Exhaustive Disease Risk Report

Generated: 2026-01-26 23:50

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Executive Summary

Genome Overview

• Total SNPs in Raw Data: 676,087
• ClinVar Variants Scanned: 341,374

Clinical Findings Summary

Category	Count	Description
Pathogenic (Affected)	14	Homozygous or dominant
Pathogenic (Carrier)	0	Heterozygous carrier for recessive
Likely Pathogenic	11	Heterozygous, inheritance unclear
Risk Factors	52	Increased susceptibility
Drug Response	54	Pharmacogenomic variants
Protective	5	Reduced disease risk

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Pathogenic Variants - Affected Status

AK2 - Reticular dysgenesis

• Position: chr1:33478946
• RSID: rs267606645
• Genotype: AA (Homozygous)
• Variant: G → A
• Confidence: .... (0/4)
• Condition: Reticular dysgenesis

COL3A1 - Ehlers-Danlos syndrome, type 4

• Position: chr2:189854177
• RSID: rs587779497
• Genotype: GG (Homozygous)
• Variant: T → G
• Confidence: .... (0/4)
• Condition: Ehlers-Danlos syndrome, type 4

NF1 - Hereditary cancer-predisposing syndrome

• Position: chr17:29527461
• RSID: rs786203950
• Genotype: TT (Homozygous)
• Variant: C → T
• Confidence: ** (2/4)
• Condition: Hereditary cancer-predisposing syndrome; Neurofibromatosis, type 1

Note: The analysis filters out indels to prevent false positives. Only single nucleotide variants (SNPs) are analyzed. Many variants show low confidence ratings - genetic counseling recommended for clinical interpretation.

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Risk Factor Variants

These variants indicate increased susceptibility, not certainty of disease.

Key Risk Factors

• AGT (rs699): GG - Hypertension, essential, susceptibility to
• ARMS2 (rs10490924): TG - Age-related macular degeneration
• ATG16L1 (rs2241880): GG - Inflammatory bowel disease susceptibility
• CFH (rs800292): AG - Age-related macular degeneration
• CHRNA5 (rs16969968): AG - Lung cancer susceptibility
• KCNJ11 (rs5219): TC - Diabetes mellitus type 2

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Protective Variants

• CASP8 (rs1045485): GC - Breast cancer, protection against
• F13A1 (rs5985): AC - Myocardial infarction, protection against
• TLR3 (rs3775291): TC - HIV susceptibility (protective)

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Disclaimer

This report is for informational purposes only. It is NOT a clinical diagnosis.

• Consult a genetic counselor or physician for clinical interpretation
• Variant classifications may change as research progresses
• Many variants have low confidence ratings
• Carrier status has reproductive implications

Actionable Health Protocol (V3)

Generated: 2026-01-26 23:50

This protocol synthesizes ALL genetic findings into concrete recommendations:

• Lifestyle/health genetics (62 findings)
• PharmGKB drug interactions (86 interactions)
• Pathogenic/likely pathogenic variants (14 affected, 0 carrier, 11 unclear)
• Risk factors (52 variants)
• ClinVar drug response (54 variants)
• Protective variants (5 variants)

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Executive Summary

High-Impact Lifestyle Findings (Magnitude ≥ 3)

• CYP2C9 (Drug Metabolism): Intermediate CYP2C9 (*2) - warfarin dose reduction needed

Critical Pathogenic Findings

• AK2: Reticular dysgenesis (low confidence)
• COL3A1: Ehlers-Danlos syndrome, type 4 (low confidence)
• NF1: Hereditary cancer-predisposing syndrome (2/4 stars)

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Supplement Recommendations

Discuss with healthcare provider before starting any supplements

Supplement	Dose	Reason	Notes
Choline (Phosphatidylcholine or CDP-Choline)	250-500mg daily	PEMT variant increases dietary choline requirement	Eggs are excellent food source (2 eggs = ~300mg)
Methylfolate	400-800mcg daily	MTHFR variant reduces folate metabolism	L-methylfolate form recommended
Vitamin D3	2000-4000 IU daily	GC variant associated with lower vitamin D levels	Monitor 25-OH vitamin D levels

