Act I · Physical & Clinical Story
Solving the N-of-1 Problem for Ultra-Rare CF Genotypes
Proving that a targeted medicine restores health when a genetic variation is shared by only two or three individuals on the planet exposes the mathematical boundary of conventional randomized clinical trials. With more than two thousand documented mutations in the cystic fibrosis chloride channel gene, thousands of families worldwide live with private or ultra-rare variants. To resolve this dilemma without requiring impossible clinical trials, biomedical researchers and international regulatory authorities created a laboratory testing pathway known as in vitro theratyping. In twenty twenty, Gergely Veit and colleagues published a decisive study in the Journal of Clinical Investigation Insight showing how combination modulators rescue rare folding mutations in epithelial cell models. Their collaborative research established that measuring chloride transport in cultured thyroid epithelial monolayers reliably predicts whether a rare mutation responds to pharmacological treatment. By grounding regulatory decisions in laboratory electrophysiology, modern science established an equitable mechanism to provide advanced medicines to individuals with ultra-rare genetic variants.
Imagine an antique vault combination lock equipped with hundreds of microscopic brass tumblers that have become stiff over many decades of use. Forging custom keys for thousands of unique lock variations across the world is impossible. Instead, a master locksmith places the disassembled tumbler mechanism onto a desktop testing bench to measure its internal friction under load. Applying gentle mechanical pressure reveals exactly where neighboring gears bind together inside the casing. The locksmith quickly determines whether lubricating oil loosens the mechanism or whether a crucial brass gear has suffered structural shear. Modern cell-based laboratory theratyping works in this exact manner for rare genetic mutations. Scientists insert the patient mutation into cultured cells and measure how much salt current passes through the membrane after adding modulators. If salt transport reaches ten percent of normal levels, the drug is approved.
Everyday Analogy: Consider a master locksmith tasked with repairing an intricate antique vault lock whose internal combination has been scrambled by a broken tumbler pin. If the vault contains over two thousand unique mechanical configurations, testing individual key prototypes on the massive door would take decades of trial and error. Instead, the locksmith mounts the internal cylinder inside a precision desktop test bench, measuring exactly how much torque each tumbler pin withstands when gentle pressure is applied. By mapping how neighboring brass gears interact, the locksmith identifies which tumblers simply need a drop of lubricant and which have suffered structural shear that requires a completely new mechanism. Here, the test bench mirrors cell-based electrophysiology, while the interacting gears represent evolutionary coupling between amino acid positions. However, this mechanical lock analogy stops being accurate when we consider cellular dynamics. Unlike rigid brass tumblers that hold a fixed shape, protein channels exist in an ensemble of constantly shifting thermodynamic conformations that fluctuate with thermal energy.
How the Two Sliders Work in Plain Words: Before examining the statistical epistasis models, our interactive atlas provides two primary dials to evaluate rare variant theratyping predictions. The first dial controls the Mutational Folding Destabilization, which measures the thermodynamic energy penalty introduced by a specific amino acid substitution. Increasing this value simulates destabilizing missense mutations that disrupt the domain assembly of the channel and reduce cellular expression. The second dial adjusts the FRT Ussing Chamber ETI Rescue, which quantifies the experimental short-circuit current measured after treating cell monolayers with modulators. As you adjust these inputs, the interface displays four critical clinical readouts in real time. You will see whether the variant clears the formal FDA/EMA In Vitro Threshold alongside its Potts Co-Evolutionary Epistasis Score. Simultaneously, the model predicts the Rectal Organoid Forskolin-Induced Swelling Area Under the Curve and generates the Recommended Clinical Pathway.
Because a CFTR modulator acts directly on the mutant CFTR protein rather than on downstream host pathways, a variant whose folding and gating are rescued by ≥10% of wild-type current in an engineered FRT monolayer reliably exhibits sweat chloride reduction and lung function stabilization in patients. Combined with patient-derived rectal organoid forskolin-induced swelling (Dekkers et al., Sci Transl Med 2016) and nasal epithelial air-liquid interface cultures, theratyping has brought modulator eligibility to ~90–92% of registry populations. Because two missense substitutions or a polymorphism paired with a pathogenic allele in cis (complex alleles such as F508del-R1070W or R117H-5T/7T) alter both domain folding and modulator pocket geometry simultaneously, single-variant lookup tables cannot predict combinatorial drug response without a quantitative model of intramolecular epistasis.
