Everything in this manual — the nervous system, the gut, the hormones, the metabolic function, the immune system, sleep — has been building to a single clinical question: how do we know what's actually going wrong in a specific person's body? Not what we suspect. Not what seems most likely from the symptom pattern. What is objectively, measurably, demonstrably happening. The answer is the five-test programme.
These five tests were not assembled arbitrarily. Each was selected because it reveals something critical about a different layer of function — and because standard medical testing consistently fails to reveal the same information. Together, they produce over 900 data points, covering 170+ validated clinical patterns, with 40+ cross-test conflict resolution protocols. No other investigation approach available in primary or functional care covers this breadth of interconnected systems simultaneously.
This module is the clinical reference for understanding each test. It explains what each panel measures, what it reveals in functional terms, how the results are interpreted using optimal rather than population-average reference ranges, and how findings across the five tests connect to each other. Read it once for understanding. Return to it every time you receive results.
Why Testing Beats Guessing — And Why Most Testing Still Misses the Point
Standard medical testing is designed to detect disease. It establishes reference ranges from population averages — ranges wide enough to include the vast majority of people, including many who are unwell. When your results fall within these ranges, you're told everything is normal. But normal, as the previous modules have made clear, is not the same as optimal. And optimal is what we're measuring for.
Optimal Ranges vs Normal Ranges
The gap between "not diseased" and "functioning optimally" is where most chronic symptoms live. Take TSH: the standard NHS reference range is 0.5–5.0 mIU/L. The functional optimal range is 1.0–2.0 mIU/L. At 3.5 — technically normal — many people experience the full constellation of hypothyroid symptoms: fatigue, weight gain, cold intolerance, hair thinning, constipation, brain fog. They're told their thyroid is fine. They're not fine. We're just not looking at the right range.
The same principle applies across every test. Fasting glucose of 5.5 mmol/L is normal. Functionally optimal is 3.9–4.7. Ferritin of 25 ng/mL is within the reference range. For adequate thyroid conversion, dopamine production, and energy metabolism, you need above 70. The functional reference ranges used throughout the TDG platform are calibrated to detect dysfunction at the stage when it's most correctable — not at the stage when it's severe enough to be called disease.
Reading Patterns, Not Just Numbers
Individual markers tell partial stories. The clinical picture emerges from relationships between markers — patterns that require the full panel to be visible. A ferritin of 28 is "low-normal." But ferritin of 28 combined with low Free T3, elevated reverse T3, low vitamin D, and elevated CRP tells a complete story: iron insufficiency is impairing thyroid conversion, systemic inflammation is simultaneously driving reverse T3 production, and vitamin D deficiency is compounding both the inflammatory and thyroid dysfunction. The intervention isn't iron. It's the full upstream picture that generated the pattern.
"I don't just look at whether markers are 'in range.' I look at optimal ranges. I look at patterns. I look at relationships between markers. The pattern tells a story that individual markers miss."
Stephen Duncan FDN-P MScBlood Chemistry — The Metabolic Foundation
Blood chemistry is the starting point for every client — not because it's the most informative test, but because it reveals the metabolic foundation on which everything else depends. Thyroid function, blood sugar, inflammation status, nutrient levels, liver function, kidney function, and critically, hydration — all visible from a single blood draw. And hydration, for reasons most practitioners never consider, is where interpretation always begins.
Hydration First — Always
The clinical rationale is personal and direct. My father had low cholesterol, exercised regularly, and had a heart attack requiring a triple bypass. His chronic dehydration — never tested, never addressed by anyone — was a significant contributing factor. Next to breathing, and before food, cellular hydration is the primary principle of human health. But it's overlooked because you can't prescribe it, can't charge for it, can't put it in a pill.
Hydration markers on the blood panel: sodium-potassium balance (cellular hydration indicators), chloride levels, BUN-to-creatinine ratio (kidney function and hydration), haematocrit (concentration — elevated when dehydrated), total protein and albumin (concentration markers). These tell me whether you're hydrated at a cellular level — not just whether you drank water today. You can drink litres of water and still be dehydrated if your electrolytes are imbalanced and you can't hold water in cells, if your kidneys are overworking and flushing water out, or if you're depleting minerals through stress, sweat, or poor absorption.
