Detects low-VAF (down to 1-2 percent) somatic variants in PIK3CA, MTOR, AKT3, AKT1, PTEN, TSC1/2, and related overgrowth-pathway genes in tissues that are more likely than blood to carry the mosaic lineage. Can use targeted deep sequencing panels (>=500x) or ddPCR of known hotspots.

• Promotes

  Somatic (mosaic) variant in the PI3K-AKT-mTOR or related overgrowth pathway

  A pathogenic low-VAF variant at a PROS / mTORopathy hotspot confirms this theory and opens pathway-targeted treatment.

• Rules out

  Germline PI3K-AKT-mTOR variant

  Although a tissue-mosaic finding is technically not germline, it would reclassify the overall category and effectively close the germline-variant branch.

A positive result would make targeted therapy (rapamycin, everolimus, or alpelisib depending on gene and variant) a real, pathway-justified option with growing pediatric safety data. A negative result, combined with the existing negative germline data, substantially narrows the genetic differential.

• →Consult medical genetics about whether a commercial PROS panel on buccal / skin is available locally or whether a research lab (e.g. Mirzaa, Aldinger, Poduri) is the better route.
• →Consider simultaneous banking of multiple tissues (skin, buccal, hair).
• →Consider re-running existing WGS BAMs with somatic callers (MuTect2-style paired tumor/normal) before collecting new tissue.

Identifies methylation defects and uniparental disomy at known overgrowth-associated imprinted loci. Several Sotos-adjacent and BWS-spectrum presentations have a methylation-only mechanism with no detectable coding-region variant.

• Refines

  Overgrowth syndrome outside the mTOR axis (epigenetic/imprinting mechanism)

  A methylation signature at 11p15 or 5q35 would confirm a specific imprinting / epigenetic etiology despite the negative germline workups. Clean panel would substantially close this residual.

Syndrome-specific surveillance changes (BWS tumor screening, Sotos skeletal and tumor surveillance) but does not by itself alter acute DEE-SWAS management.

• →Order through Stanford Medical Genetics (Melanie Manning MD / Devon Bonner LCGC) or directly via a reference lab that offers MS-MLPA for BWS + Sotos + other imprinted loci (GeneDx, Baylor, or equivalent).
• →Consider a methylome array (genome-wide methylation) as a single test covering multiple loci if available.

Direct compartmental measurement of CNS inflammation and neurotransmitter/pterin/folate physiology. Distinguishes compartmentalized cell-mediated CNS inflammation from a purely peripheral cytokine signal. Adds CSF AE panel, addressing the one missing piece of the classical AE workup. Rules in or out CNS folate/pterin disorders.

• Refines

  Seronegative cell-mediated / Th1-Th17-biased neuroinflammatory contribution

  Elevated CSF IL-1beta / TNF / IL-6 / IL-17 or elevated neopterin would be the strongest single-test evidence for CNS inflammation and would promote this theory. A clean CSF cytokine profile off steroids would substantially down-weight it.

• Refines

  Classical antibody-positive autoimmune encephalitis

  Positive CSF AE antibody (particularly NMDA-R) with negative serum is the classic pediatric pattern. Negative CSF AE panel combined with the negative March 2026 serum panel effectively excludes this theory.

CSF-documented inflammation justifies sustained immunomodulation (repeat IV steroid pulses, IVIG, possibly rituximab or tocilizumab in refractory cases). Clean CSF off steroids makes continued immunomodulation harder to justify and may shift toward genetic or idiopathic-DEE-SWAS management.

• →Coordinate with UCSF neurology team (Aylin Ulku and Genesis Trejo).
• →Time the LP relative to steroid taper so results are interpretable.
• →Pre-order the specific add-on assays (CSF cytokine panel including IL-6, CSF NMDA-R and full AE panel, neopterin, HVA/5-HIAA, folate). 2026-04-19 - explicitly include IL-6 since Kessi 2019 implicates IL-6 in CSWS pathogenesis and IL-6 is a canonical HPA-axis activator (Papanicolaou 1998); a positive CSF IL-6 finding would strengthen both the seronegative-cell-mediated-neuroinflammation theory and the new hypothalamic-hpa-axis-contribution theory simultaneously.