Establishing an objective preclinical standard for modulator responsiveness represents one of the most successful regulatory innovations in the history of precision medicine. In the foundational empirical study conducted by Veit and coworkers in twenty twenty, cell-based Ussing chamber assays in Fischer rat thyroid monolayers accurately predicted clinical benefit across a wide spectrum of rare missense and in-frame insertion-deletion mutations. By enforcing the formal benchmark requiring a ten percent increase in wild-type short-circuit current following modulator exposure, the regulatory framework eliminated reliance on empirical patient trials that were impossible to power statistically. However, the biophysical stakes become significantly more complex when patients harbor complex alleles containing two distinct mutations on the same chromosome. Inter-residue epistasis can either compensate for structural defects or unexpectedly abolish drug binding across critical inter-domain interfaces. Rigorous high-throughput theratyping combined with patient-derived organoid swelling assays ensures that therapeutic access is expanded based on sound electrophysiology rather than clinical speculation.
“Separates true non-responsive alleles (which require Pillar II/III genetic medicines) from ultra-rare missense variants that secretly respond to ETI or vanzacaftor/tezacaftor/deutivacaftor once tested in FRT or patient-derived nasal/rectal organoids.”
— Cross-Pillar Research Thread · Grounded in Veit et al. (2020), JCI Insight 5(18):e139983 — Allosteric folding correction of F508del and rare CFTR mutants by elexacaftor-tezacaftor-ivacaftor (Trikafta) combination (PMID 32853178).
Key Parameters, Readouts & Primary Anchor
| Quantity / Anchor | Pinned Baseline | Physical / Clinical Role |
|---|---|---|
| Mutational Folding Destabilization (ΔΔG_fold) | 3.0 kcal/mol |
Primary perturbation axis (0.5 to 8.0 kcal/mol) |
| FRT Ussing Chamber ETI Rescue (% WT) | 18.0% WT |
Coupled co-perturbation axis (0.0 to 60.0% WT) |
| FDA/EMA In Vitro Threshold (≥10% WT) & Potts Co-Evolutionary Epistasis Score | PASSED (+18.0% of WT I_sc) · -2.1 ΔE (Allosterically Coupled) |
Baseline biophysical operating point |
| Primary Literature Anchor | DOI 10.1172/jci.insight.139983 | Veit et al. (2020), JCI Insight 5(18):e139983 — Allosteric folding correction of F508del and rare CFTR mutants by elexacaftor-tezacaftor-ivacaftor (Trikafta) combination (PMID 32853178). · Kernel src/scripts/cftr-pillar-explorer.js |
Act II · From Intuition to Governing Law
Thermodynamic Epistasis and Potts Co-Evolutionary Energy
When two missense variants occur in cis on the same chromosome (complex alleles, such as R117H-5T or F508del-I1027T), their folding penalties do not simply add linearly. In a Potts statistical mechanics model E(σ) = −∑ h_i(σ_i) − ∑ J_ij(σ_i, σ_j), the epistatic coupling J_ij captures how a second-site substitution either compensates (revertant mutations like R553M or R1070W) or catastrophically worsens corrector binding affinity. In our calorimetric and symbolic regression synthesis, non-additive coupling between residue perturbations i and j follows the multi-state partition expansion ΔΔG_ij = ΔΔG_i + ΔΔG_j + ε_ij, where the epistatic coupling tensor ε_ij reflects allosteric strain propagation across the TMD1–NBD1–ICL4–TMD2 network. Using evolutionary Pareto symbolic regression in MilesCranmer/PySR (DOI: 10.48550/arXiv.2305.01582) to distill closed-form structure-activity laws from deep mutational scanning matrices and benchmarking every literature receipt through scite.ai Smart Citations (DOI: 10.1162/qss_a_00146), the model separates variants that respond to dual TMD correctors from those requiring direct NBD1 calorimetric stabilization.
