GC157 Paediatric Chemical Pathology
Paediatric chemical pathology is the subspecialty of clinical biochemistry focused on the diagnosis and monitoring of metabolic, endocrine, and biochemical disorders in neonates, infants, and children.
Paediatric Chemical Pathology
This lecture (GC 157) sits at the intersection of paediatric medicine and chemical pathology. The overarching message is deceptively simple but profoundly important: "Children are not small adults." In chemical pathology, this means reference ranges, differential diagnoses, investigations, sample handling, and management all differ from adult practice. The lecture centres on four core paediatric biochemical problems—neonatal cholestasis, hyperlactatemia, hyperammonemia, and hypoglycemia—and then pivots to the broader topic of inborn errors of metabolism (IEM), including their classification, clinical presentation, laboratory approach, epidemiology, and the expanding role of newborn screening. Two illustrative cases round out the lecture: an OTC deficiency case and a primary CoQ10 deficiency case.
Learning Objectives (per slide 2) [1]:
- Enhance understanding of "children are not small adults" from a chemical pathology perspective.
- Discuss chemical pathology approaches to common paediatric biochemical problems: neonatal cholestasis, hyperlactatemia, hyperammonemia, and hypoglycemia.
- Understand general principles and laboratory investigations for suspected IEM.
- Understand the importance and latest updates on newborn screening for IEM and genetic diseases.
High Yield: Every learning objective maps directly to past exam stems. The examiners love giving a neonatal/infant case and asking you to interpret biochemistry, narrow the DDx, and order the right confirmatory test.
"In Chemical Pathology perspective: Reference intervals are different; DDx are different; Tests are different; Sample requirement and considerations are different; Treatment and monitoring are different." [1]
| Aspect | Adult Practice | Paediatric Difference | Why It Matters |
|---|---|---|---|
| Reference intervals | Standard adult ranges | Age-, sex-, and sometimes Tanner-stage-specific | e.g. ALP is physiologically high in growing children (bone isoenzyme); bilirubin reference differs in neonates |
| DDx | Acquired diseases dominate | IEM, congenital anomalies, genetic syndromes far more common | A "rule-out sepsis" picture in a neonate may actually be an IEM |
| Tests | Standard panels | Specialised metabolic screens (plasma amino acids, urine organic acids, acylcarnitines) | These tests are rarely ordered in adult medicine but are first-line in paediatrics |
| Sample requirements | 5–10 mL tubes | Micro-samples; capillary/heel-prick; smaller tubes | Over-sampling can cause iatrogenic anaemia in neonates |
| Treatment | Standard dosing | Weight-based dosing; different drug metabolism; some drugs contraindicated | e.g. aspirin → Reye syndrome in children |
2. Neonatal Cholestasis
Neonatal cholestasis = conjugated (direct) hyperbilirubinaemia in early infancy. Current NASPGHAN/ESPGHAN guidance defines an abnormal direct/conjugated bilirubin as > 1.0 mg/dL (> 17 µmol/L), regardless of the percentage of total bilirubin; the older “> 20% of total” rule should not be used to delay evaluation [11]. Any infant still jaundiced after 2 weeks should have total and direct/conjugated bilirubin measured (a well breastfed infant may be reviewed at 3 weeks under the guideline's specified pathway) [11].
Why this matters: Unconjugated neonatal jaundice (physiologic, breast-milk, haemolytic) is extremely common and usually benign. Conjugated jaundice is ALWAYS pathological and demands urgent workup.
"Surgical: Bile duct abnormalities — then need to exclude biliary atresia since infants need to undergo surgery ASAP before the age of 60 days. Medical causes: Infections, Toxins/drugs, Endocrine diseases, IEM, Chromosomal diseases." [1]
| Category | Examples | Key Points |
|---|---|---|
| Surgical | Biliary atresia, choledochal cyst | Biliary atresia is time-critical: outcomes are generally better when Kasai portoenterostomy is performed earlier. Day 60 is not a safe deadline to wait for—refer and investigate urgently. |
| Infections | TORCH (Toxoplasma, Others, Rubella, CMV, HSV), UTI (especially E. coli), hepatitis B/C, sepsis | CMV is the most common congenital infection causing cholestasis |
| Toxins/Drugs | TPN-associated cholestasis, drugs | Prolonged parenteral nutrition in preterm neonates is a classic cause |
| Endocrine | Hypothyroidism, hypopituitarism, cortisol deficiency | Congenital hypothyroidism can cause prolonged conjugated jaundice |
| IEM | Galactosemia, tyrosinemia type I, alpha-1 antitrypsin deficiency, Niemann-Pick type C, CF | Galactosemia = jaundice + E. coli sepsis + cataracts in a milk-fed neonate |
| Chromosomal | Alagille syndrome (JAG1 mutation), Down syndrome | Alagille = paucity of intrahepatic bile ducts + butterfly vertebrae + posterior embryotoxon + characteristic facies |
Critical Time Window
Suspected biliary atresia needs urgent paediatric hepatology/surgical assessment. Earlier Kasai portoenterostomy is associated with better native-liver outcomes; the lecture's “before 60 days” phrase is a teaching landmark, not permission to wait until day 60. Do not attribute persistent jaundice to breast-milk jaundice without fractionating bilirubin [11].