A dedicated re-read focuses on (1) whether any subtle FCD is present at higher-resolution sequences, (2) whether mosaic-overgrowth patterns (hemispheric asymmetry, periventricular nodular heterotopia, subtle cortical-subcortical abnormalities, focal cortical thickening) are present, and (3) a more specific characterization of the R>L periventricular FLAIR signal than "nonspecific / may represent sequela of prior injury."

• Refines

  Germline or mosaic variant in the PI3K-AKT-mTOR axis

  A subtle cortical tuber, FCD, or hamartomatous lesion on expert re-read would promote the mTORopathy hypothesis. Clean re-read through an mTORopathy lens meaningfully reduces the prior.

• Refines

  Structural or vascular/perinatal etiology

  Subtle FCD may be missed on summary reads and would promote this theory. Clean expert re-read reduces it.

A cortical tuber or FCD would redirect the workup toward possible surgical evaluation. Clean re-read supports continued medical/immunomodulatory management.

• →Obtain the full radiology report from UCSF or Stanford PACS.
• →Request re-read by a pediatric neuroradiologist experienced with mTORopathies and DEE-SWAS.
• →2026-04-19 - explicitly enumerate the hypothalamus and pituitary (sellar/parasellar region) in the re-read request, given the new hypothalamic-hpa-axis-contribution theory and the 1.5-year nocturnal arousal/hyperphagia phenotype documented in `content/vault/records/2026-04-19-note-nocturnal-hyperphagia-addendum.md`. Question to ask the re-reader - is there any subtle hypothalamic asymmetry, pituitary-stalk abnormality, posterior-pituitary bright-spot loss, or pituitary-size/morphology deviation that might be missed on a general read?
• →Extract into content/vault/records/.

Confirms whether the April 6 Th1/Th17 serum signature reflects active ongoing inflammation or residual effect / treatment artifact. Glucocorticoid exposure is a well-documented confounder of TH17 differentiation (JACI 2018) so off-steroid reassessment is essential for interpretation.

• Refines

  Seronegative cell-mediated / Th1-Th17-biased neuroinflammatory contribution

  Persistent elevation off steroids raises the prior for an active inflammatory process. Normalization off steroids meaningfully lowers it.

Persistent serum cytokine elevation off steroids, together with CSF data, would tilt toward sustained immunomodulation. Normalization argues against additional immunotherapy absent new evidence.

• →Schedule after steroid taper completes.
• →Include sIL-2R, IFN-gamma, TNF-alpha, IL-17, IL-13 at minimum, plus IL-6 (now explicitly required), IL-10, and IL-1beta. 2026-04-19 - IL-6 elevated to required because Kessi 2019 specifically implicates IL-6 in CSWS pathogenesis and IL-6 is a canonical HPA-axis activator (Papanicolaou 1998); a positive serum IL-6 elevation off steroids would simultaneously strengthen the seronegative-cell-mediated-neuroinflammation theory and the new hypothalamic-hpa-axis-contribution theory.

Quantitative SWI during sleep confirms durability of the April 6-7 near-resolution and provides the first objective SWI benchmark for Levi. Establishes the baseline against which future steroid decisions and adjunct therapy can be measured.

• Context

  Idiopathic multifactorial DEE-SWAS

  EEG documents syndrome severity and durability but does not adjudicate underlying etiology.

• Refines

  Seronegative cell-mediated neuroinflammatory contribution

  Rapid relapse off steroids would strengthen the inflammatory-driver interpretation; durable suppression through a steroid taper makes ongoing active inflammation less likely.

A rebound in SWI triggers a pre-specified rule for further steroid pulses, slower taper, or escalation to IVIG / other immunomodulation. Durable suppression supports staying the course with developmental support.

• →Coordinate with Stanford pediatric epileptology (Christopher Lee-Messer, MD, PhD).
• →Request quantitative SWI rather than qualitative reads.

