Whole genome SNP genotype piecemeal imputation
Bibliographic record
Abstract
BACKGROUND: Despite ongoing reductions in the cost of sequencing technologies, whole genome SNP genotype imputation is often used as an alternative for obtaining abundant SNP genotypes for genome wide association studies. Several existing genotype imputation methods can be efficient for this purpose, while achieving various levels of imputation accuracy. Recent empirical results have shown that the two-step imputation may improve accuracy by imputing the low density genotyped study animals to a medium density array first and then to the target density. We are interested in building a series of staircase arrays that lead the low density array to the high density array or even the whole genome, such that genotype imputation along these staircases can achieve the highest accuracy. RESULTS: For genotype imputation from a lower density to a higher density, we first show how to select untyped SNPs to construct a medium density array. Subsequently, we determine for each selected SNP those untyped SNPs to be imputed in the add-one two-step imputation, and lastly how the clusters of imputed genotype are pieced together as the final imputation result. We design extensive empirical experiments using several hundred sequenced and genotyped animals to demonstrate that our novel two-step piecemeal imputation always achieves an improvement compared to the one-step imputation by the state-of-the-art methods Beagle and FImpute. Using the two-step piecemeal imputation, we present some preliminary success on whole genome SNP genotype imputation for genotyped animals via a series of staircase arrays. CONCLUSIONS: From a low SNP density to the whole genome, intermediate pseudo-arrays can be computationally constructed by selecting the most informative SNPs for untyped SNP genotype imputation. Such pseudo-array staircases are able to impute more accurately than the classic one-step imputation.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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; a candidate call from one teacher head, 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".