Documenting Trofinetide Treatment Phenotypes in Rett Syndrome with a Dual-LLM Consensus Pipeline

Objective: Trofinetide, approved in 2023 as the first Rett syndrome treatment, lacks scalable real-world monitoring because chart review is labor-intensive. We developed a dual large language model (LLM) consensus pipeline to extract 18 treatment-response phenotypes, comprising 4 adverse effects, 13 Rett clinical features, and medication refusal, from clinical notes. Materials and Methods: We analyzed 26,763 notes from 108 patients with confirmed sustained trofinetide exposure at Texas Children's Hospital. The pipeline filters notes by keyword, classifies each through two LLMs requiring consensus, and aggregates a patient-by-timepoint matrix. Architecture and prompt were selected on a diarrhea development set, then frozen and applied to the other 17 phenotypes with the phenotype definition substituted, as an out-of-sample test. The reported prompt comparison scores 183 expert-labeled cells. Results: A prompt requiring diarrhea to be active and severe performed best (84.2 $\pm$ 0.0% accuracy; F1 = 0.674), 47 percentage points above regular-expression matching ($p < 0.0001$). Expert reviewers judged six of the pipeline's calls per phenotype, three positive and three negative, and agreed with 90.2% (92/102). The 13 Rett clinical features are manifestations of the disorder itself rather than adverse effects of trofinetide. Gross and fine motor impairment, language/communication, and stereotypy were documented present in 92-100% of patients at every visit. Discussion: In-context LLM extraction captured multi-domain treatment responses. The outcome is documented presence at each visit, not a direction-of-change judgment. Conclusion: Coupling in-context LLM reasoning with a consensus architecture offers a scalable alternative to keyword and regular-expression extraction for real-world evidence, adapting to new phenotypes and medications through configuration alone.