"First-line Investigations of Neonatal Cholestasis" [1] (slide 6)
The image-based checklist on the slide lists the following historical first-line screen:
| Initial tests | Extra steps if the infant is acutely unwell |
|---|---|
| Blood count | Plasma ammonia, glucose and lactate |
| Blood and urine cultures | Acid–base status |
| Prothrombin time | Urinary pH and ketones |
| Plasma urea, electrolytes and glucose | Chest X-ray |
| Total and unconjugated bilirubin | Freeze plasma and urine for future analysis before treatment changes the biochemical pattern |
| Urinalysis for reducing substances | — |
Current-practice correction: the essential bilirubin pair is total plus direct/conjugated bilirubin, not merely total plus unconjugated bilirubin [11]. Urine reducing substances are nonspecific and are not a reliable stand-alone exclusion test for galactosaemia; use the local newborn-screen result and definitive enzyme/metabolite testing in consultation with the metabolic team. Obtain time-sensitive metabolic samples promptly when feasible, but never delay resuscitation, glucose, antibiotics or other urgent treatment to complete the panel.
This biochemical/sepsis screen is followed by problem-directed testing such as a full liver panel, coagulation assessment, thyroid and metabolic tests and abdominal ultrasound, with specialist-directed imaging, biopsy and/or genomic testing where indicated. The urgent clinical branch remains exclusion of biliary atresia.
3. Hyperlactatemia
Lactate is the end-product of anaerobic glycolysis. Pyruvate is normally converted to acetyl-CoA (via pyruvate dehydrogenase) and enters the TCA cycle. When oxygen is insufficient OR when specific metabolic pathways are blocked, pyruvate is shunted to lactate by lactate dehydrogenase.
Normal plasma lactate: < 2 mmol/L. Hyperlactatemia is generally defined as > 2 mmol/L; lactic acidosis when > 5 mmol/L with pH < 7.35.
"Type A lactic acidosis: With hypoxia. Type B lactic acidosis: Without hypoxia (Acquired / Genetic)." [1]
| Type | Mechanism | Examples |
|---|---|---|
| Type A | Tissue hypoxia → anaerobic glycolysis → excess lactate | Shock, severe anaemia, cardiac arrest, severe hypoxia, CO poisoning |
| Type B — Acquired | Raised lactate without systemic tissue hypoxia, from altered production or clearance | Recent generalised seizure/strenuous exercise, thiamine deficiency, liver failure, malignancy, medicines/toxins |
| Type B — Genetic | Enzyme defects in lactate-pyruvate metabolism | See below |
"Disorders of lactate-pyruvate oxidation; TCA cycle deficiencies; Respiratory chain defects; Disorders of gluconeogenesis; Disorders of glycogen metabolism" [1]
| Genetic Cause | Example | Mechanism |
|---|---|---|
| Pyruvate metabolism defects | Pyruvate dehydrogenase deficiency, pyruvate carboxylase deficiency | Cannot convert pyruvate → acetyl-CoA or oxaloacetate → lactate accumulates |
| TCA cycle deficiencies | Fumarase deficiency | Block in Krebs cycle → upstream metabolite build-up including lactate |
| Respiratory chain (mitochondrial) defects | MELAS, Complex I/II/III/IV deficiency | Cannot oxidise NADH → NAD+ ratio falls → pyruvate shunted to lactate |
| Gluconeogenesis defects | Fructose-1,6-bisphosphatase deficiency | Cannot convert lactate back to glucose via gluconeogenesis |
| Glycogen metabolism defects | GSD type I (von Gierke) | Glucose-6-phosphatase deficiency → excess glycolysis → lactate |
Read the specimen before the pathway
A difficult venepuncture, prolonged tourniquet, struggling/crying, recent seizure or delayed separation can raise lactate. If the result does not fit the child, repeat a free-flowing sample with minimal stasis and rapid local-laboratory handling—while treating genuine shock or hypoxia immediately. Interpret lactate with perfusion, blood gas, glucose and ketones, not in isolation.
Clinical tip: a simultaneously collected lactate-to-pyruvate (L:P) ratio can support pathway localisation only when lactate is genuinely elevated and both analytes were handled correctly. A high ratio may support respiratory-chain/redox dysfunction, whereas a normal ratio can occur in pyruvate dehydrogenase deficiency; neither pattern is diagnostic by itself.
4. Hyperammonemia
Ammonia (NH₃/NH₄⁺) is produced by amino acid catabolism, gut bacterial urease activity, and renal glutaminase. It is detoxified in the liver via the urea cycle, which converts ammonia to urea for renal excretion. In neonates and infants, the urea cycle can be immature or defective.
Normal plasma ammonia: < 60 µmol/L in older children; neonates may have slightly higher levels but should still be < 100 µmol/L.
