Methylation Cycle

claw-methylation-cycle

Methylation cycle analysis skill for ClawBio. Produces enzymatic activity profiles, Net Methylation Capacity (NMC), BH4 axis estimates, compound heterozygosity detection, and clinician-review genotype findings from raw SNP genotype data.

Trigger

Fire this skill when:

• The user asks about methylation, MTHFR variants, folate cycle, or homocysteine risk from a genotype file.
• A raw SNP file (23andMe / ADNTRO / Ancestry format) is provided and the clinical question involves methylation, BH4, dopamine/serotonin synthesis capacity, or neurodevelopmental contexts (ADHD, depression, anxiety).
• The upstream workflow (PharmGx Reporter, NutriGx Advisor) has flagged MTHFR or MTRR and the clinician needs the full methylation panel.
• Keywords present: methylation, MTHFR, BH4, folate cycle, metilación, ciclo de metilación, homocysteine, 5-MTHF, methylcobalamin, neurotransmitter synthesis, dopamine upstream.

Do NOT fire this skill when:

• The question is purely about folic acid supplementation without a genotype file.
• The user is asking about MTHFR in the context of thrombophilia/clotting only — use PharmGx Reporter for warfarin/anticoagulation questions.
• Only N-GENE polygenic risk data is available (no raw SNP file) — this skill requires genotype-level input; PRS percentiles are not sufficient.
• The SNP file format is VCF, FASTQ, BAM, or PLINK binary — these require preprocessing before this skill can run.
• The clinical question is exclusively pharmacogenomic (CYP enzymes) — use PharmGx Reporter instead.

Workflow

1. Receive input — Accept either a raw genotype file path or a pre-parsed snp_dict. If a file is provided, call parse_genotype_file() to extract the rsID → genotype mapping.

2. Panel coverage check — Compare detected rsIDs against the 9-gene methylation panel. Log missing SNPs. For any SNP absent from the input, mark the corresponding gene as not_assessed — do NOT silently assume normal activity (Safety Rule 6).

3. Enzymatic activity scoring — For each gene, map the diplotype to an estimated activity percentage. Heterozygous risk variants reduce activity by their assigned weight; homozygous variants apply the full reduction.

4. Compound heterozygosity detection — Check MTHFR C677T (rs1801133) and A1298C (rs1801131) simultaneously. If both are heterozygous, set compound_heterozygosity = True and apply the combined activity reduction (~15% of normal — more severe than either variant alone).

5. Net Methylation Capacity (NMC) — Compute the weighted average of all enzyme activities. Clamp to [0, 100]. Expose coverage_pct and snps_missing; flag NMC as partial if key SNPs are absent.

6. BH4 axis capacity — Derive BH4 from MTHFR activity and MTRR modifier. Report clinical implications for dopamine and serotonin synthesis in neurodevelopmental presentations.

7. Prioritised recommendations — Generate PRIORITY 1 / 2 / 3 recommendations based on active findings. Lead with highest clinical impact (compound het MTHFR or severely reduced BH4).

8. Output — Write report.md (human-readable) and result.json (structured, for downstream integration).

Example Output

╔══════════════════════════════════════════════════════════════╗
║  ClawBio · Methylation Cycle Analysis Report                 ║
║  Author: Samuel Carmona Aguirre · RUO — Not a medical device ║
╚══════════════════════════════════════════════════════════════╝

Executive Summary
─────────────────
Net Methylation Capacity : 53 / 100  🔴 Reduced
BH4 Axis Capacity        : 31 / 100  🔴 Reduced
MTHFR Compound Het.      : YES ⚠️   (C677T + A1298C)
Dopamine Synthesis       : Severely Reduced
Serotonin Synthesis      : Severely Reduced

Enzymatic Activity Profile
──────────────────────────
Gene    Activity  Status                Key Variants
MTHFR    15%     🔴 Severely reduced   C677T, A1298C
MTRR     60%     🟡 Moderately reduced A66G
MTR     100%     🟢 Normal             –
CBS     100%     🟢 Normal             –
BHMT     40%     🔴 Moderately reduced R239Q
SHMT1    80%     🟢 Mildly reduced     C1420T
COMT     55%     🟡 Moderately reduced Val158Met
AHCY    100%     🟢 Normal             –

Clinical Recommendations — FOR CLINICIAN REVIEW ONLY
──────────────────────────────────────────────────────
⚠️  The following is genotype-based information for qualified clinician use.
    Do not self-administer. All nutrients listed are reported in the peer-reviewed
    literature for the pathways indicated; dosing and indication require
    individualised clinical assessment.