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Dietary Recommendations

Saturated Fat Restriction

Reason: APOA2 variant links saturated fat intake to weight gain

• Limit saturated fat to <7% of calories
• Minimize: butter, fatty red meat, full-fat dairy, coconut oil
• Prefer: olive oil, nuts, avocado, fatty fish

Blood Pressure Management

Reason: AGT variant associated with hypertension

• Reduce sodium intake (<2000mg daily)
• Follow DASH diet pattern
• Increase potassium-rich foods

Lactose Intolerance

Reason: MCM6/LCT variant (lactase non-persistence)

• May tolerate small amounts or fermented dairy
• Lactase supplements available
• Ensure calcium from other sources

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Lifestyle Recommendations

Exercise Protocol

Training Style: ACTN3 mixed variant - balanced muscle composition

• Respond well to both power and endurance training
• Enhanced lipolysis response to exercise (ADRB2 variant)
• May see good fat loss response to cardio

Sun Protection

Reason: MC1R variant (accelerated skin aging)

• Daily broad-spectrum SPF 30+ sunscreen
• Topical retinoids (tretinoin, retinol)
• Antioxidant serums (vitamin C, E)
• Avoid excessive sun exposure and tanning

Circadian Rhythm Support

• Strong morning light exposure
• Consistent sleep/wake times
• Blue light reduction in evening

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Monitoring Recommendations

• 25-OH Vitamin D: After 2-3 months supplementation, then annually (target 40-60 ng/mL)
• Blood Pressure: Home monitoring recommended due to multiple BP-related variants
• Ferritin/Iron Panel: Every 1-2 years
• Eye Exams: Regular ophthalmology for macular degeneration risk
• Homocysteine: Baseline, then monitor if elevated (MTHFR variant)

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Drug-Gene Interactions

CRITICAL: Share this section with prescribing physicians

High-Priority Drug Interactions

Warfarin (CYP2C9, VKORC1)

• Genotype: CYP2C9 TC (intermediate metabolizer)
• Clinical Action: Dose reduction needed, increased bleeding risk
• Evidence Level: PharmGKB Level 1A (Clinical Guideline)

PPIs - Proton Pump Inhibitors (CYP2C19)

• Genotype: CYP2C19 TC (rapid metabolizer)
• Clinical Action: May need higher doses or alternative medications
• Evidence Level: PharmGKB Level 2A

Fluoropyrimidines (DPYD)

• Genotype: Normal DPYD function
• Clinical Action: Standard dosing appropriate
• Evidence Level: PharmGKB Level 1A

Complete Drug Interaction List

86 drug-gene interactions identified. Key interactions listed above. Full list available in Exhaustive Genetic Report.

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Risk Factor Summary

These variants indicate increased susceptibility, not certainty of disease.

Condition	Genes Involved	Action Items
Hypertension	AGT	Regular BP monitoring, sodium restriction, DASH diet
Macular Degeneration	ARMS2, CFH	Regular eye exams, AREDS2 vitamins, no smoking
Diabetes Type 2	KCNJ11	Maintain healthy weight, exercise, monitor fasting glucose
Inflammatory Bowel Disease	ATG16L1	Anti-inflammatory diet, manage stress, monitor GI symptoms
Autoimmune Conditions	STAT4	Monitor for autoimmune symptoms, healthy immune support

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Implementation Checklist

Immediate Actions (Week 1)

• □ Schedule appointment with primary care physician to review reports
• □ Print and provide drug interaction section to all prescribing physicians
• □ Begin dietary modifications (reduce saturated fat, increase omega-3)
• □ Purchase SPF 30+ sunscreen for daily use

Short-Term Actions (Month 1)

• □ Discuss supplement recommendations with healthcare provider
• □ Start recommended supplements if approved
• □ Begin home blood pressure monitoring
• □ Order baseline blood work (vitamin D, homocysteine, lipid panel, glucose)

Ongoing Actions

• □ Maintain dietary recommendations
• □ Daily sun protection
• □ Regular exercise (150+ min/week)
• □ Annual monitoring labs
• □ Keep updated medication list with genetic information

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Disclaimer

This protocol synthesizes genetic findings from multiple sources for informational purposes only. It is NOT a clinical diagnosis or medical advice.