Why ammonia is toxic: Ammonia freely crosses the blood-brain barrier. In astrocytes, glutamine synthetase converts glutamate + NH₃ → glutamine. Excess glutamine causes osmotic swelling of astrocytes → cerebral oedema → encephalopathy → coma → death.
Ammonia is a pre-analytically fragile emergency test
Use an age- and laboratory-specific reference interval. Send a free-flowing venous or arterial sample without fist clenching, transport/process it immediately according to the local laboratory protocol, and repeat an unexpected result promptly. Marked hyperammonaemia with encephalopathy is a metabolic emergency: repeat confirmation must not delay specialist metabolic treatment [14].
| Category | Examples |
|---|---|
| Urea cycle defects (UCD) | OTC deficiency (X-linked), CPS1 deficiency, ASS deficiency (citrullinemia), ASL deficiency (argininosuccinic aciduria), arginase deficiency |
| Organic acidemias | Propionic acidemia, methylmalonic acidemia, isovaleric acidemia |
| Fatty acid oxidation defects | MCAD, VLCAD, LCHAD |
| Liver failure | Any cause — viral, drug, metabolic |
| Transient hyperammonemia of the newborn (THAN) | Preterm infants; resolves spontaneously |
| Infections | Severe sepsis, herpes |
| Others | Valproate therapy, urinary tract infection with urease-producing organisms |
"3-yo Hong Kong Chinese boy; full term; non-consanguineous parents; unremarkable history; good past health and normal development; 3 days of repeated vomiting and diarrhea; bizarre behavior on day 2; comatose on day 3." [1]
Key investigation findings [1]:
- CBP, LFT, RFT, ABG: normal
- Plasma ammonia: 54 µmol/L (< 60 — i.e. normal at presentation!)
- Urine toxicology: negative
- EEG: generalised slowing with transient sharp slow wave
- CT brain: normal
- CSF and blood cultures for viruses: negative
- Plasma and urine amino acids: normal
- Stool culture: positive for rotavirus
- Urinary organic acids: marked elevation of orotic acid
Exam Trap — Normal Ammonia Does NOT Rule Out UCD
In this case, ammonia was normal at the time of sampling. UCD patients can have intermittent hyperammonemia triggered by catabolic stress (infection, fasting). Between crises, ammonia may normalise. The KEY clue was the elevated urinary orotic acid.
"Plasma urea: LOW. Ammonia: HIGH. Plasma amino acids: low arginine, elevated glutamine. All are normal in this patient, except the urine orotic acid." [1]
Why these patterns?
- Low urea: The urea cycle is blocked, so less urea is produced
- High ammonia: Cannot convert ammonia to urea
- Low arginine: Arginine is the immediate precursor of urea; in most UCDs it is consumed/not produced
- High glutamine: Ammonia is detoxified to glutamine as a compensatory mechanism
- Orotic acid elevation: Specific to OTC deficiency — carbamoyl phosphate (which cannot enter the blocked urea cycle) spills into the pyrimidine synthesis pathway → orotic acid
"DDx of Orotic Aciduria" [1] (slide 18)
The lecture table grades the differential by the degree of increase:
| Degree of orotic acid increase | Causes shown on the slide |
|---|---|
| Slight | Premature birth; pregnancy |
| Slight–moderate | Alcoholism; cerebral infection; diabetes; heart failure; hypertension; malignancy; trauma |
| High | Arginase deficiency; argininosuccinate lyase deficiency; argininosuccinate synthetase deficiency; hyperornithinaemia–hyperammonaemia–homocitrullinuria syndrome; lysinuric protein intolerance; OTC deficiency; Rett syndrome; UMP synthase deficiency |
Mechanistically, OTC deficiency diverts excess carbamoyl phosphate into pyrimidine synthesis, whereas UMP synthase deficiency causes hereditary orotic aciduria and classically produces megaloblastic anaemia that does not respond to folate or vitamin B12.
The image-table discriminator is the surrounding phenotype: OTC deficiency typically pairs orotic aciduria with hyperammonaemia, low/low-normal citrulline and often low urea; UMP synthase deficiency causes persistent orotic aciduria with failure to thrive and megaloblastic anaemia without hyperammonaemia. Orotic acid alone is not diagnostic [14].
"Genetic analysis of OTC gene unraveled a hemizygous missense mutation of arginine-to-glutamine substitution on amino acid 277 (p.R277Q)" [1]
Why hemizygous? OTC deficiency is X-linked. Males have only one X chromosome, so a single pathogenic variant = disease. This is the only common X-linked UCD; all others are autosomal recessive.
Why so atypical? The p.R277Q mutation is a known "late-onset" or partial OTC deficiency variant. The enzyme has residual activity (unlike null mutations that present in the neonatal period with severe hyperammonemia). These patients may be well for years and only decompensate during catabolic stress (e.g. the rotavirus infection in this case).
"The child remained unconscious for three days under intensive care. He regained consciousness spontaneously without any neurological deficit. He was discharged on the third hospital day with a diagnosis of transient encephalopathy of undetermined cause." [1]
Clinical lesson: Without the orotic acid finding and subsequent genetic testing, this child would have been discharged without a diagnosis and would be at risk of fatal hyperammonemic crisis in the future.