Submicroscopic deletions/duplications across the genome (CMA-class resolution). CNVs in 16p11.2, 22q11.2, 15q11-q13, and several other regions are classic neurodevelopmental contributors. Also large runs of homozygosity (ROH) indicating UPD or consanguinity.

• Refines

  Idiopathic multifactorial DEE-SWAS

  A pathogenic CNV would have reclassified the case away from idiopathic-multifactorial. Result normal; remains idiopathic from this assay's perspective.

• Rules out

  Germline PI3K-AKT-mTOR axis

  No large CNV / ROH at PTEN, PIK3CA, TSC1, TSC2, AKT, or mTOR loci (CMA-class resolution only; does not exclude point variants).

• Refines

  Sotos / Weaver / chromatinopathy / imprinting

  No large CNV / ROH at 5q35 (NSD1/Sotos), 11p15 (BWS imprinted region), 2q23.1 (MBD5), or other imprinted regions detected. Methylation-mechanism disease remains untested (MS-MLPA outstanding), so this is a partial refinement rather than full elimination.

None; negative result.

• →No further action required; closes the CMA coverage gap.

Detects the cutaneous and retinal findings that are specific for TSC (hypomelanotic macules, angiofibromas, retinal hamartomas) and PTEN-associated disease (trichilemmomas, mucocutaneous lesions). Very low cost; very high yield if positive.

• Refines

  Germline or mosaic variant in the PI3K-AKT-mTOR axis

  Positive findings would promote TSC or PTEN specifically and would accelerate pathway-targeted testing. Clean exam meaningfully down-weights TSC while not excluding the broader axis.

Positive findings may accelerate the decision to start mTOR-pathway-directed therapy and triggers syndrome-specific surveillance.

• →Request from dermatology or geneticist during the next visit.
• →Add ophthalmology referral if not already in place.

Characterizes whether the borderline-low April 6 total IgG 518 reflects a broad humoral deficit (all four subclasses down), a selective subclass deficiency (e.g., IgG2 in a subset of children), or a transient post-steroid or post-infection dip. Relevant both for infection-risk counseling and as context for IVIG candidacy if immunomodulation is escalated.

• Context

  Seronegative cell-mediated neuroinflammatory contribution

  IgG subclass status is a safety / candidacy question rather than a mechanistic test for this theory.

A clinically significant humoral deficiency shifts IVIG candidacy from "adjunct immunomodulation" toward "replacement therapy with incidental immunomodulation" and changes dose / frequency decisions. Normal subclasses remove that consideration.

• →Order IgG subclasses 1-4.
• →Repeat total IgG, IgA, IgM, IgE in 4-8 weeks.

Completes the organic acidemia / fatty acid oxidation / urea cycle workup not fully covered by the January 2026 plasma panels. Expected to be normal given prior normal plasma amino acids, acylcarnitines, MMA, homocysteine, ammonia, and creatine disorder panel.

• Rules out

  Classical inborn error of metabolism

  Clean urine organic acids combined with the existing normal plasma metabolic panel effectively closes the IEM bucket.

Clean result removes IEM from active consideration; would not by itself change current management.

• →Confirm whether already done in the Stanford record set; if not, order.

Identifies whether a specific infection or febrile illness was documented around Jan 16, 2026. A pulled symptom history (late Dec 2025 – Jan 2026) may also reveal encounters not captured in current extractions and can redirect convalescent serology.

• Refines

  Post-infectious or peri-inflammatory trigger (January 2026)

  Identifying a specific infection promotes this theory and may trigger targeted convalescent serology (mycoplasma, EBV, HHV-6, SARS-CoV-2). No documented illness keeps the theory plausible but unverified.

Documented post-infectious trigger can motivate inclusion of post-infectious immunomodulation in the longitudinal plan. No change to acute DEE-SWAS management.

• →Pull all Stanford encounters in late December 2025 and January 2026.
• →If an infectious workup was started and not completed, consider catching up with convalescent serologies.