Metabolic & Glucose
- Fasting glucose and HbA1c (blood sugar patterns — optimal vs normal ranges)
- Fasting insulin (rarely tested by standard medicine — reveals insulin resistance 10 years before glucose elevates)
- HOMA-IR calculation (quantifies insulin resistance from fasting glucose + insulin)
- Triglycerides and triglyceride-to-HDL ratio (insulin resistance surrogate marker)
Thyroid
- TSH (pituitary signal — but standard testing stops here)
- Free T4 (what the thyroid produces — inactive form)
- Free T3 (the active hormone — regulates cellular energy production)
- Reverse T3 (inactive form blocking T3 receptors — elevated by stress, inflammation)
- Anti-TPO and anti-thyroglobulin antibodies (Hashimoto's autoimmunity)
Nutrients & Deficiencies
- Ferritin and full iron panel (ferritin optimal: 70–100 ng/mL; required for thyroid conversion, dopamine synthesis, energy production)
- Vitamin D (optimal 75–150 nmol/L — UK population typically 25–50)
- B12 and folate (functional deficiency visible long before frank deficiency)
- Magnesium (red blood cell magnesium more accurate than serum)
- Zinc (plasma or serum zinc — context-dependent interpretation)
Inflammation & Liver
- hs-CRP (high-sensitivity — optimal below 1.0 mg/L)
- Homocysteine (methylation and cardiovascular inflammation — optimal below 7 µmol/L)
- ALT, AST, GGT (liver function and detoxification capacity — GGT is the earliest liver stress marker)
- Ferritin as inflammation marker (must be interpreted alongside CRP to distinguish iron overload from inflammatory elevation)
- Cholesterol pattern (HDL, LDL, total — interpreted in context, not as isolated risk markers)
GI-MAP Stool Analysis — The Gut-Everything Connection
The GI-MAP uses quantitative PCR technology — the same DNA-based detection methodology used in the most sophisticated medical laboratories — to identify and quantify gut organisms at levels of precision that standard culture-based stool testing cannot approach. A standard NHS stool culture detects perhaps 20–30 species under ideal conditions. The GI-MAP detects hundreds of organisms simultaneously, including parasites, fungi, and bacteria that do not grow on culture media.
The clinical decision to use DNA-based stool analysis is not a preference for novel technology. It's a precision requirement. The organisms most commonly driving chronic gut dysfunction — Blastocystis hominis, Cryptosporidium, Dientamoeba fragilis, SIBO-associated organisms, many Clostridia species — are systematically missed by culture methods. The test you don't run cannot tell you what you need to know.
My own stool testing revealed Blastocystis hominis — a parasite that had been causing years of constipation, bloating, and digestive discomfort I'd normalised as "just how I am." I wasn't just like that. I had an infection creating dysfunction. And this is exactly the pattern I see with clients who come to me for fatigue, skin issues, mood problems, or hormonal symptoms — and when we test their gut, we find infections, dysbiosis, inflammation, leaky gut. Fix the gut. Watch the other symptoms improve. Because the gut isn't just about digestion. It's about everything.
Stephen Duncan FDN-P MSc — personal accountPathogens & Infections
- H. pylori (with virulence factors — not all strains equally pathogenic)
- Parasites: Blastocystis, Cryptosporidium, Giardia, Dientamoeba, Entamoeba
- Pathogenic bacteria: E. coli O157, Campylobacter, Salmonella, C. difficile
- Fungal/yeast: Candida species quantified
- Opportunistic organisms: Klebsiella, Pseudomonas, Citrobacter, Morganella
Microbiome Balance
- Keystone species: Akkermansia muciniphila, Faecalibacterium prausnitzii (anti-inflammatory, barrier-supporting)
- Bifidobacterium and Lactobacillus species — beneficial bacteria levels
- Bacteroidetes-to-Firmicutes ratio — metabolic health indicator
- Overall microbiome diversity score
Digestive Function
- Pancreatic elastase (exocrine function — below 200 µg/g indicates enzyme insufficiency)
- Fat in stool (steatocrit) — bile flow and fat absorption adequacy
- Total short-chain fatty acids — fermentation and microbiome metabolic activity
Immune & Barrier Markers
- Secretory IgA — mucosal immune defence (depleted by cortisol)
- Calprotectin — active intestinal inflammation marker (elevated in IBD, infections)
- Zonulin — gut barrier permeability (elevated = leaky gut)
- Anti-gliadin antibodies — gluten immune reactivity in gut
- Beta-glucuronidase — oestrogen recirculation enzyme (drives oestrogen dominance)
- Eosinophil protein X — allergic/parasitic inflammation marker
DUTCH Hormone Panel — Patterns, Not Snapshots
Standard hormone blood testing gives you a snapshot — one moment in time, one number, no context about rhythm or pattern. DUTCH testing gives you something categorically different: patterns. How hormones fluctuate across the day. How you're metabolising them, not just producing them. What pathways they're taking through your body. This distinction matters profoundly because hormone metabolites — not just hormone levels — determine health outcomes.