"Liver biopsy: Refused by parents; Invasive; Sending overseas; Patients have to pay. Genetic analysis: Non-invasive; Definitive; Local expertise available." [1]
The slide's Sanger workflow is blood → DNA extraction/quantification → PCR → sequencing reaction → purification → capillary sequencing → chromatogram review. Modern testing may instead use a targeted panel, exome or genome. A pathogenic/likely pathogenic variant that fits the inheritance and biochemical phenotype can establish a diagnosis; a variant of uncertain significance does not, and a negative test does not exclude every biochemical disorder. Liver OTC enzyme assay is now reserved for selected unresolved cases and is unreliable for excluding disease in heterozygous females because of X-inactivation [14].
5. Hypoglycemia
"Definition of plasma glucose level" [1]
There is no single universal glucose cut-off for every neonatal age and clinical context. The lecture's < 2.6 mmol/L value is a commonly used operational threshold, but local neonatal protocols determine when to feed, recheck, investigate or give IV glucose. Persistent/recurrent hypoglycaemia—especially beyond the transitional newborn period—needs evaluation for an underlying disorder [12]. Confirm a low bedside value with a laboratory plasma glucose where feasible, but treat a symptomatic or dangerously low value immediately.
Why it matters: The developing brain is critically dependent on glucose. Prolonged or recurrent hypoglycemia causes irreversible neurological damage.
"Ketone +/−? Urine stix vs quantitative measurement of ketone. Acetoacetate vs beta-hydroxybutyrate. Insulin – check any hemolysis in the sample. Glucose transfusion rate." [1]
| Consideration | Explanation |
|---|---|
| Ketone status | The MOST important discriminator. Normal fasting → ketones should be present (ketotic hypoglycemia). Absent ketones = non-ketotic = hyperinsulinism or fatty acid oxidation defect |
| Urine dipstick ketones | Detects acetoacetate only; misses beta-hydroxybutyrate. In early fasting, the predominant ketone body is beta-hydroxybutyrate |
| Quantitative blood beta-hydroxybutyrate | More accurate; preferred in paediatric workup |
| Insulin measurement | Must check for sample haemolysis — RBC contain insulin-degrading enzyme; haemolysed sample gives falsely LOW insulin, masking hyperinsulinism |
| Glucose infusion rate (GIR) | The amount of IV glucose (mg/kg/min) needed to maintain euglycaemia. A requirement > 8 mg/kg/min in a neonate is evidence of excessive insulin action; this neonatal threshold should not be applied unchanged to older children [13]. |
The lecture's image uses urine ketones and then serum insulin as its main branches [1]. The visual principle remains useful, but current evaluation branches on quantitative plasma beta-hydroxybutyrate (BOHB) and free fatty acids (FFA)—the metabolic actions of insulin—not on urine dipstick or insulin concentration alone [12,13]:
The diagram's logic is: appropriate ketosis directs the work-up toward fasting/illness, endocrine, organic-acid, glycogen and gluconeogenesis causes; hypoketosis directs it toward insulin excess, fatty-acid oxidation or ketogenesis defects. A low or undetectable insulin concentration does not exclude hyperinsulinism if BOHB and FFA are suppressed, GIR is excessive or glucose rises inappropriately after glucagon [13].
Critical Sample
When a child presents with hypoglycaemia, draw a critical sample during the low glucose if this can be done without delaying treatment: laboratory glucose, insulin, C-peptide, cortisol, GH, FFA, BOHB, lactate, ammonia and context-directed amino-acid/acylcarnitine studies, plus first urine for organic acids. Treatment changes these analytes quickly, but preventing neuroglycopenic injury comes first [12].
6. Inborn Errors of Metabolism (IEM) — General Principles
"Phenotypically and genetically heterogeneous group of disorders. Defective enzyme or transporter in metabolic pathways — leading to disease due to metabolic malfunction and/or accumulation of toxic intermediate metabolites." [1]
Think of a metabolic pathway as an assembly line. If one worker (enzyme) is missing:
- The product downstream is deficient (e.g. low cortisol in CAH)
- The substrate upstream accumulates and may be toxic (e.g. phenylalanine in PKU)
- Alternative pathways may be activated, producing abnormal metabolites (e.g. orotic acid in OTC deficiency)
The lecture lists all 15 SSIEM groups [1]:
| # | Group | Classic Example |
|---|---|---|
| 1 | Amino acid & peptide metabolism | PKU, MSUD, homocystinuria |
| 2 | Carbohydrate metabolism | Galactosemia, GSD |
| 3 | Fatty acid & ketone body metabolism | MCAD deficiency |
| 4 | Energy metabolism | Mitochondrial disorders, PDH deficiency |
| 5 | Purine, pyrimidine & nucleotide metabolism | Lesch-Nyhan syndrome |
| 6 | Sterol metabolism | Smith-Lemli-Opitz syndrome |
| 7 | Porphyrin & haem metabolism | Acute intermittent porphyria |
| 8 | Lipid & lipoprotein metabolism | Familial hypercholesterolaemia |
| 9 | Congenital disorders of glycosylation | CDG syndromes |
| 10 | Lysosomal disorders | Gaucher, Fabry, MPS |
| 11 | Peroxisomal disorders | Zellweger syndrome, X-linked ALD |
| 12 | Neurotransmitter metabolism | AADC deficiency |
| 13 | Vitamin & cofactor metabolism | Biotinidase deficiency |
| 14 | Trace element & metal metabolism | Wilson disease |
| 15 | Xenobiotic metabolism | Variants in drug metabolism |
Historical classification
This 15-group SSIEM table reflects the lecture's older teaching framework. The internationally endorsed ICIMD published in 2021 contained 1,450 disorders in 24 categories and 124 groups, and its online database continues to evolve [15]. Use the slide's list for lecture recall, but use ICIMD/OIMD for current taxonomy rather than memorising old disease counts.