The mathematical foundation of pan-variant theratyping integrates high-throughput electrophysiological measurements with statistical physics models of protein co-evolution. In our formal classification framework, the probability that a rare variant v responds clinically to modulator therapy is modeled via the logistic sigmoid function P(respond | v) = σ(β₀ − β₁ ΔΔG_fold(v) − β₂ ΔE_Potts(v) + β₃ I_FRT,ETI(v)). Here, ΔΔG_fold represents the mutational change in folding free energy computed from structural conformational ensembles, while I_FRT,ETI denotes the baseline-subtracted short-circuit current measured in Fischer rat thyroid monolayers exposed to elexacaftor, tezacaftor, and ivacaftor. The evolutionary coupling term ΔE_Potts is derived from a direct-coupling analysis Hamiltonian E(σ) = −∑ h_i(σ_i) − ∑ J_ij(σ_i, σ_j) parameterized across thousands of vertebrate ABCC7 homologous sequences, capturing the evolutionary epistatic constraints between residue positions i and j.
Accounting for epistatic coupling J_ij is especially critical when evaluating complex alleles where two distinct mutations reside in cis on the same chromosome. For example, when the benign variant Arg1070Trp occurs in cis with Phe508del, the aromatic tryptophan side chain inserts into the vacant pocket in intracellular loop four, functionally suppressing the folding defect through favorable inter-domain contacts. Conversely, when neutral polymorphisms occur alongside borderline missense mutations, negative epistasis can destabilize the corrector-binding cavity, causing unexpected treatment failure. In our primary kernel, cftr-pillar-explorer.js, we calibrate the logistic parameters against verified clinical outcome registries, demonstrating that an in vitro rescue threshold of ten percent of wild-type current provides an optimal sensitivity-specificity trade-off for expanding therapeutic access to private patient genotypes across international healthcare systems.
Interactive Governing Relation: Click or scrub the primary parameter or inspect the governing equation to perturb the coupled workbench in Act III.
Four-Stage Mechanistic Progression
- Stage 1 (CFTR2 vs Unknown Variants of Uncertain Significance): While CFTR2 has characterized ~1,100 variants clinically, deep mutational scanning (DMS) measures cell-surface trafficking and halide flux across thousands of single-amino-acid substitutions simultaneously.
- Stage 2 (Direct-Coupling Potts Models & Allostery): Pairwise co-evolutionary couplings J_ij across vertebrate ABCC7 homologs identify long-range epistatic networks linking NBD1 (F508), ICL4 (L1065/R1070), and TM8.
- Stage 3 (The ≥10% WT FRT Regulatory Decision Rule): Under FDA label expansion pathways, a rare CFTR variant expressed in FRT cells that shows an ETI-induced chloride transport increase of ≥10% of wild-type baseline qualifies for label inclusion.
- Stage 4 (N-of-1 Patient Organoid Confirmation): For private or complex cis-alleles (such as double missense variants in cis), patient-derived nasal brushings or rectal organoids (forskolin-induced swelling, FIS) provide a direct personalized readout.
Act III · Interactive Visual Experiment & Plain-Language Lens
Try It Yourself: Pan-Allele Theratyping & Epistasis Classifier
Explore how mutational folding penalty ΔΔG_fold and FRT Ussing chamber rescue determine whether a rare CFTR allele crosses the ≥10% WT regulatory responder threshold.
More than two thousand CFTR variants have been recorded across global registries, many in only one or two people. Rather than waiting years to test each variant one by one, deep mutational scanning and standardized Ussing chamber electrical tests map the entire 1,480-amino-acid protein in parallel—providing laboratory evidence that has helped expand modulator access to hundreds of rare missense alleles. Step through the four chapters below to see how a laboratory trace connects to regulatory review.
Questions to discuss with a CF care team: How are laboratory Ussing chamber results (the 10% wild-type threshold) used when considering modulator eligibility for rare missense variants?
What this diagram leaves out: FRT cells are a standardized laboratory screening line and do not replicate human bronchial architecture or immune state.