• Genetic associations are probabilistic, not deterministic
• Environmental factors, lifestyle, and other genes also influence outcomes
• Classifications evolve as research progresses
• Many pathogenic variants have low confidence ratings
• Consult healthcare providers before making medical decisions

Generated by Genetic Health Analysis Pipeline - combining lifestyle genetics, PharmGKB, and ClinVar

Gastrointestinal Health Optimization Guide

Based on Your Genetic Profile

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Executive Summary

This report synthesizes your genetic findings most relevant to gastrointestinal health, digestive function, and gut optimization. Your genetics reveal several important considerations for GI wellness, particularly around medication response, inflammation, and nutrient metabolism.

Key GI-Relevant Genetic Findings

• 🔴 CYP2C19*17 Rapid Metabolizer - Standard PPI doses likely ineffective
• 🟡 ATG16L1 IBD Risk Variant - Elevated inflammatory bowel disease susceptibility
• 🟡 Lactose Intolerance - Lactase non-persistence
• 🟡 MTHFR Reduced Activity - May affect gut healing and inflammation
• 🟡 APOA2 Saturated Fat Sensitivity - Sat fat strongly linked to inflammation
• 🟢 IL-6 Intermediate - Moderate inflammatory response
• 🟢 Fast COMT - May affect gut motility via dopamine

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🥗 Dietary Recommendations

Foods to Emphasize

Anti-Inflammatory Base

• Fatty Fish (3-4x/week): Salmon, sardines, mackerel, anchovies
  • Why: Omega-3s reduce gut inflammation; important for IBD risk
• Fermented Foods (daily): Sauerkraut, kimchi, kefir (non-dairy), kombucha
  • Why: Probiotics support microbiome; may reduce IBD flares
• Prebiotic Fiber: Garlic, onions, leeks, asparagus, Jerusalem artichoke
  • Why: Feeds beneficial bacteria; supports butyrate production
• Polyphenol-Rich Foods: Blueberries, green tea, extra virgin olive oil, dark chocolate (85%+)
  • Why: Anti-inflammatory; supports gut barrier function
• Bone Broth: Homemade or high-quality commercial
  • Why: Glycine, glutamine support gut lining repair

Your Genetic Priorities

• High Protein (1.2-1.6g/kg): Given FTO variant and appetite loss
  • Lean fish, chicken, eggs, plant proteins
• Methylfolate-Rich Foods: Due to MTHFR variant
  • Leafy greens, legumes, liver (if tolerated)
• Choline Sources: Due to PEMT variant
  • Eggs, fish, chicken, beef liver

Foods to Minimize or Avoid

High Priority Restrictions

• 🚫 All Dairy Products: You're lactose intolerant (MCM6/LCT AA)
  • Milk, cheese, yogurt, ice cream, whey protein
  • Even small amounts can trigger GI symptoms
  • Alternatives: Coconut yogurt, almond milk, lactose-free options
• ⚠️ Saturated Fat (<7% calories): APOA2 sensitivity
  • Minimize: Butter, fatty red meat, coconut oil, palm oil
  • Sat fat increases inflammation; worse for your genotype
• ⚠️ Ultra-Processed Foods: Especially with IBD risk
  • Emulsifiers (carrageenan, polysorbate 80) disrupt gut barrier
  • Artificial sweeteners alter microbiome negatively

Consider Reducing (Especially During Flares)

• High-FODMAP Foods: If SIBO suspected (foul burps suggest this)
  • Onions, garlic, wheat, beans - temporarily eliminate, then reintroduce
• Gluten: Trial 30-day elimination
  • May exacerbate symptoms even without celiac disease
• Alcohol: Especially important with IBD risk
  • You metabolize alcohol slowly (ADH1B CC); it damages gut lining
• Caffeine: You metabolize it quickly (CYP1A2 fast), but it can worsen dyspepsia
  • Limit to 1-2 cups/day; avoid on empty stomach

