel biological hypotheses should be testable, either using computational or laboratory approaches. Evaluation will be based on the narrative description of the design of testable experiments, which could examine the novel biological hypothesis identified through these new genes or combinations of genes, genetic variants, or sets of genomic features associated with breast cancer. The format should mirror an outline of grant-specific aims. NOTE: The “Evidence of Novel Biological Hypothesis(es)” criteria (4) is distinct from the “Identification of Novel Findings” criteria (1). The “Evidence of Novel Biological Hypothesis(es)” criteria (4) is based on the narrative description of hypotheses generated from the findings and proposed follow up experiments. In contrast, the “Identification of Novel Findings” criteria (1) are the identification of new genes or combinations of genes, genetic variants, or sets of genomic features associated with breast cancer susceptibility.
5. Collaboration (15 points) – Points will be awarded based on (a) the number of different fields represented on the Team; (b) the number of new collaborations represented on the Team (defined as individuals not having published together in the past 5 years); and (c) the number of individuals invited to participate in the Challenge by Team members resulting in Entries to the Challenge
How To EnterRegistration Process for Participants To register for this Challenge, Challenge participants may access the registration on the Challenge website (https://www.synapse.org/upforachallenge). Access to this website may also be found by searching the www.challenge.gov site for “Up For A Challenge.” Individuals may participate in the Challenge as individuals or as Teams. Details about participating as a Team are provided below:
- After registration, you may participate alone or on a Team with other Challenge participants. To work on a Team, you may either create a new Team or join a pre-existing Team.
- There is no maximum Team size.
- All Teams must designate a Team Captain. Each individual member of a Team must be a registered participant in the Challenge.
- Individuals may participate on multiple Teams, and Challenge Teams may merge (requiring mutual agreement of Team Captains). Individuals are allowed to leave a Team to work alone or join another Team.
Data Access Process Once registered for the Challenge, participants must apply for controlled access to the designated Challenge genetic datasets following instructions on the Challenge website. Challenge participants may use any of these dbGaP datasets or any other datasets available to anyone (either publically available or available through controlled access) such as data from the Cancer Genome Atlas (TCGA) (http://cancergenome.nih.gov/) or the ENCyclopedia Of DNA Elements (ENCODE) project (http://www.genome.gov/encode/). Data will be requested through database of Genotypes and Phenotypes (dbGaP) application process. Details regarding the process for requesting data are provided on the Challenge website (https://www.synapse.org/upforachallenge). Data Access Requests will be reviewed by the appropriate NIH Data Access Committees (DAC) to ensure that the proposed project is consistent with any Data Use Limitations for the requested dataset(s).
NOTE: that any scientific collaborators, including contractors, who are not at the same institution as the PI must submit their own DAR. Data cannot be shared with collaborators from other institutions until they have submitted an application (and explicitly named this collaborators) to use the dataset(s) from their institution(s) and have received approval. If Approved Users are provided access to NIH genomic datasets for inter-institutional collaborative research described in the research use statement of the DAR, and all members of the collaboration are also Approved Users through their home institution(s), data obtained through this DAR may be securely transmitted within the collaborative group. Challenge participants who obtain data from dbGaP should note that they are agreeing to the NIH Genomic Data User Code of Conduct (http://gds.nih.gov/pdf/Genomic_Data_User_Code_of_Conduct.pdf) and they are agreeing to the terms of specific Data Use Certificates for each individual dataset requested (The model Data Use Certificate can be found here -- http://gds.nih.gov/pdf/Model_DUC.pdf). Note that individual datasets may have additional limitations in regards to use of the data. As the GWAS datasets obtained from dbGaP are considered controlled access data, individuals approved to use these data must abide by dbGaP security best practices in regards to the data (http://www.ncbi.nlm.nih.gov/projects/gap/pdf/dbgap_2b_security_procedures.pdf).
If submitting a request to dbGaP for use of data for the Challenge, participants should be aware that the data requested should be used solely for the research purpose described in the Data Access Request, i.e. solely for the Challenge. New uses of these data outside this Challenge will require submission of a new Data Access Request. Challenge Entries As used in this notice, “Entry” is the information submitted in the manner and format specified on the Up For A Challenge (U4C) website (https://www.synapse.org/upforachallenge). All Entries must be received by the applicable deadline. Entries submitted after a posted Challenge deadline will not be considered. Entries may be submitted on behalf of a Team by any of its participants. It is up to each Team to organize its Entry(ies) and to follow the Challenge submission requirements. On submission of an Entry, Challenge participants must include the Team name under which they are submitting. All final Entries must be submitted through the Challenge website on Synapse, following website instructions and should provide necessary and sufficient detail and annotation for reproduction of the submitted results.Information accompanying each Entry should include:
- Title of project
- Name of Team
- Names and field of expertise of Team members
- List of new pair-wise collaborations on Team (defined as individuals not having published together in the past 5 years)
- Information about how Team learned about the Challenge
- Identification of datasets used (1 page)
- A description of methods used to generate the findings (4 pages maximum)
- Narrative which addresses the evaluation criteria (identification of novel findings, replication of findings, innovation of approach, evidence of novel biological hypothesis(es), and collaboration) (6 pages maximum)
- The corresponding source code so that the Challenge organizers can re-run and manually review and verify that the code affiliated with the top scoring Entries yield the submitted results. Warranties
- By submitting an Entry to the Challenge, Challenge participants represent and warrant that all information provided in their Entries and as a result of the Challenge registration process is true and complete, that Challenge participants have the right and authority to submit such Entry on their own behalf or on behalf of the persons and entities specified within the Entry, and that the Entry:
- Only complete Entries, which follow application instructions, will be reviewed and eligible to win. Top performing Entries will be reviewed thoroughly. The NCI reserves the right to disqualify any Challenge participants in instances where cheating or other misconduct is identified. Details regarding the dispute resolution process are provided on the Challenge website (https://www.synapse.org/upforachallenge).
- Is the Challenge participant’s or Team’s (as applicable) own original work, or is used by permission with full and proper credit given within the Entry;
- Does not contain confidential information or trade secrets (the Team’s or anyone else’s);
- Does not violate or infringe upon the patent rights, industrial design rights, copyrights, trademarks, rights of privacy, publicity or other intellectual property or other rights of any person or entity;
- Does not contain malicious code, such as viruses, timebombs, cancelbots, worms, trojan horses or other potentially harmful programs or other material or information;
- Does not and will not violate any applicable law, statute, ordinance, rule or regulation; and
- Does not trigger any reporting or royalty obligation to any third party.