"Mostly autosomal recessive" [1]
- In the pedigree image, each carrier parent has one normal and one pathogenic allele. For each pregnancy, two carrier parents have a 25% chance of an unaffected non-carrier child, 50% chance of an unaffected carrier, and 25% chance of an affected child.
- This is a recurrence probability, not a prediction that every four children will include one affected child.
- Notable exceptions to autosomal recessive inheritance include OTC deficiency and Hunter syndrome (X-linked), mitochondrial-DNA disorders (maternal inheritance), and several autosomal-dominant metabolic disorders.
"Usually presented at birth, early infancy and childhood (but some can present in adulthood) — with nonspecific clinical symptoms (esp. in neonatal period) such as appetite, vomiting, acute or chronic encephalopathy, myopathy, hypoglycaemia or hepatic syndromes, rule out sepsis pattern." [1]
High Yield — The 'Rule-Out Sepsis' Pattern
A neonate who presents with poor feeding, lethargy, vomiting, acidosis, and a "septic" picture but whose cultures are negative should be investigated for IEM. This is one of the most important clinical pearls in paediatric chemical pathology.
"Group 1: leading to intoxication. Group 2: with energy metabolism defects. Group 3: involving complex molecules." [1]
| Group | Mechanism | Examples | Key Features |
|---|---|---|---|
| Group 1 — Intoxication | Accumulation of toxic metabolites proximal to the enzyme block | UCDs, organic acidemias, MSUD, galactosemia | Symptom-free interval after birth (toxin needs to accumulate); acute decompensation triggered by feeds/catabolism; potentially treatable by removing the toxic substrate (dietary restriction, dialysis) |
| Group 2 — Energy deficiency | Defects in energy production (mitochondria, glycolysis, gluconeogenesis) | Mitochondrial respiratory chain defects, FAO defects, GSD, PDH deficiency | Chronic symptoms (hypotonia, myopathy, cardiomyopathy); lactic acidosis; hypoglycemia; less responsive to acute dietary manipulation |
| Group 3 — Complex molecules | Defects in synthesis or degradation of complex molecules | Lysosomal storage disorders, peroxisomal disorders, CDG | Progressive, often with organomegaly, coarse facies, skeletal dysplasia; storage diseases — symptoms develop gradually |
The lecture provides an extensive list [1] (slide 35). Key indications:
- Failure to thrive
- Neurological abnormalities: developmental delay, lethargy, hypotonia, seizures, encephalopathy, stroke, psychiatric problems
- Movement, sensory or skin clues: dystonia/ataxia, unexplained visual or hearing loss, unusual pigmentation or recurrent unexplained rash
- Unexplained episodic illness with "rule-out sepsis" picture
- Abnormal biochemical findings: high anion gap metabolic acidosis, ketosis, hypoglycemia, Type B lactic acidosis, hyperammonemia
- Organomegaly, cardiomyopathy, myopathy, rhabdomyolysis
- Family history of unexplained sudden death or life-threatening event
- Maternal history of AFLP or HELLP syndrome (suggests FAO defect in fetus — fetal FAO defect → maternal liver injury)
- Jaundice, Reye syndrome, unexplained liver/renal derangement
- Abnormal odour (e.g. "sweaty feet" in isovaleric acidemia, "maple syrup" in MSUD, "musty" in PKU)
"Individually rare; collectively common. Collective incidence overseas amounted to about 1:4,000 newborns screened. Local collective incidence of IEM ranges from 1 in 4,122 to 1 in 7,580 — comparable to worldwide figures." [1]
These are historical slide estimates, not directly comparable prevalence figures: the country table combines different years, screening panels, populations and ascertainment methods. The durable teaching point is that IEMs are individually rare but collectively important; use a defined programme, panel and period when quoting incidence.