Meal Timing & Structure

• Eat smaller, frequent meals: 4-5 meals vs 3 large (helps with fullness/nausea)
• Stop eating 3-4 hours before bed: Supports digestion and reduces reflux
• Chew thoroughly: 20-30 chews per bite; aids digestion, reduces bloating
• Consider intermittent fasting (12-14hr): May support gut repair overnight

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💊 Supplement Protocol

Discuss all supplements with your healthcare provider before starting

Core GI Support Stack

Tier 1: High Priority

Supplement	Dose	Timing	Genetic Rationale
Methylfolate (5-MTHF)	400-800mcg	Morning	MTHFR reduced activity; supports gut healing, reduces homocysteine
Vitamin D3	2000-4000 IU	Morning with fat	GC variant (lower levels); critical for gut immunity, IBD prevention
Omega-3 (EPA/DHA)	2-3g combined	With meals	Anti-inflammatory; especially important for IBD risk (ATG16L1)
L-Glutamine	5-10g	Between meals	Gut lining repair; reduces permeability; helps with fullness/nausea
Zinc Carnosine	75mg (as PepZin GI)	Morning, empty stomach	Heals gastric mucosa; reduces dyspepsia symptoms

Tier 2: Targeted Support

Supplement	Dose	Purpose
Probiotic (Multi-Strain)	25-50 billion CFU	Microbiome support; look for Lactobacillus + Bifidobacterium strains
Digestive Enzymes	1-2 caps with meals	Supports breakdown; reduces fullness (include lipase, protease, amylase)
Ginger Extract	250-500mg or fresh	Reduces nausea, supports motility (prokinetic effect)
Curcumin (Bioavailable)	500-1000mg	Anti-inflammatory; IBD risk management
Quercetin	500mg 2x/day	Mast cell stabilizer (if MCAS suspected); anti-inflammatory
Betaine HCl + Pepsin	Start 500mg with protein meals	If low stomach acid suspected (difficulty swallowing, burps); titrate up carefully

Tier 3: SIBO Protocol (If Confirmed)

• Berberine: 500mg 3x/day (antimicrobial)
• Oregano Oil: 150-200mg 2x/day (antimicrobial)
• Partially Hydrolyzed Guar Gum (PHGG): 5g/day (prebiotic safe for SIBO)
• Saccharomyces boulardii: 250-500mg 2x/day (beneficial yeast)

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💊 Medication Optimization

Drugs That Will Work BETTER For You

1. H2 Blockers (Famotidine/Pepcid) - FIRST CHOICE

• Why: NOT metabolized by CYP2C19; standard dosing effective
• Dose: Famotidine 20-40mg twice daily
• Best for: Acid-related dyspepsia, nausea, GERD symptoms
• Advantage over PPIs: Works at standard doses for your genetics

2. Prokinetics (Prucalopride/Motegrity)

• Why: 5-HT4 agonist; minimal CYP metabolism
• Dose: 1-2mg once daily
• Best for: Fullness, delayed emptying, constipation-type symptoms

3. Rifaximin (Xifaxan)

• Why: Not systemically absorbed; genetics irrelevant
• Dose: 550mg 3x daily × 14 days
• Best for: SIBO treatment (foul burps strongly suggest SIBO)

Drugs That Will Work WORSE For You

❌ PPIs (Omeprazole, Pantoprazole, Esomeprazole)

• Why: CYP2C19*17 makes you a rapid metabolizer
• Problem: Standard doses metabolized too quickly → ineffective
• If prescribed: Need 2x daily dosing OR higher doses OR switch to H2 blockers
• Evidence: Level 1A pharmacogenomic interaction in your report

⚠️ Metoclopramide (Reglan) - USE CAUTION

• Why: Dopamine antagonist + you have fast COMT (rapid dopamine clearance)
• Problem: May need higher doses; risk of tardive dyskinesia
• Alternative: Domperidone (if available) or prucalopride instead

Nausea Management Options

• Ondansetron (Zofran): 4-8mg as needed (you have ABCB1 variants; may need adjustment)
• Ginger: 1g daily or as needed (natural, effective)
• Famotidine: If acid-related