My own DUTCH results showed a flattened cortisol curve — low morning output when it should have been high, elevated evening cortisol when it should have declined. The result was that I couldn't wake up properly in the morning and couldn't switch off at night. My high oestrogen — which caused the fertility challenges and contributed to the frozen shoulder period — was made worse by gut dysfunction preventing proper oestrogen elimination, liver stress impairing oestrogen metabolism, and a low-fat diet that didn't provide the substrate for healthy hormone pathways. Everything was connected. And DUTCH testing showed me exactly how.
Stephen Duncan FDN-P MSc — personal accountCortisol Patterns — What We're Mapping
Four collection points across the day reveal the complete cortisol curve: cortisol awakening response (CAR — the morning surge that should occur within 30–45 minutes of waking, indicating HPA axis competence), peak morning, afternoon, evening, and midnight. The rhythm matters as much as the absolute level. Common patterns and their clinical interpretations: Elevated throughout (Stage 1 — Alarm, driving the "wired" presentation); High morning then flat or inverted (Stage 2 — Resistance, the exhausted-but-wired pattern); Low throughout (Stage 3 — Exhaustion, HPA burnout, post-exertional malaise, inability to handle stress); High evening (onset insomnia, racing mind, blood sugar dysregulation); Flat morning with high evening (reversed cortisol pattern — often post-traumatic, shift worker, or severely sleep-disrupted presentation).
Sex Hormone Production & Levels
- Oestradiol, oestrone, oestriol — the three oestrogen forms and their balance
- Progesterone and pregnanediol (metabolite) — production and clearance
- Testosterone and DHEA-S — production levels, cortisol-to-DHEA ratio (stress resilience buffer)
- SHBG (sex hormone binding globulin) — determines free hormone fraction available to cells
Hormone Metabolism — What Standard Testing Misses
- Oestrogen metabolites: 2-OH (protective), 4-OH (genotoxic), 16-OH (proliferative) — the ratio determines cancer risk independent of oestrogen levels
- Methylation capacity — ability to clear oestrogen metabolites through 2-methylation pathway
- 5-alpha reductase activity — testosterone-to-DHT conversion (hair loss, prostate risk)
- Aromatase activity — testosterone-to-oestrogen conversion rate
Neurotransmitter Metabolites
- Dopamine metabolites (HVA) — motivation, focus, reward circuitry
- Noradrenaline/adrenaline (VMA) — stress reactivity, sympathetic overdrive
- Serotonin (5-HIAA) — mood, sleep, gut function; low = impaired melatonin production
Melatonin & Nutritional Markers
- 6-OH-melatonin sulphate — nighttime melatonin production (sleep quality, cancer protection)
- B12 and B6 functional status
- Methylation pathway markers (direct clinical utility for MTHFR variants)
- Oxidative stress markers
- Glutathione conjugation capacity
Organic Acids Test — Under the Hood
The OAT measures organic acid metabolites — the byproducts of cellular metabolism that spill into urine — providing a snapshot of what's happening inside your cells. Blood chemistry shows you the dashboard warning lights. The OAT shows you what's malfunctioning in the engine. It's the test that connects the dots between symptoms that appear unrelated: the fatigue, the anxiety, the brain fog, the weight that won't shift, the gut symptoms — all visible simultaneously in the metabolic picture the OAT reveals.
