EP09.06: Chromosomal microarray as a first tier test following diagnostic prenatal procedures: the Toronto Mount Sinai Hospital experience
Bibliographic record
Abstract
To evaluate the clinical utility of this new service in a heterogeneous population in terms of: turn-around times, ability to obtain DNA on direct specimen vs the need for cell culture, diagnostic yield, and prevalence of VOUS based on the indications for testing. Our study population included women undergoing prenatal diagnostic testing referred from 7 prenatal diagnosis centres in Ontario and analysed at the cytogenetic lab at Mount Sinai Hospital during a one year period. There were 1152 samples. QF-PCR was preformed initially and if normal, followed by CMA. The prevalence of positive CMA results, were compared between groups based on clinical indications for testing. Strict reporting guidelines were designed in accordance with international guidelines, and locally discussed by a committee, which consists of cytogeneticists, clinical geneticists and MFM specialists. There were a total of 1152 samples. The overall diagnostic yield was 24.2%, which included 17.96% detected by QF-PCR and an additional 6.25% by CMA when QF-PCR was normal. The abnormal CMA results included clinically significant microdeletions/microduplications 2.34% (n = 27), aneuploidies 0.87% (n = 10), sex chromosomes aneuploidies 1.13% (n = 13), unbalanced translocations 0.17% (n = 2), chromosomal deletions (>5Mb) 0.35% (n = 4), susceptibility loci to neurodevelopment conditions 0.17% (n = 2), and VOUS 0.26% (n = 3). In addition to CMA abnormalities, SNP-array detected absence of hetrozygosity in 27 cases (2.34%). CMA showed clinically significant abnormalities in 9.2% with ultrasound abnormalities and 4.2% when the indication for testing was LMA, anxiety or positive prenatal screening. Our turn-around time was 12.8 days (ranged between 5–32 days). Abnormal results were detected in 4.2% of the low risk group, which is higher than previously reported. A larger sample size is needed to confirm our findings and to establish CMA as a primary tool for prenatal diagnosis.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".