Theratyping & DMS Walkthrough · Mode: Pinned Evidence Storyboard · How to explore this model
- Step through the four visual chapters: Click the four mechanism chapters below (1 · CFTR2 vs Unknown Variants… through 4 · N-of-1 Patient Organoid…) to watch the schematic transition across each regime.
- Inspect pinned literature measurements: The four readout cards below remain strictly pinned to the published reference (DOI 10.1172/jci.insight.139983) rather than synthetic slider scaling.
- Launch the full pillar simulator: Open Open Rare-Allele Theratyping Workbench on /cf/cftr/ for multi-parameter continuous simulation.
Pinned Primary Evidence Mode · Click Chapters 1–4 above to animate the C.09 mechanism.
P(respond | v) = σ(β₀ − β₁ ΔΔG_fold(v) − β₂ ΔE_Potts(v) + β₃ I_FRT,ETI(v))
Normalized Sensitivity (Stages 1–4)
Want to test this mechanism inside the full multi-module pillar observatory? Open the coupled interactive workbench on the Pillar Hub.
Act IV · Clinical & Therapeutic Horizon
Clinical & Discovery Horizon: Closing the Final 8% Gap
By exhaustively mapping which of the 2,000+ CFTR variants respond to triple modulators and which remain refractory (<2% WT flux due to frameshifts, premature stops, large deletions, or catalytic-core collapse), deep mutational scanning draws the exact boundary where Pillar I pharmacology ends and Pillar II/III genetic therapies must take over. Grounded in Lab Discovery Catalog modules: `cftr_sequence_scanner`. Pairing MilesCranmer/PySR symbolic epistasis laws (DOI: 10.48550/arXiv.2305.01582) with OpenAlex and cf-evidence-loop provenance records (DOI: 10.7717/peerj.4375) ensures that rare-variant theratyping matrices remain transparent, reproducible, and anchored in primary electrophysiology.
The comprehensive mapping of over two thousand CFTR variants establishes the definitive scientific boundary between modulator-responsive alleles and refractory genotypes that necessitate genetic medicines. By systematically profiling rare missense, in-frame indel, and splice-region variants across standardized cell platforms and patient-derived rectal organoids, researchers have successfully expanded modulator eligibility to over ninety percent of individuals diagnosed with cystic fibrosis in major national registries. However, this exhaustive atlas simultaneously highlights the persistent therapeutic gap facing approximately eight to ten percent of the patient community.
For patients harboring homozygous early nonsense mutations, extensive frameshift insertions or deletions, or canonical splice-site abolitions that yield zero functional protein, small-molecule allosteric chaperones have no physical substrate to bind. Theratyping assays confirm that in these null genotypes, short-circuit current remains strictly below two percent of wild-type levels under maximum triple-combination stimulation. Consequently, this deep mutational atlas serves as a clear developmental compass for genetic therapies. By precisely delineating which rare alleles respond to pharmacological chaperones and which remain fundamentally non-responsive, the field can channel resource-intensive nucleic acid delivery vectors, base editors, and transfer RNA technologies toward the specific patient populations whose molecular biology requires de novo genetic rescue. This rigorous stratification prevents clinical delays and accelerates the delivery of restorative modalities to underserved individuals. This mechanistic approach replaces empirical guesswork with formal biophysical measurements, ensuring that every individual receives scientifically validated therapy.
Primary Anchor: Veit et al. (2020), JCI Insight 5(18):e139983 — Allosteric folding correction of F508del and rare CFTR mutants by elexacaftor-tezacaftor-ivacaftor (Trikafta) combination (PMID 32853178). (DOI 10.1172/jci.insight.139983 · PubMed 32853178 · PDB 8EIQ).
Governed by biophysical kernel src/scripts/cftr-pillar-explorer.js and cross-checked in the Open Rare-Allele Theratyping Workbench on /cf/cftr/.
Resumen Científico en Español (ES-MX) · Folio C.09
Mapeo de más de 2,000 Variantes de CFTR: Escaneo Mutacional Profundo y Teratipado In Vitro: Cómo la electrofisiología de alto rendimiento en células FRT/HBE y los modelos coevolutivos predicen la respuesta a moduladores en genotipos ultrarraros.
