Additional file 2 of Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Bibliographic record
Abstract
Additional file 2: Table S1. Clinical parameters, cohort classification and chr5:60,111,983 genotypes of 35 Dobermanns evaluated in Uppsala, Sweden. Table S2. A list of 393 public or in-house genomes from wolves and 87 dog breeds used in filtering and variant screening. Table S3. Distribution of the chr5:53,109,178G>A variant in 321 array genotyped Dobermanns, 10 Dobermann whole genomes and 393 non-Dobermann whole genomes. Table S4. Primer sequences, total concentration in reaction (Conc.), annealing temperature (An. temp) and assays used in transcript analyses. Table S5. Phenotype definitions used with UK Biobank data. CAD = coronary artery disease, LVSD = left ventricular systolic dysfunction. Table S6. Results of various univariate linear mixed model association analyses in GEMMA with different case subcohorts. Table S7. Association of sex and risk SNPs chr53:109,178 and chr5:60,531,090 with echocardiographic changes in the logistic regression analysis. Table S8. Association of sex and risk SNPs chr53:109,178 and chr5:60,531,090 with echocardiographic changes. Cases from the replication cohort were included. Table S9. Variants in the minor locus region (chr5:50-54 Mb) shared by two DCM-affected Dobermanns with A/A at the risk SNP chr5:53,109,178 and present in less than 10 % of 366 non-Dobermann genomes. Table S10. Variants in the minor locus region (chr5:50-54 Mb) shared by three DCM-affected Dobermanns with G/G at the risk SNP chr5:53,109,178 and present in less than 10 % of 366 non-Dobermann genomes. Table S11. Variants in the major locus region (chr5:58.2-63.3 Mb) shared by eight DCM-affected Dobermanns with A/A (N = 7) or G/A (N = 1) at the risk SNP chr5:60,531,090 and present in less than 10 % of 366 non-Dobermann genomes. Table S12. Gene content and annotation of the minor locus and flanking regions (chr5:50.0-54.0 Mb). Table S13. Gene content and annotation of the major locus and flanking regions (chr5:58.2-63.3 Mb). Table S14. Partial amino acid sequences and conservation of 94 Eutherian RNF207 orthologs. Table S15. Distribution of the chr5:60,111,983G>A variant in 9 RNA sequenced Dobermanns, 10 whole-genome sequenced Dobermanns and 393 non-Dobermann whole genomes from wolves and 87 dog breeds. Table S16. Distribution of the chr5:60,111,983G>A variant in 14230 dogs from 319 breeds or breed varieties genotyped on a commercial platform. Table S17. Potentially damaging variants in RNF207 identified in cardiomyopathy patients (UMCU and AMC), in UK Biobank participants diagnosed with DCM (UKBiobank) or in cardiomyopathy patients in the FinnGen consortium. Table S18. Potentially damaging variants in PRKAA2 identified in cardiomyopathy patients (UMCU and AMC), in UK Biobank participants diagnosed with DCM (UKBiobank) or in cardiomyopathy patients in the FinnGen consortium.
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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 | 0.002 | 0.023 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.840 | 0.157 |
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".