1 · Mitochondrial Function
- Krebs cycle intermediates (citrate, aconitate, isocitrate, alpha-ketoglutarate, succinate, fumarate, malate) — elevated at specific points indicate blockages at those enzymatic steps
- Pyruvate and lactate — ratio reveals whether glucose is entering mitochondria for efficient ATP production or being shunted to anaerobic metabolism
- Carnitine markers (suberate, adipate) — fatty acid transport into mitochondria; impaired = can't burn fat for fuel
- HMG elevation — CoQ10 deficiency indicator
2 · Neurotransmitter Metabolism
- 5-HIAA (serotonin metabolite) — low indicates poor gut serotonin production impairing melatonin and mood
- HVA (dopamine metabolite) — motivation, focus, drive; low in chronic fatigue and ADHD presentations
- VMA (noradrenaline/adrenaline) — high indicates chronic sympathetic activation
- Quinolinic acid — neuroinflammation and tryptophan shunting away from serotonin toward inflammatory pathway
- HPHPA — Clostridia neurotoxic metabolite affecting dopamine, behaviour, mood
3 · Gut Microbial Markers
- Arabinose and tartaric acid — Candida and yeast overgrowth confirmation (complements GI-MAP findings)
- HPHPA — Clostridia species producing dopamine-disrupting metabolites
- Bacterial metabolites indicating SIBO and dysbiosis patterns
- 3-oxoglutaric acid — yeast activity marker
4 · Nutrient Deficiencies
- B vitamin functional status: xanthurenate (B6 deficiency), methylmalonate (B12 deficiency), formiminoglutamate (folate deficiency)
- CoQ10 functional status (HMG marker)
- Carnitine functional status (adipate, suberate)
- Biotin deficiency markers
- Vitamin C (oxalate pathway)
5 · Detoxification Capacity
- Pyroglutamic acid — glutathione depletion marker; elevated = Phase II conjugation compromised
- Sulfate — total sulfur pool supporting Phase II detoxification
- Alpha-hydroxybutyrate — glutathione synthesis capacity
- Glucarate — Phase II glucuronidation activity
- Hippuric acid — aromatic compound exposure and Phase II load
6 · Oxidative Stress
- 8-OHdG (8-hydroxy-2-deoxyguanosine) — oxidative DNA damage marker
- Isoprostanes — lipid peroxidation from free radical damage to cell membranes
- Overall antioxidant capacity indicators
- Chronic oxidative stress pattern: elevated damage markers with depleted protective markers
Food Sensitivity Panel — The Hidden Inflammatory Triggers
This is IgG food sensitivity testing, not IgE allergy testing. The distinction is fundamental to clinical utility.
IgE reactions are immediate — eat peanuts, throat swells, you know within minutes. Dramatic, unmistakable, already managed. This is what conventional allergy testing identifies.
IgG reactions are delayed — symptoms appear hours to days after eating the reactive food. You eat eggs on Monday and feel terrible on Wednesday. No obvious connection. You've eliminated gluten and dairy (the obvious culprits) but still feel awful because you're actually reacting to eggs, almonds, and chicken. Nobody would guess that without testing.
IgG sensitivities drive chronic, low-grade inflammation contributing to digestive symptoms, skin conditions (eczema, acne, rosacea), joint pain and inflammation, headaches and migraines, fatigue and brain fog, autoimmune flare-ups, and mood disturbances. The delayed, unpredictable nature of these reactions makes them essentially impossible to identify through dietary trial and error alone.
Three clinical caveats apply to food sensitivity testing. First: food sensitivities often heal once the gut is fixed. Many sensitivities are a consequence of intestinal permeability — partially digested food proteins entering the bloodstream through a compromised gut barrier, triggering immune reactions. Fix the gut, heal the permeability, and many sensitivities resolve over 3–6 months. The foods aren't the primary problem. The leaky gut is. Second: sequence matters. If the gut is severely dysfunctional, you'll react to everything. Better to test and treat gut dysfunction first, then test food sensitivities, remove reactive foods while healing, then retest for reintroduction decisions. Third: this test is the last run, not the first. Used in context of the full picture, it guides a temporary elimination period with a clear reintroduction pathway. Used in isolation, it can produce unnecessary food restriction that impairs nutritional status.