"Plasma amino acids (PAA), Plasma acylcarnitines (PAC), Urine organic acids (UOA)" [1]
| Test | Method | What It Detects | Classic Findings |
|---|---|---|---|
| Plasma amino acids (PAA) | Ion-exchange chromatography or MS/MS | Aminoacidopathies, UCDs | ↑Phe in PKU; ↑Leucine/Isoleucine/Valine in MSUD; ↓Arginine + ↑Glutamine in UCD |
| Urine organic acids (UOA) | GC-MS (gas chromatography–mass spectrometry) | Organic acidemias, FAO defects, other IEMs | ↑Methylmalonic acid in MMA; ↑3-OH isovaleric acid in IVA; ↑Orotic acid in OTC deficiency |
| Plasma acylcarnitines (PAC) | Tandem mass spectrometry (MS/MS) | FAO defects, organic acidemias | ↑C8 (octanoylcarnitine) in MCAD; ↑C3 in propionic acidemia; ↑C5 in isovaleric acidemia |
How to read the three instrument images: PAA produces an amino-acid chromatogram, PAC an MS/MS spectrum, and UOA a GC–MS chromatogram. Diagnosis comes from a pattern of peaks/ratios plus the clinical state, not from one isolated peak. Samples collected during acute decompensation and before disease-specific therapy often have the highest yield; diet, transfusion, medication and recovery can attenuate the pattern. A normal screen outside a crisis does not exclude every IEM.
Additional tests (context-dependent):
- Plasma lactate and L:P ratio
- Plasma ammonia (free-flowing sample, transported and processed immediately under the local laboratory protocol)
- Very long chain fatty acids (peroxisomal disorders)
- Urine purines and pyrimidines
- CSF amino acids and neurotransmitters (for neurotransmitter defects)
- Enzyme assays (on fibroblasts, lymphocytes, or liver tissue)
- Phenotype-directed genomic testing, interpreted alongside the biochemical pattern
8. IEM Diagnosis and Management
"Confirmatory test: mainly through biochemical testing, supplemented with genetic testing." [1]
Modern evaluation may add a targeted gene panel, exome or genome after initial biochemical/phenotypic assessment, particularly when:
- Biochemical results are ambiguous
- Enzyme assay requires invasive tissue (liver biopsy)
- Local genetic expertise is available (as in the OTC case) [1]
"Dietary control; Enzyme replacement therapy; Steroid treatment; Surgical: liver & kidney transplantation; Genetic counselling." [1]
| Strategy | Examples |
|---|---|
| Dietary restriction | Low-phenylalanine diet in PKU; low-protein diet in UCD/organic acidemias; galactose-free diet in galactosemia |
| Cofactor supplementation | Biotin in biotinidase deficiency; CoQ10 in CoQ10 deficiency; B12 in B12-responsive MMA |
| Enzyme replacement therapy (ERT) | Gaucher (imiglucerase), Fabry (agalsidase), Pompe (alglucosidase alfa), MPS I (laronidase) |
| Substrate reduction / pathway inhibition | Miglustat in selected lysosomal disorders; nitisinone blocks an upstream tyrosine-catabolism step in tyrosinaemia type I |
| Transplantation | Liver transplant in UCD (provides the missing enzyme); kidney transplant in some; bone marrow transplant in some lysosomal diseases |
| Phenotype-specific symptomatic treatment | e.g. hormonal therapy for infantile epileptic spasms in the CoQ10 case; corticosteroids are not a generic treatment for IEM |
| Emergency management | Reverse catabolism (often IV glucose), temporarily withhold protein under a metabolic protocol, give disease-specific nitrogen scavengers and use renal replacement therapy when indicated |
| Genetic counselling | Recurrence risk, carrier testing, prenatal diagnosis |
Acute treatment is disorder-specific and specialist-led. The general priorities are to stabilise airway/breathing/circulation, reverse catabolism (often with glucose), temporarily stop the offending substrate when advised, remove toxic metabolites where indicated, give disease-specific cofactors/scavengers and collect critical samples without delaying resuscitation.
9. Newborn Screening (NBS)
Historical slide wording: "Newborn screening becoming the gold standard worldwide." [1]
Newborn screening is a jurisdiction-specific public-health programme, not a universal diagnostic panel. The conditions, timing and assays vary by programme. An out-of-range result requires prompt confirmatory testing; a normal result does not exclude a disorder that is not on the panel or one missed because of timing, transfusion, parenteral nutrition, prematurity or biological/analytical limitations.
Wilson & Jungner criteria (adapted for NBS):
- Important health problem
- Accepted treatment available
- Facilities for diagnosis and treatment available
- Recognisable latent or early symptomatic stage
- Suitable test available
- Test acceptable to the population
- Natural history of the disease understood
- Agreed policy on whom to treat
- Cost of case-finding economically balanced with cost of treatment
- Continuous process, not a "once and for all" project
"Conventional screening test: one analysis of one metabolite (e.g. PKU). Nowadays screening test: many metabolites for different diseases in one analysis — by tandem mass spectrometry (MS/MS). MS/MS might be more cost-effective." [1]
| Method | How It Works | Advantage |
|---|---|---|
| Guthrie test (conventional) | Bacterial inhibition assay for Phe on dried blood spot | Simple, cheap; one test = one disease |
| Tandem mass spectrometry (MS/MS) | Analyses amino acids and acylcarnitines simultaneously from a single dried blood spot | One blood spot → screening for 20–50+ diseases; fast; small sample volume |
The heel-prick photograph shows several fully saturated dried-blood-spot circles on filter paper. Each circle must be filled through from one side without layering or contamination; collection quality matters because an insufficient or uneven spot can produce an invalid, false-positive or false-negative result. The US “50 years of newborn screening” infographic on the preceding slide is a historical US timeline (PKU screening, hearing and pulse-oximetry milestones), not a Hong Kong programme specification.