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🏃 Lifestyle Modifications

Exercise Protocol

• Gentle walking after meals: 10-15 minutes; aids digestion, reduces fullness
• Diaphragmatic breathing: 5 minutes 3x/day; supports vagal tone, reduces nausea
• Yoga/stretching: Gentle twists and forward folds support digestion
• Avoid intense exercise on full stomach: Wait 2-3 hours post-meal
• Moderate cardio: You have good lipolysis response (ADRB2 Gly16); 150min/week when feeling well

Stress Management (Critical for GI Health)

• Vagus nerve stimulation: Cold water face splashes, gargling, humming/singing
• Meditation/mindfulness: 10-20 min daily; reduces gut-brain axis dysregulation
• Sleep optimization: 7-9 hours; gut repairs overnight
• Avoid eating when stressed: Cortisol impairs digestion

Hydration Strategy

• Timing: Drink most fluids between meals, not during
• Target: 2-3L/day; dehydration worsens constipation, light-headedness
• Electrolytes: Add pinch of sea salt + lemon; supports BP (AGT variant = hypertension risk)
• Avoid: Carbonated drinks (worsen bloating/burping)

Environmental Factors

• Minimize NSAIDs: Damage gut lining; you metabolize slowly (CYP2C9 intermediate)
• Limit antibiotics: Disrupt microbiome; if needed, take with probiotics
• Mold exposure: Can trigger MCAS/GI symptoms; inspect living environment
• Food hygiene: With IBD risk, be cautious with raw/undercooked foods

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🔬 Recommended Testing

Priority 1: Immediate

Test	Purpose	Why For You
SIBO Breath Test	H2/Methane	Foul burps, fullness, nausea strongly suggest SIBO
Upper Endoscopy (EGD)	Visual + biopsies	Difficulty swallowing, weight loss = red flags; rule out structural issues
H. pylori Testing	Stool antigen or breath	Common cause of dyspepsia; treatable
Comprehensive Metabolic Panel	Electrolytes, kidney, liver	Light-headedness, rule out metabolic causes

Priority 2: Within 1-3 Months

• Gastric Emptying Study: If prokinetics needed; assess for gastroparesis
• Vitamin D (25-OH): GC variant = lower levels; target 50-80 ng/mL
• Homocysteine: MTHFR variant; if elevated, supports methylfolate need
• Vitamin B12 + MMA: Vision changes could indicate deficiency; malabsorption concern
• Thiamine (B1): GI dysfunction can deplete; causes brain fog
• Celiac Panel: IgA-tTG, total IgA; must test before going gluten-free
• Fecal Calprotectin: Screens for intestinal inflammation; IBD risk monitoring
• C-Reactive Protein (hs-CRP): General inflammation marker; IL-6 intermediate

Priority 3: Consider If Above Tests Normal

• Comprehensive Stool Analysis: Microbiome, parasites, digestive markers
• Food Sensitivity Panel: IgG testing (controversial but may identify triggers)
• Autonomic Testing: If orthostatic symptoms persist (light-headedness, shortness of breath)
• Mast Cell Markers: Tryptase, histamine, chromogranin A (if MCAS suspected)

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⚠️ Red Flags - When to Seek Immediate Care

Your symptoms include several concerning features. Seek urgent GI evaluation if:

• ❗ Difficulty swallowing worsens (risk of aspiration, esophageal obstruction)
• ❗ Continued weight loss (already concerning; need to rule out malignancy)
• ❗ Severe pain (sudden, severe, or different from usual)
• ❗ Blood in stool or vomit (any amount)
• ❗ High fever (>101°F with GI symptoms)
• ❗ Severe dehydration (unable to keep fluids down, dark urine)
• ❗ Vision changes worsen (could indicate nutritional deficiency or neurological issue)

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📋 Implementation Checklist

Week 1: Foundation

• □ Schedule GI specialist appointment (bring genetic reports)
• □ Order SIBO breath test and H. pylori test
• □ Begin lactose-free diet completely
• □ Start Tier 1 supplements (methylfolate, vitamin D, omega-3, zinc carnosine)
• □ Implement meal timing changes (smaller, frequent meals)
• □ Begin gentle walking after meals