My own food sensitivity panel showed gluten — not surprising given the Italian restaurant pasta consumption and the lifelong pace of eating. But also some other foods I'd been eating regularly, confident they were "healthy." Once I removed them, inflammation decreased, digestion improved, energy returned. Whether IgG testing perfectly predicts reactivity is less relevant to me than what I've observed clinically across decades: remove the reactive foods while healing the gut, and people improve. The theory can catch up to the clinical reality.
Stephen Duncan FDN-P MSc — personal accountCross-Test Integration — Where the Clinical Picture Emerges
The diagnostic power of the five-test programme is not in any individual test but in the cross-referencing of findings across all five simultaneously. Clinical patterns that are invisible in any single test become unmistakable when seen across the full panel. These are the most clinically important cross-test connections.
The Flexible 3-Test Option — When Not All Five Are Needed Immediately
Not every client requires all five tests simultaneously. When symptom patterns clearly point to specific systems, or when investment in a full panel isn't immediately possible, a targeted three-test combination provides the majority of clinical insight for the majority of presentations.
Always: Blood Chemistry
The metabolic foundation for every investigation. Thyroid, blood sugar, inflammation, nutrients, hydration — provides the context for interpreting every other test and reveals the systemic picture.
+ GI-MAP Stool Analysis
The gut connects to everything. Added for any presentation with digestive symptoms, immune dysfunction, hormonal imbalance, skin conditions, mood issues, or unexplained fatigue — which covers the vast majority of chronic health presentations.
+ DUTCH Hormones
Stress and sex hormone patterns are major drivers in most chronic cases. The DUTCH adds the HPA axis picture, cortisol rhythm, and hormone metabolism to blood chemistry's snapshot. These three together catch the majority of driving dysfunction.
The OAT is added when: fatigue is prominent and mitochondrial dysfunction is suspected, neurotransmitter symptoms (anxiety, depression, motivation, brain fog) are present, detoxification issues are clinically apparent, or gut dysbiosis markers from the GI-MAP need metabolic confirmation. The food sensitivity panel is added when: multiple food-related symptoms are present, autoimmune conditions are involved, or after gut restoration when reintroduction decisions need objective data.
What this module establishes
- Standard medical testing is designed to detect disease, not to identify dysfunction before it becomes disease. Functional testing uses optimal reference ranges — calibrated to detect dysfunction at the stage when it's correctable, not at the stage when it's diagnosable
- Pattern reading across the full panel is more clinically valuable than any individual marker result. The story is in the relationships between findings, not in isolated numbers
- Blood chemistry always begins with hydration assessment — sodium-potassium balance, BUN-to-creatinine ratio, haematocrit, and concentration markers. Cellular dehydration impairs everything else and is never addressed if never measured
- The GI-MAP uses quantitative PCR technology, identifying organisms that culture-based stool testing systematically misses — including most parasites, Candida, SIBO-associated organisms, and key Clostridia species
- DUTCH testing measures hormone metabolites and diurnal patterns — not just hormone levels at a single moment. The oestrogen metabolite ratios (2-OH vs 4-OH vs 16-OH) reveal cancer risk and detoxification capacity independent of oestrogen production levels
- The OAT is the window into cellular metabolism: mitochondrial function, neurotransmitter production, gut microbial activity, nutrient cofactor sufficiency, detoxification capacity, and oxidative stress — all from a single urine collection
- IgG food sensitivity testing identifies delayed immune reactions (hours to days after eating) that are invisible to IgE allergy testing and clinically impossible to identify through dietary elimination alone without objective data
- Food sensitivities are frequently a consequence of intestinal permeability, not the primary problem. Treating the leaky gut while temporarily eliminating reactive foods produces better long-term outcomes than indefinite food avoidance
- The five tests work as an integrated investigation system — cross-test connections consistently produce clinical insights that no single test can generate. Oestrogen dominance driven by gut beta-glucuronidase, serotonin depletion explaining sleep and mood through the gut-melatonin pathway, and H. pylori-driven nutrient deficiencies all require at minimum two tests to identify correctly
- The minimum effective combination for the majority of chronic presentations is blood chemistry plus GI-MAP plus DUTCH. OAT and food sensitivity are added based on clinical indication from the initial three