File S1 - <i>MTHFR</i> Glu429Ala and <i>ERCC5</i> His46His Polymorphisms Are Associated with Prognosis in Colorectal Cancer Patients: Analysis of Two Independent Cohorts from Newfoundland
Bibliographic record
Abstract
<p><b>Supporting information.</b> Figure S1 The circled SNP is rs1801131 (<i>MTHFR</i> Glu429Ala), which lies in a 12kb LD block. The black squares indicate other highly correlated SNPs (r<sup>2</sup>>0.80). Figure S2 The circled SNP is rs1046678 (<i>ERCC5</i> His46His), which lies in a 23kb LD block. The black squares indicate other highly correlated SNPs (r<sup>2</sup>>0.80). Table S1 n: number. Table S2 <sup>*</sup>Assay ID by Applied Biosystems (CA, USA). Underlined are the sequences on probes that are complementary to alleles they recognize. Assays for rs1799750 in <i>MMP1</i> gene and rs1799889 in <i>SERPINE1</i> gene were custom designed. Assays for rs1801131 in <i>MTHFR</i> gene and rs1047768 in <i>ERCC5</i> gene were predesigned by Applied Biosystems. Primer and probe sequences for these assays are not available since they are proprietary of Applied Biosystems. Seq: sequence. Table S3 n/a: not applicable. Polymorphisms with χ2 value greater than 3.84 were considered to be deviating from HWE (p<0.05). *For these gene deletions, since heterozygote genotype cannot be determined by the genotyping method applied, HWE was not calculated. All polymorphisms were investigated in this study regardless of their deviations from the HWE as these deviations may also be attributed to the fact that the Newfoundland population is considered a genetically isolated population <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061469#pone.0061469-Kweekel1" target="_blank">[49]</a>. Nevertheless, it is worth noting that while the <i>OGG1</i> Ser326Cys polymorphism that deviated from the HWE was included in the DFS multivariable model of the discovery cohort, its genotype data was not available for the validation cohort patients. Thus, the main conclusion on the disease-free survival analysis that the <i>ERCC5</i> His46His polymorphism was associated with DFS in both the discovery and the validation patient cohorts is not affected by including this polymorphism in the DFS analysis of the discovery cohort. Table S4 CI: confidence interval, HR: hazard ratio, MSI: microsatellite instability, n: number of patients, vs: versus. Table S5 CI: confidence interval, HR: hazard ratio, MSI: microsatellite instability, n: number of patients, vs: versus. Table S6 CI: confidence interval, HR: hazard ratio, MSI: microsatellite instability, n: number of patients, vs: versus. Table S7 CI: confidence interval, HR: hazard ratio, MSI: microsatellite instability, n: number of patients, vs: versus. Methods S1 Genotyping reactions. Methods S2 Construction of linkage disequilibrium (LD) maps.</p> <p>(DOC)</p>
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.003 | 0.003 |
| Meta-epidemiology (broad) | 0.007 | 0.001 |
| Bibliometrics | 0.008 | 0.013 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.001 | 0.003 |
| Open science | 0.006 | 0.005 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.007 | 0.000 |
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; both teacher heads agree on what is shown here.
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".