"Expanded Newborn Screening" [1] (slide 38)
The table shown in the lecture is explicitly dated January 2023. Its green ticks identify the conditions then available in the HA/HK programme:
| Category | Conditions ticked on the lecture slide |
|---|---|
| Organic acid disorders | Propionic acidaemia; methylmalonic acidaemia due to methylmalonyl-CoA mutase; methylmalonic acidaemia due to cobalamin disorders; isovaleric acidaemia; 3-hydroxy-3-methylglutaric aciduria; holocarboxylase synthetase deficiency; β-ketothiolase deficiency; glutaric acidaemia type I |
| Fatty-acid oxidation disorders | Carnitine uptake/transport defect; MCAD deficiency; VLCAD deficiency |
| Amino-acid disorders | Argininosuccinic aciduria; citrullinaemia type I; MSUD; homocystinuria; classic PKU; tyrosinaemia type I |
| Endocrine disorders | Primary congenital hypothyroidism; congenital adrenal hyperplasia |
| Other disorders | Biotinidase deficiency; classic galactosaemia; hearing loss; severe combined immunodeficiencies; spinal muscular atrophy due to homozygous SMN1 deletion |
Date the programme list
Use the January 2023 list to answer questions about this lecture slide. Screening panels change over time, so do not silently treat it as a current policy list.
Current Hong Kong context (June 2026): the HKSAR Government reports that the HA programme now screens for 30 IEM conditions plus SCID and SMA, reaches more than 99% of babies born in public hospitals, and has been extended to babies born in participating private hospitals where eligibility criteria are met [16]. This supersedes the slide's January 2023 “available in HA/HK” ticks; the slide also compares that former local subset with the US Recommended Uniform Screening Panel, which should not be mistaken for a Hong Kong mandate.
"Preventable Morbidities & Mortalities: Biochemical and Molecular Diagnosis of Tyrosinemia Type I — Recommendation for Expanded Newborn Screening in Hong Kong — Preventable liver transplantation." [1]
This slide emphasises that tyrosinaemia type I is a treatable IEM. The disease-specific screening marker is succinylacetone (tyrosine alone is insufficiently sensitive/specific); early confirmation and nitisinone plus a low-tyrosine/low-phenylalanine diet markedly improve survival and reduce liver and renal complications. Treatment reduces but does not eliminate hepatocellular-carcinoma risk, so biochemical and liver surveillance remains necessary [17].
The companion VLCAD-deficiency example makes the same prevention point for fatty-acid oxidation: an apparently well screened newborn may need confirmatory testing, a fasting-avoidance plan and rapid carbohydrate/IV-glucose support during illness to prevent hypoketotic decompensation, cardiomyopathy or death. Newborn screening reduces diagnostic delay but is not infallible [19].
10. Case 2 — Primary CoQ10 Deficiency (Infantile Spasm)
"FTNSD, AN/PN unremarkable; Chinese, non-consanguineous; first child in family, FHx unremarkable; noted developmental delay then infantile spasm at 6 months; spasm resolved after short course of steroid; P/E: microcephaly, hypotonia; no positive findings from extensive blood/urine tests." [1]
"WES (Classified as pathogenic): Compound heterozygous for COQ4 c.370G>A, p.Gly124Ser and c.371G>T, p.Gly124Val" [1]
- Whole exome sequencing (WES) was used because standard metabolic workup was negative
- COQ4 gene encodes a protein involved in CoQ10 biosynthesis
- Compound heterozygous = two different pathogenic variants, one on each allele (consistent with autosomal recessive inheritance)
"Also known as coenzyme Q10, CoQ10, ubiquinone, ubidecarone. Non-protein-bound lipid-soluble prosthetic group. Ubiquitous in animals and most bacteria. Component of electron transport chain — Carrier of both proton and electrons — Accepts electrons from complex I or II — Donates electrons to complex III." [1]
Why CoQ10 deficiency causes disease: CoQ10 is a lipid-soluble redox carrier. It cycles between ubiquinone (oxidised), a semiquinone intermediate and ubiquinol (reduced) while carrying electrons/protons. In the respiratory chain it shuttles electrons from complexes I and II to complex III; deficiency impairs oxidative phosphorylation and disproportionately affects brain, muscle, heart and kidney.
What the two pathway diagrams show:
- In the inner mitochondrial membrane, complexes I and II donate electrons to CoQ, CoQ transfers them to complex III, cytochrome c carries them to complex IV, and oxygen is reduced to water. Complexes I, III and IV pump protons to build the gradient used for ATP generation.