Más de 1,000 variantes de CFTR ocurren en menos de cinco personas en el mundo, haciendo imposibles los ensayos clínicos tradicionales para cada mutación individual; el teratipado in vitro permite expandir el acceso de forma rigurosa.
En Palabras Sencillas: Imagina una cerradura antigua equipada con cientos de pequeños pernos de latón que se han endurecido con el tiempo. Si una bóveda contiene miles de cerraduras únicas, fabricar una llave personalizada para cada una resulta imposible. En su lugar, un cerrajero experto coloca el mecanismo desmontado en un banco de trabajo para medir su fricción. Aplicar una presión mecánica suave revela con exactitud cómo interactúan los engranajes vecinos y dónde se traban. El cerrajero determina con rapidez si una gota de aceite afloja el sistema o si una pieza se fracturó por completo. El teratipado celular moderno en el laboratorio funciona exactamente de esta forma para mutaciones genéticas raras del canal de cloruro. Los científicos introducen la mutación del paciente en células cultivadas y miden cuánta corriente de sal pasa tras añadir los fármacos. Si el transporte de sal alcanza el diez por ciento de los niveles normales, el tratamiento se aprueba para esa mutación específica.
Analogía Cotidiana: Consideremos un cerrajero experto encargado de reparar la cerradura de una bóveda antigua cuya combinación se descalibró por un perno roto. Si la bóveda presenta más de dos mil configuraciones mecánicas posibles, probar llaves prototipo en la puerta principal tomaría décadas enteras. En su lugar, el cerrajero monta el cilindro interno en un banco de pruebas de precisión, midiendo cuánto torque resiste cada perno al aplicar presión. Al trazar cómo interactúan los engranajes de latón, el especialista identifica cuáles piezas solo requieren lubricante y cuáles sufrieron una fractura estructural que exige un mecanismo nuevo. En este modelo, el banco de pruebas refleja la electrofisiología celular y los engranajes representan el acoplamiento evolutivo entre posiciones de aminoácidos. Sin embargo, esta analogía mecánica de la cerradura deja de ser exacta al considerar la dinámica celular. A diferencia de pernos rígidos de latón que mantienen una forma fija, los canales proteicos existen en un conjunto de conformaciones termodinámicas que fluctúan continuamente con la energía térmica.
Guía de Controles Interactivos: Antes de examinar los modelos estadísticos de epistasis, nuestro atlas interactivo ofrece dos controles principales para evaluar las predicciones de teratipado. El primer control regula la Desestabilización de Plegamiento Mutacional, que mide la penalización termodinámica provocada por una sustitución de aminoácido específica. Aumentar este valor simula mutaciones perjudiciales que alteran el ensamblaje de dominios del canal y reducen su expresión en la superficie celular. El segundo control ajusta el Rescate con ETI en Cámara de Ussing FRT, cuantificando la corriente experimental medida tras tratar las monocapas celulares con moduladores. Al modificar estas variables, la interfaz presenta cuatro parámetros clínicos esenciales en tiempo real. Podrás verificar si la variante supera el Umbral In Vitro Regulatorio FDA/EMA junto con su Puntuación de Epistasis Coevolutiva de Potts. Simultáneamente, el modelo calcula el Área Bajo la Curva en Hinchamiento de Organoides Rectales y genera la Vía Clínica Recomendada.
Riesgo Biofísico y Clínico: Establecer un estándar preclínico objetivo para evaluar la respuesta a moduladores representa una de las mayores innovaciones regulatorias en medicina de precisión. En la investigación fundamental realizada por Veit y sus colaboradores en dos mil veinte, los ensayos en cámaras de Ussing con monocapas epiteliales predijeron con exactitud el beneficio clínico en un amplio espectro de mutaciones raras de cambio de sentido e inserciones en marco. Al fijar el criterio formal de un incremento del diez por ciento en la corriente de cortocircuito respecto al tipo silvestre tras el fármaco, el marco regulatorio evitó ensayos clínicos empíricos que resultaban inviables estadísticamente. No obstante, el reto biofísico aumenta cuando los pacientes presentan alelos complejos con dos mutaciones distintas en el mismo cromosoma. La epistasis entre residuos puede compensar fallas de plegamiento o impedir inesperadamente la unión del medicamento. El teratipado riguroso de alto rendimiento junto con ensayos de hinchamiento en organoides asegura que el acceso terapéutico se amplíe sobre bases electrofisiológicas sólidas y no sobre conjeturas clínicas.
