Abstract 43: The Colon Cancer Family Registry: A major resource for post-GWAS gene-environment studies.
Bibliographic record
Abstract
Abstract Background: The Colorectal Cancer Family Registry (Colon CFR) has served as an international resource for studies of the genetics and epidemiology of colorectal cancer (CRC) since 1997. It is the largest family-based resource in the world for the study of CRC and other cancers, such as endometrial cancer, that occur in CRC families. The Colon CFR has recruited participants via six institutions: Cancer Care Ontario, Fred Hutchinson Cancer Research Center, Mayo Clinic, University of Hawaii, University of Southern California Consortium, and University of Melbourne. Methods: CRC cases were recruited from both population-based cancer registries and family cancer clinics. Controls were recruited from population-based sources. Relatives were recruited via cases and controls. Participants were asked to: donate a blood sample; give permission to access any tumor tissue; complete a detailed personal and family history of cancer including degree of relationship, site of cancer and age of diagnosis; and complete a detailed baseline lifestyle questionnaire that was administered across all recruitment sites, which included items on established and suspected risk factors for colorectal cancer: personal characteristics including age, sex, height and weight, country of birth, ethnicity, race and religion; history of exercise, alcohol consumption and smoking; medication use including NSAIDs, cholesterol-lowering agents, diabetes medication and post- menopausal hormone use; history of colorectal cancer screening including fecal occult blood test, sigmoidoscopy, colonoscopy; personal history of surgery including polypectomy, other bowel surgery and hysterectomy; frequency of meat consumption and method of cooking; reproductive history (for women). Participants were also asked for detail information on the frequency of food consumption and portion size using a food frequency questionnaire. Follow-up of participants has been conducted every five years, by questionnaire, to update vital status, surgery, cancer screening, polypectomy, and personal and family history of cancer history. Participants have been characterized for major known predisposing CRC gene mutations and have undergone a genome-wide SNP testing and tested for known CRC SNPs. Results: The Colon CFR has enrolled 35,297 participants (11,635 affected with CRC, 3,629 affected with other cancers, and 20,033 unaffected) who have completed baseline questionnaires. We have 5-year follow-up data on 24,692 participants (6,329 affected with CRC, 2,261 affected with other cancers, and 16,102 unaffected) and 10-year follow-up data on 10,467 (3,654 affected with CRC, 1,182 affected with other cancers, and 5,631 unaffected). We have GWAS data on 3,830 participants, candidate SNP data on 18,000 participants, and mismatch repair gene mutation data on 2,697 participants (and observed 1,697 carriers with a deleterious mutation). Conclusion: This largest and best characterized CRC cohort in the world will facilitate post-GWAS research to provide insight into the role of environmental factors, and how they interact with genetic factors on CRC risk. Researchers are encouraged by the National Cancer Institute (USA) and the Colon CFR investigators to apply for access to this unique resource of data and biospecimens for collaborative research. Citation Format: Aung Ko Win, Daniel D. Buchanan, Noralane M. Lindor, Robert W. Haile, Polly A. Newcomb, Loic Le Marchand, Steven Gallinger, Hopper L. John, Casey Graham, Mark A. Jenkins. The Colon Cancer Family Registry: A major resource for post-GWAS gene-environment studies. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 43.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.012 | 0.055 |
| Meta-epidemiology (narrow) | 0.001 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.001 |
| Bibliometrics | 0.009 | 0.016 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.004 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.150 | 0.088 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".