Post-acute-event snapshot of Levi's gut microbiome against the May 2025 baseline. Detects shifts in diversity, histamine-producer abundance, Akkermansia level, and LPS index that may correlate with the January 2026 event and the April 2026 spike-wave escalation.

• Refines

  Gut microbiome-driven neurodevelopmental phenotype

  Dramatic post-acute dysbiosis would promote the gut-brain hypothesis. A pattern similar to May 2025 would confirm the low-likelihood interpretation.

Substantial dysbiosis could motivate targeted dietary / probiotic intervention. A preserved pattern supports not prioritizing microbiome-directed intervention.

• →Decide whether the gut-brain hypothesis is being actively pursued.
• →If yes, run now before any planned dietary or probiotic intervention.

An actual cooperative baseline QTc measurement and pediatric-electrophysiology interpretation. The 460 and 452 ms values from the 2024 tracings are automated reads from non-cooperative acquisitions and do not count as a usable baseline.

A cooperative repeat EKG with a truly normal QTc lifts the caution for QT-prolonging candidate regimens. A prolonged QTc on a cooperative tracing restricts the candidate AED / stimulant / psychopharm list (avoid sotalol, amiodarone, citalopram, methylphenidate combinations, certain atypical antipsychotics) and changes the safety calculus around several DEE-SWAS second-line options.

• →Schedule a cooperative repeat EKG, ideally with pediatric-friendly positioning and desensitization, before any new QT-prolonging drug regimen is considered.
• →Request pediatric-cardiology / electrophysiology review (Henry Chubb, MD at Stanford / LPCH is documented as the most recent reader).
• →2026-04-17 - the prior framing of a "persistent borderline QTc signal" across the 460 -> 452 sequence is superseded; treat baseline as unknown.

A morning cortisol below the pediatric AM threshold (Improda 2024 - <150 nmol/L = adrenal insufficiency; >=317 nmol/L = recovered) flags primary or secondary AI. A low cortisol with low/inappropriate ACTH localizes the lesion to pituitary or hypothalamus (consistent with the hypothalamic-hpa-axis-contribution theory). A low cortisol with appropriately elevated ACTH points to primary adrenal insufficiency. A normal AM cortisol meaningfully (but not completely) reduces the probability of a clinically significant HPA-axis defect.

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  Low AM cortisol with low/inappropriate ACTH directly supports a central HPA defect and promotes this theory. Normal AM cortisol with normal ACTH reduces the prior but does not exclude (a single AM draw misses circadian-shift and stimulated-response abnormalities).

A confirmed low cortisol motivates pediatric endocrinology consult, stress-dose policy education for the family in advance of any future steroid pulse or acute illness, and (depending on degree) maintenance hydrocortisone replacement. A normal value removes acute stress-dose concern but does not invalidate the case for further characterization (diurnal salivary cortisol).

• →Coordinate with UCSF pediatrics or pediatric endocrinology; can be added to the next routine blood draw.
• →Time after steroid taper completes so glucocorticoid suppression is not the cause of a low value (or, if drawn before taper completes, document the steroid context explicitly).

Detects (a) an elevated or earlier-than-normal cortisol awakening response (CAR), which would correlate with the 3 AM stimmy hyperarousal phenotype, (b) a flattened diurnal slope, which reflects HPA dysregulation, and (c) loss of the normal late-evening nadir. Sleep-HPA bidirectionality (Balbo 2010) means a disturbed cortisol curve and disturbed sleep can each cause the other; this test characterizes the cortisol-side signature.

• Promotes

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  A phase-advanced cortisol curve, an exaggerated CAR, or a flattened diurnal slope would directly support this theory and would tie the 3 AM nocturnal awakening phenotype to a measurable circadian-HPA signature.

• Refines

  Seronegative cell-mediated neuroinflammatory contribution

  A flattened cortisol curve in the presence of elevated IL-6 (when measured) would be consistent with a cytokine-driven HPA dysregulation pattern, supporting convergence between this theory and the hypothalamic-HPA theory.