Genotype findings:
  • 5-MTHF (methylfolate) preferred over synthetic folic acid (MTHFR C677T/A1298C).
    Ref: Lamers Y et al. (2004) Am J Clin Nutr 80(5):1234-41.
  • MTHFR compound het: methylcobalamin co-administration reported in literature.
    Ref: Ledford AW et al. (2021) Nutrients 13(3):768.
  • BH4 capacity at 31%: riboflavin (B2) reported as MTHFR cofactor supporting BH4
    regeneration. Ref: McNulty H et al. (2017) Am J Clin Nutr 106(1):128-36.
  • MTRR A66G: methylcobalamin preferred over cyanocobalamin per functional studies.
    Ref: Olteanu H et al. (2002) Biochemistry 41(45):13378-85.
  • BHMT R239Q: betaine and choline-rich foods reported as alternative methyl donors.
    Ref: Slow S et al. (2004) Clin Chim Acta 340(1-2):57-67.

Some literature reports an association between BH4 deficiency and
ADHD/depression/anxiety phenotypes. This genotype indicates reduced BH4
production capacity. A clinician should contextualise this finding with
the patient's clinical history.
Where clinically relevant, a clinician may evaluate whether neurodevelopmental
symptoms correlate with BH4 capacity for potential non-pharmacological support.

Gotchas

1. Missing SNPs must never be silently normalised. The current implementation (line 471) defaults to assuming normal activity for SNPs absent from the input. This produces an artificially high NMC. When key SNPs are missing, always expose coverage_pct and snps_missing so downstream consumers know the score is partial.

2. Compound heterozygosity is synergistic, not additive. C677T and A1298C affect different MTHFR domains. Their combined effect (~15% activity) is greater than either variant alone. Do not compute as activity(677) × activity(1298).

3. BH4 capacity is an estimate, not a measured value. The BH4 score is derived from MTHFR activity and literature-based weights. It does not account for DHFR variation or dietary cofactor availability. Always include the RUO disclaimer.

4. COMT Val158Met has a dual role. rs4680 appears in both methylation (SAM consumption) and dopamine/catecholamine panels. Always note this — do not report it in isolation.

5. DTC array coverage varies by platform. ADNTRO covers all 9 panel SNPs for most European-ancestry samples. 23andMe v3 and Ancestry v1 may not include rs1801394 (MTRR) or rs3733890 (BHMT). Always check snps_missing.

6. This skill does not cover pharmacogenomics. SLCO1B1, CYP enzymes, and statin/warfarin risk belong to PharmGx Reporter, not this skill.

Domain Decisions

Genes and Variants Assessed

Enzymatic Activity Estimates

Activity is estimated as a percentage of normal function based on homozygous vs. heterozygous status of risk alleles. These are approximations derived from published functional studies — they are NOT direct enzyme assays.

Gene-specific estimates (homozygous risk):

• MTHFR C677T homozygous: ~30% of normal
• MTHFR A1298C homozygous: ~60% of normal
• MTHFR compound heterozygous (C677T + A1298C): ~15% of normal
• MTRR A66G homozygous: ~60% of normal
• BHMT R239Q homozygous: ~40% of normal
• COMT Val158Met homozygous (Met/Met): ~25% of normal
• SHMT1 C1420T homozygous: ~60% of normal

Source: Nazki FH et al. (2014) Gene 533(1):11-20; Ledford AW et al. (2021) Nutrients 13(3):768.

Net Methylation Capacity (NMC) Score

NMC is a composite index (0–100) derived from weighted enzymatic activities:

• MTHFR: weight 0.35 (primary rate-limiting enzyme)
• MTRR: weight 0.15
• BHMT: weight 0.15
• COMT: weight 0.10
• MTR: weight 0.10
• CBS: weight 0.05 (inverse — upregulation diverts homocysteine)
• SHMT1: weight 0.05
• AHCY: weight 0.05

NMC < 40: Severely reduced NMC 40–60: Moderately reduced NMC 60–80: Mildly reduced NMC > 80: Within normal range

Note (ACMG 2013): Routine population screening for MTHFR variants is not recommended for thrombosis risk assessment. This tool reports genotype facts for clinician contextualisation; NMC bands are descriptive outputs, not intervention triggers. Clinical decisions require individual patient evaluation.

BH4 Axis Capacity

BH4 (tetrahydrobiopterin) is an essential cofactor for tyrosine hydroxylase (dopamine) and tryptophan hydroxylase (serotonin). MTHFR activity directly constrains BH4 regeneration via the folate cycle.

