Fluorescent, Multiplexed, Automated, Primer-Extension Assay for 3120+1G→A and I148T Mutations in Cystic Fibrosis
Bibliographic record
Abstract
Cystic fibrosis [(CF); Online Mendelian Inheritance in Man No. 602421] is an autosomal recessive disorder characterized by chronic broncho-pulmonary disease, pancreatic insufficiency, and increased sweat electrolytes (1). The CF transmembrane conductance regulator ( CFTR ) gene was identified by three groups (2)(3)(4) and was mapped to the long arm of chromosome 7 (7q31). The CFTR contains 24 exons, encodes a protein of 1480 amino acids, functions as a chloride channel, and regulates other transport pathways. Over 900 disease-causing mutations in the CFTR gene have been identified. The American College of Medical Genetics has recommended a core mutation panel for general population CF carrier screening (5). This panel contains 25 of the known CF mutations, including 3120+1G→A and I148T . 3120+1G→A (intron 16) is the second most common CF mutation in the African American population and accounts for 9–14% of the African American CF chromosomes (6). I148T (exon 4) is the second most common CF mutation in the French Canadian population and accounts for 9.1% of the French Canadian CF chromosomes (7). Most of the 25 mutations recommended by the American College of Medical Genetics can be detected with commercially available methods [Roche Molecular Biochemicals, Applied Biosystems and Innogenetics (ABI)], but no assays test for both the 3120+1G→A and I148T mutations, and two of the three assays do not detect either mutation. Therefore, we developed a multiplex primer-extension assay that rapidly and simultaneously detects these two CF mutations using the ABI Prism® SNaPshotTM ddNTP Primer-Extension assay. We believe this is the first demonstration of the use of this assay in the literature. The method uses a dideoxynucleotide primer-extension reaction (PER) in conjunction with an ABI genetic analyzer to detect the addition of a fluorescently labeled ddNTP to the 3′ end of a sequencing primer (Fig. …
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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 | 0.001 | 0.012 |
| 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".