An abnormal curve motivates pediatric endocrinology consult and may motivate (a) a pre-bedtime carbohydrate-protein snack trial, (b) sleep hygiene optimization, and (c) consideration of melatonin to address the circadian-phase component independently of HPA. A normal curve substantially down-weights the HPA-axis theory (without fully excluding it).

• →Order through pediatric endocrinology; many reference labs (LabCorp, Quest, ZRT, Genova) offer 4-point salivary cortisol home collection kits.
• →Coordinate with the structured sleep diary so the cortisol samples and the sleep/arousal log are time-aligned.

IGF-1 + IGF-BP3 screen the somatotropic axis (relevant to both Hage 2019 TBRS and to overgrowth/PI3K-AKT-mTOR pathway); these are particularly important if the overgrowth-dnmt3a-tbrs theory stays live. Prolactin screens hypothalamic dopaminergic restraint (loss = hypothalamic dysfunction or stalk effect). TSH + free T4 screen central vs. primary hypothyroidism. Fasting leptin screens hypothalamic appetite regulation (relevant to the Prader-Willi / ROHHAD / MC4R / leptin-POMC axis differential motivated by the nocturnal hyperphagia phenotype - Lazea 2021 ROHHAD review).

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  Multiple-axis pituitary output abnormalities (e.g., low IGF-1 + central hypothyroidism + abnormal prolactin) would suggest a multi-axis hypothalamic / pituitary defect and substantially promote this theory. Isolated abnormalities still inform but with less weight.

• Refines

  TBRS (DNMT3A overgrowth)

  Hage 2019 documents a GH-secreting pituitary macroadenoma in TBRS. An elevated IGF-1 / IGF-BP3 in Levi would be a specific positive signal for TBRS-spectrum pituitary involvement and would motivate a dedicated pituitary MRI.

• Refines

  Germline or mosaic PI3K-AKT-mTOR variant

  PI3K-AKT-mTOR pathway directly couples to GH/IGF-1 and somatotroph development. Abnormal IGF-1 in either direction would be consistent with this theory.

Specific pituitary-output abnormalities trigger pediatric endocrinology consultation, axis-specific replacement (e.g., levothyroxine for central hypothyroidism), and re-prioritization of the genetic differential. Abnormal leptin would prompt a hypothalamic-obesity / Prader-Willi-spectrum workup.

• →Order through pediatric endocrinology; bundle with the AM cortisol + ACTH draw to minimize needlesticks.
• →Time after steroid taper completes so prolactin and IGF-1 are not glucocorticoid-suppressed.

Quantifies (a) frequency and timing distribution of nocturnal awakenings (parent-reported \"around 3 AM\" -> objective time-of-night histogram), (b) sleep-onset latency, (c) total sleep time, (d) sleep efficiency, (e) whether the awakenings cluster in the 1-5 AM window or are more broadly distributed. Establishes the durable baseline so intervention effects are interpretable.

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  A confirmed circadian-clustered arousal pattern (rather than randomly distributed awakenings) would support a hypothalamic / circadian-HPA driver. A randomly distributed pattern would be more consistent with a behavioral or epileptiform-arousal driver.

• Context

  Idiopathic multifactorial DEE-SWAS

  Sleep characterization documents phenotype severity but does not adjudicate underlying etiology of the DEE-SWAS itself.

A documented circadian-clustered pattern justifies (a) a structured pre-bedtime snack trial, (b) a structured melatonin trial, and (c) sleep-hygiene optimization, all of which need a pre/post benchmark to evaluate. A randomly distributed pattern with high behavioral-reinforcement features would tilt toward behavioral / sleep-medicine consultation rather than endocrine intervention.

• →Coordinate with sleep medicine or pediatric neurology; many centers (UCSF, Stanford) loan actigraphy devices for 2-week home studies.
• →Provide family with a structured diary template that captures wake time, perceived arousal character (calm vs. stimmy vs. distressed), pantry-seeking behavior, and re-settling time.
• →Time-align with the 4-point salivary cortisol collection.