• Base BH4 capacity = MTHFR_activity × MTRR_modifier
• MTRR_modifier: homozygous risk = 0.75; heterozygous = 0.88; WT = 1.0

BH4 thresholds:

• < 40%: Severely reduced — neurotransmitter synthesis substantially constrained
• 40–65%: Moderately reduced — may be clinically relevant; clinician to contextualise

• 65%: Within normal range

Compound Heterozygosity

MTHFR compound heterozygous (C677T + A1298C simultaneously) is the most clinically significant single-gene methylation finding. Total MTHFR activity is reduced more than either variant alone. Flagged explicitly in output.

Author and Attribution

Developed by Samuel Carmona Aguirre (samuel@unimed-consulting.es) as part of a contribution to the ClawBio open-source bioinformatics library.

Conflict of Interest (COI): The author develops clinical genomics workflows in a private practice context and may use tools derived from this skill as a component in those workflows. This skill is contributed as a standalone open-source genotype reporting tool; its output is not specific to any proprietary clinical platform. All clinical integration decisions rest with the qualified end-user clinician.

ACMG caveat on MTHFR testing (Green et al., Genet Med 2013, 15:153–156): Routine population screening for MTHFR variants is not currently recommended by ACMG for assessment of thrombosis risk, neural tube defect risk, or psychiatric phenotypes. Genotype findings from this tool should be interpreted in the context of the individual patient's clinical history by a qualified clinician.

Safety Rules

1. Never report a clinical diagnosis. Always include the RUO disclaimer.
2. Never recommend specific drug dosages or prescribe medication changes.
3. Always flag MTHFR compound heterozygous status as requiring clinical review.
4. Flag BH4 capacity < 40% with an explicit neurodevelopmental warning.
5. Never extrapolate to ancestries not represented in source studies (validated primarily in European-ancestry populations).
6. Unknown SNPs or SNPs not in the input must be reported as "Not assessed" — never assume wildtype.
7. All supplementation suggestions are Priority-ranked guidance for a clinician, not direct patient instructions.

Agent Boundary

In Scope

• Genotype extraction for 9 methylation-cycle genes from raw DTC files
• Enzymatic activity estimation (percentage of normal function)
• Net Methylation Capacity (NMC) composite index calculation
• BH4 axis capacity estimation and neurotransmitter synthesis impact
• MTHFR compound heterozygosity detection and flagging
• Prioritised clinical recommendations for clinician review
• JSON output for integration with downstream clinical decision-support systems

Out of Scope

• Dosing recommendations (requires clinical context and prescribing authority)
• Diagnosis of methylation disorders or neurodevelopmental conditions
• Drug-drug interaction analysis (see PharmGx Reporter)
• Epigenetic state (methylation is a phenotype; this skill assesses genotype only)
• Whole-genome or whole-exome sequencing data (SNP array input only)
• Direct patient communication (output is for qualified clinician use)

Usage

python skills/claw-methylation-cycle/methylation_cycle.py \
  --input path/to/genotype.txt \
  --output results/

References

• Nazki FH et al. (2014). Folate: metabolism, genes, polymorphisms. Gene, 533(1), 11-20.
• Ledford AW et al. (2021). MTHFR and BH4 pathway in neuropsychiatric disorders. Nutrients, 13(3):768.
• Stover PJ (2009). One-carbon metabolism-genome interactions. J Nutr, 139(12), 2402-5.
• Lamers Y et al. (2004). Supplementation with [6S]-5-methyltetrahydrofolate or folic acid equally reduces plasma total homocysteine. Am J Clin Nutr, 80(5):1234-41.
• McNulty H et al. (2017). Riboflavin lowers homocysteine in children and adults with common MTHFR polymorphism. Am J Clin Nutr, 106(1):128-36.
• Olteanu H et al. (2002). Differences in the efficiency of reductive methylation of cob(II)alamin. Biochemistry, 41(45):13378-85.
• Slow S et al. (2004). Plasma betaine and homocysteine. Clin Chim Acta, 340(1-2):57-67.
• Esteller M. (2014). Introduccion a la epigenetica. SEBBM, 179:4-6.
• Spuch C, Agis-Balboa RC. (2014). Epigenetica en neurociencias. SEBBM, 179:18-21.
• Green RC et al. (2013). ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med, 15(7):565-74.
• ClawBio (2026). https://github.com/ClawBio/ClawBio

Changelog