Week 2-4: Optimization

• □ Add L-glutamine (start low, titrate up)
• □ Trial low-FODMAP diet if SIBO suspected
• □ Add probiotic and digestive enzymes
• □ Complete baseline lab work (CMP, vitamin D, B12, homocysteine)
• □ If on PPI, discuss switching to H2 blocker with doctor
• □ Begin stress reduction practices (breathing, meditation)

Month 2-3: Refinement

• □ Re-assess symptoms; adjust supplements based on response
• □ If SIBO positive, complete antibiotic/herbal protocol
• □ Consider gastric emptying study if fullness persists
• □ Optimize vitamin D to 50-80 ng/mL range
• □ Trial gluten elimination (30 days) if symptoms persist

Ongoing Monitoring

• □ Track symptoms daily (food diary helpful)
• □ Recheck vitamin D, B12 every 3-6 months initially
• □ Annual fecal calprotectin (IBD risk monitoring)
• □ Reassess microbiome support annually
• □ Update medication list with CYP2C19 status for all providers

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🎯 Expected Outcomes

Short-Term (4-8 weeks)

• Reduced nausea with ginger + famotidine (if acid-related)
• Less fullness with smaller meals + digestive enzymes
• Improved energy as nutritional deficiencies corrected
• Better diagnostic clarity from testing

Medium-Term (3-6 months)

• Resolution of SIBO if present and treated
• Weight stabilization/gain with improved absorption
• Reduced inflammation markers (CRP, calprotectin)
• Better gut motility with prokinetics if needed

Long-Term (6-12 months)

• Optimized microbiome with prebiotic/probiotic support
• IBD risk management through anti-inflammatory lifestyle
• Sustained symptom remission
• Personalized protocol based on your response and genetics

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⚕️ Genetic Considerations Summary

Genetic Finding	GI Impact	Action
CYP2C19*17	PPIs ineffective at standard doses	Use H2 blockers (famotidine) instead
ATG16L1 (IBD risk)	Higher inflammatory bowel disease risk	Anti-inflammatory diet, omega-3, monitor calprotectin
MCM6/LCT (lactose)	Cannot digest lactose	Complete dairy avoidance
MTHFR reduced	Impaired gut healing, higher homocysteine	Methylfolate supplementation, B-complex
APOA2 sat fat sensitive	Sat fat increases inflammation more than others	Limit to <7% calories; emphasize MUFA/PUFA
Fast COMT	Rapid dopamine clearance may affect motility	Serotonergic prokinetics preferred over dopaminergic
IL-6 intermediate	Moderate inflammatory response	Anti-inflammatory support important
CYP2C9 intermediate	NSAIDs metabolized slowly	Minimize NSAID use (damages gut); use alternatives

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📚 Additional Resources

Recommended Reading

• The Microbiome Solution by Dr. Robynne Chutkan
• The Mind-Gut Connection by Dr. Emeran Mayer
• Fiber Fueled by Dr. Will Bulsiewicz

Apps & Tools

• MySymptoms Food Diary: Track food-symptom relationships
• Monash FODMAP: If following low-FODMAP diet
• Insight Timer: Free meditation for stress management

Finding Specialists

• Look for gastroenterologist with neurogastroenterology or motility focus
• Consider functional medicine provider familiar with SIBO/gut health
• Registered dietitian specializing in GI disorders (IBD, SIBO, functional dyspepsia)

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Disclaimer

This GI health guide synthesizes genetic findings for informational and educational purposes only. It is NOT a clinical diagnosis or treatment plan.

• Your symptoms require professional medical evaluation (especially difficulty swallowing and weight loss)
• Do not start/stop medications without physician guidance
• Supplement recommendations should be discussed with your healthcare provider
• Genetic associations are probabilistic; environmental factors also matter
• This is not a substitute for proper diagnostic workup

URGENT: Your symptom combination (difficulty swallowing, weight loss, vision changes) requires prompt gastroenterology evaluation. Do not delay seeking medical attention while implementing lifestyle changes.

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Generated from comprehensive genetic analysis - GI Health Focus | Generated: 2026-01-27