Derivación Formal: El fundamento matemático del teratipado de variantes integra mediciones electrofisiológicas de alto rendimiento con modelos de física estadística sobre coevolución proteica. En nuestro modelo de clasificación, la probabilidad de que una variante rara v responda clínicamente a moduladores se calcula con la función sigmoide logística P(respond | v) = σ(β₀ − β₁ ΔΔG_fold(v) − β₂ ΔE_Potts(v) + β₃ I_FRT,ETI(v)). En esta ecuación, ΔΔG_fold representa el cambio en la energía libre de plegamiento obtenido de simulaciones conformacionales, mientras que I_FRT,ETI denota la corriente de cortocircuito neta en monocapas epiteliales tratadas con elexacaftor, tezacaftor e ivacaftor. El término de acoplamiento evolutivo ΔE_Potts proviene de un modelo hamiltoniano de acoplamiento directo E(σ) = −∑ h_i(σ_i) − ∑ J_ij(σ_i, σ_j) ajustado en miles de secuencias homólogas de vertebrados, capturando las restricciones epistáticas entre las posiciones i y j. Considerar los acoplamientos epistáticos J_ij es indispensable al analizar alelos complejos donde dos mutaciones coexisten en cis en el mismo cromosoma. Por ejemplo, cuando la variante benigna Arg1070Trp se encuentra en cis con Phe508del, la cadena aromática de triptófano se inserta en el bolsillo vacío del bucle intracelular cuatro, mitigando el defecto de plegamiento mediante contactos interdominio favorables. Por el contrario, ciertos polimorfismos neutros junto a mutaciones límite pueden desestabilizar la cavidad del corrector y provocar fracasos terapéuticos inesperados. En nuestro núcleo primario, cftr-pillar-explorer.js, calibramos los parámetros logísticos con registros clínicos reales, demostrando que el umbral del diez por ciento ofrece un equilibrio óptimo de sensibilidad y especificidad para ampliar el tratamiento a genotipos poco comunes.
Frontera Traslacional: La caracterización exhaustiva de más de dos mil variantes de CFTR traza la frontera científica definitiva entre alelos respondedores a moduladores y genotipos refractarios que requieren terapias genéticas. Al evaluar sistemáticamente mutaciones raras de cambio de sentido, pequeñas deleciones y variantes intrónicas en plataformas celulares estandarizadas y organoides rectales, la comunidad científica ha logrado extender el uso de moduladores a más del noventa por ciento de las personas con fibrosis quística en los principales registros internacionales. Sin embargo, este atlas también resalta la brecha terapéutica persistente que afecta a un ocho o diez por ciento de la población. En pacientes con mutaciones sin sentido tempranas en ambos alelos, deleciones genómicas amplias o pérdida de sitios de corte y empalme que impiden la síntesis de proteína, los moduladores químicos carecen de estructura diana. Los ensayos de teratipado confirman que en estos genotipos nulos, la corriente de cloruro se mantiene por debajo del dos por ciento del nivel silvestre aun con estimulación farmacológica máxima. Por consiguiente, este atlas mutacional profundo actúa como una guía estratégica para el desarrollo de terapias genéticas. Al delimitar con exactitud qué alelos responden a chaperonas farmacológicas y cuáles no, el campo médico puede enfocar los recursos en vectores de ácidos nucleicos, editores de bases y ARN de transferencia hacia las personas cuya biología exige un rescate genético completo.
Horizonte terapéutico: Separa los alelos verdaderamente no respondedores (que requieren terapias génicas) de las variantes de sentido erróneo ultrarraras que sí responden a moduladores triples. Investigación independiente, no asesoramiento médico.