A simultaneous glucose, cortisol, insulin, and GH at the moment of a nocturnal arousal directly tests (a) whether the awakening is driven by hypoglycemia (Maines 2021 PI3K-AKT-mTOR -> hypoglycemia, or hyperinsulinism), (b) whether the cortisol counter-regulatory response is appropriate, and (c) whether GH secretion is appropriately suppressed (high GH at this time would be unusual). The calm/stimmy presentation argues against severe hypoglycemia clinically, but a single confirmed normal glucose during one awakening would meaningfully close the question.

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  An exaggerated cortisol/ACTH surge at the moment of awakening would directly support a mistimed pre-waking HPA surge. A flat cortisol response at the moment of awakening would argue against an HPA-driven awakening.

• Refines

  Germline or mosaic PI3K-AKT-mTOR variant

  A documented hypoglycemia +/- hyperinsulinism at the moment of awakening would be a specific positive signal for a PI3K-AKT-mTOR pathway defect (Maines 2021).

Documented hypoglycemia at awakening is itself a treatment indication (pre-bedtime carbohydrate-protein snack, possibly cornstarch, possibly continuous glucose monitoring). A documented exaggerated HPA surge motivates a different conversation about evening melatonin or alpha-2-agonist (clonidine, already on board) optimization.

• →Pre-specify the panel to draw and the labels to use during any future inpatient admission, sleep study, or overnight EEG.
• →Equip the family with a home glucometer to capture point-of-care glucose at the time of an awakening (cannot capture cortisol/insulin/GH at home, but home glucose alone would partly answer the question).
• →Lower priority than ranks 14-17 because of the calm/stimmy/non-distressed phenotype, but worth capturing opportunistically.

An EEG-correlated nocturnal arousal answers a question that is otherwise unanswerable - is the awakening time-locked to a subclinical epileptiform burst (peri-ictal arousal driven by residual SWI), or does it arise from clean background (consistent with an endocrine / circadian / behavioral driver)? This separates the seronegative-cell-mediated-neuroinflammation / DEE-SWAS branch of explanations from the hypothalamic-HPA / circadian branch.

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  A documented arousal arising from clean EEG background promotes the HPA / circadian explanation. An arousal time-locked to a subclinical epileptiform burst weakens the HPA branch and points to peri-ictal arousal.

• Refines

  Seronegative cell-mediated neuroinflammatory contribution

  An arousal time-locked to a residual epileptiform burst would point to ongoing nocturnal SWI-driven physiology and would tilt toward continued or escalated immunomodulation / SWI-suppressive treatment.

An EEG-clean awakening tilts toward HPA / circadian / behavioral interventions (snack, melatonin, sleep hygiene, endocrinology workup). An EEG-correlated awakening tilts toward neurology-led management (taper decisions, possible second steroid pulse, possible alternate SWI suppressant).

• →Add to the order set / clinical request for the next planned repeat overnight EEG (item 6).
• →Brief the EEG tech on what to annotate (any nocturnal arousal, with timestamp, character, and pantry-seeking behavior if observed).

A structured score across 9 domains (sleep / circadian, appetite / weight, body temperature, water/sodium balance, anterior pituitary axes, posterior pituitary, autonomic, behavioral, neurocognitive). Levi already meets criteria across multiple domains based on existing data (hyperphagia, temperature instability, high pain threshold, sleep/circadian disruption). Formal scoring provides (a) a defensible framework for endocrinology referral, (b) identification of any unscored domains worth probing, and (c) a baseline for longitudinal reassessment.

• Refines

  Hypothalamic-pituitary-adrenal axis dysfunction contributing to DEE-SWAS phenotype

  A high van Santen score with multiple involved domains substantially promotes this theory and supports endocrinology referral. A low score across all 9 domains substantially down-weights it.

A high score is the strongest case for pediatric endocrinology consultation as a longitudinal partner rather than as a one-time consultation. Drives the diagnostic workup priority order.

• →Run the scoring exercise as a research-note-style document under content/research/notes/ once ranks 14-17 results return.
• →Use the score as the lead exhibit in any pediatric endocrinology referral letter.