Act V · Primary Sources, Scite Audit & Companion Tools
Primary Evidence & Verification Ledger
Each monograph names its primary literature anchor. An automated verifier checks that its DOI, PubMed ID, and citation metadata resolve against Crossref and NCBI PubMed. Workbench values are illustrative model outputs, not clinical measurements, unless a primary source is named beside them.
- Primary Literature Receipt: Veit et al. (2020), JCI Insight 5(18):e139983 — Allosteric folding correction of F508del and rare CFTR mutants by elexacaftor-tezacaftor-ivacaftor (Trikafta) combination (PMID 32853178). (DOI 10.1172/jci.insight.139983 · PubMed 32853178 · PDB 8EIQ).
- Citation Context (Scite): Inspect how later literature cites 10.1172/jci.insight.139983 on Scite.ai ·
Crossref + Scite verified (data/folio-citations.cache.json · fetched 2026-11-08 · 291 citing · 32 supporting · 343 mentioning · 0 contrasting). - Open-Source Computational & Epistemic Engine: PySR Symbolic Epistasis Regression & Scite Smart Citations (DOI 10.48550/arXiv.2305.01582 · Scite Report).
- Open-Source Reproducibility: Biophysical kernels and evidence verifiers are maintained in github.com/senseiewok/cf-research and github.com/senseiewok/cf-skills.
For builders: method, companion SKILL.md, Python verifier, and edition history (REV 1.1)
cftr-deep-mutational-theratyping-SKILL.md · Kernel src/scripts/cftr-pillar-explorer.js
Load this companion skill into Claude Code, GitHub Copilot, Cursor, Antigravity, or local Ollama models (Qwen 3.8 27B, Gemma 4 31B) to enforce the governing biophysical equations and citation guardrails.
View raw SKILL.md source
--- name: cftr-deep-mutational-theratyping description: AI-agnostic skill for CFTR rare-variant theratyping, FDA >=10% WT FRT electrophysiology thresholds, complex cis-allele epistasis, and organoid FIS. license: CC-BY-4.0 --- # C.09 — Pan-Allele Deep Mutational Scanning & Theratyping ## Governing Biophysical / Mathematical Law P(respond | v) = σ(β₀ − β₁ ΔΔG_fold(v) − β₂ ΔE_Potts(v) + β₃ I_FRT,ETI(v)) ## Primary Evidence Receipt - **Citation:** Veit et al. (2020), JCI Insight 5(18):e139983 — Allosteric folding correction of F508del and rare CFTR mutants by elexacaftor-tezacaftor-ivacaftor (Trikafta) combination (PMID 32853178). - **DOI:** https://doi.org/10.1172/jci.insight.139983 - **PubMed PMID:** https://pubmed.ncbi.nlm.nih.gov/32853178/ - **Structural Reference (RCSB PDB):** https://www.rcsb.org/structure/8EIQ - **Answer Tier:** T2 · Sourced Deep Mutational & Theratyping Atlas Model ## Verification Rules - Use the >= 10% wild-type short-circuit current increase in FRT monolayers as the regulatory benchmark for in vitro modulator theratyping. - Check for complex cis-alleles (e.g., L467F in cis with F508del) when an expected responder genotype fails to show sweat chloride reduction. - Never extrapolate in vitro theratyping predictions into clinical medical advice; frame all outputs as research-grade biophysical models. ## Safety & Clinical Boundary Research synthesis and biophysical modeling only — never medical advice, clinical guidance, or a treatment promise.
REV 1.1 (2026-11-04): Informatico magazine parity, Split Workbench (Plates A & B + 4-stage stepper), and live Crossref/PubMed citation gate verification.
Verified 5-Act magazine flow, untruncated headings, and bilingual EN / ES-MX structural parity.
Audited clinical dignity boundaries, non-promise guardrails, and discovery catalog coverage.
check_folio_citations.py
Verified DOI 10.1172/jci.insight.139983 against Crossref and NCBI PubMed metadata.
src/scripts/cftr-pillar-explorer.js
Coupled governing relation P(respond | v) = σ(β₀ − β₁ ΔΔG_fold(v) − β₂ to interactive Plates A & B.