- CoQ synthesis joins an aromatic ring derived from tyrosine → 4-hydroxybenzoate (4HB) to a ten-unit prenyl side chain derived from acetyl-CoA → mevalonate → farnesyl-PP → decaprenyl-PP.
- The slide places COQ4 at the centre of the mitochondrial COQ biosynthetic complex (with COQ2/3/5/6/7), reflecting its role in organisation/stabilisation rather than a single catalytic arrow. The finished CoQ is delivered within the inner-membrane system by proteins including COQ10A/COQ10B.
This connects the case directly to the figure: biallelic COQ4 variants impair assembly/function of the biosynthetic complex, reducing CoQ available to carry electrons in the respiratory chain.
"Incidence in Italy < 1:100,000. Autosomal recessive." [1]
| System | Manifestations |
|---|---|
| Neurological | Fatal neonatal encephalopathy with hypotonia; Dystonia/Spasticity; Parkinsonism/Ataxia; Seizure; Intellectual disability |
| Multisystem | Severe infantile multisystem disease |
| Renal | Steroid-resistant nephrotic syndrome |
| Cardiac | Hypertrophic cardiomyopathy |
| Muscular | Isolated myopathy |
| Ocular | Retinopathy / optic atrophy |
| Auditory | Sensorineural hearing loss |
Historical slide regimen: high-dose oral CoQ10 as early as possible; adult 2400 mg/day and paediatric 30 mg/kg/day in three doses [1].
Potentially treatable—but specialist prescribed
Current GeneReviews describes oral CoQ10 doses across primary deficiencies ranging roughly 5–50 mg/kg/day, with response depending on genotype, severity and formulation; soluble formulations may be more bioavailable [18]. The slide's exact doses and “no serious side effects” wording are not universal prescribing instructions. Start early under a mitochondrial/metabolic specialist because treatment may slow progression or improve some features, but established severe neurological or renal injury may not reverse [18].
Case outcome [1]:
- Started CoQ10 at 9 months old
- Parents reported increased alertness
- Developmentally making slight progress; head control improved
- Still cannot sit alone by age 3
- CoQ10 dose escalated to 41 mg/kg/day (liposomal preparation)
This is a single case observation, not proof of efficacy or a general dosing protocol. The limited developmental gains despite improved alertness/head control illustrate both the potential benefit of early molecular diagnosis and the variable, often incomplete CNS response.
11. Integration with Related Lectures
GC 154 [2] covers the general principles of screening (sensitivity, specificity, PPV, NPV, Wilson-Jungner criteria). The newborn screening section of GC 157 directly applies these principles to neonatal metabolic screening via MS/MS.
This seminar [3] provides deeper dives into specific IEMs and their biochemical diagnosis, complementing the overview in GC 157.
The data interpretation sessions [4] practice interpreting panels of biochemical results in clinical scenarios, including paediatric metabolic emergencies.
GC 078 [5] covers glucose metabolism, diabetes mellitus, and DKA. Hypoglycemia in children can present similarly to adult DKA in reverse (altered consciousness, metabolic derangement), and the approach to blood glucose abnormalities overlaps.
The electrolytes lecture [6] covers acid-base disorders and electrolyte disturbances that often accompany IEM presentations (e.g. high anion gap metabolic acidosis in organic acidemias).
12. Exam Intelligence
- Neonatal cholestasis: Distinguish conjugated from unconjugated; urgency of excluding biliary atresia
- Hypoglycemia workup: time-sensitive critical sample; BOHB/FFA response; age-appropriate GIR significance
- Hyperammonemia: UCD vs organic acidemia; orotic acid significance; OTC as X-linked
- IEM general principles: Autosomal recessive inheritance; "not small adults"; newborn screening
- Lactic acidosis: Type A vs Type B; L:P ratio interpretation
- Newborn screening: MS/MS; expanded screening; why it's done
| Trap | Why Students Fall For It | Correct Approach |
|---|---|---|
| Normal ammonia at one time point excludes UCD | Ammonia fluctuates; may be normal between crises | Look for other clues (orotic acid, amino acid patterns); repeat ammonia during illness |
| Urine dipstick negative for ketones = no ketosis | Dipstick detects acetoacetate, not beta-hydroxybutyrate | Order quantitative blood beta-hydroxybutyrate |
| Haemolysed sample insulin = true insulin level | Haemolysis degrades insulin → falsely low | Reject haemolysed sample; re-draw |
| Breast-milk jaundice explains conjugated jaundice | Breast-milk jaundice causes UNCONJUGATED hyperbilirubinaemia | Always fractionate bilirubin; conjugated = pathological |
| All IEM present in neonatal period | Late-onset forms exist (e.g. partial OTC deficiency) | Metabolic stress can unmask late-onset IEM at any age |
| All mitochondrial disorders are untreatable | Primary CoQ10 deficiency is potentially treatable | Early specialist supplementation may slow progression or improve selected features; response is variable |
| Scenario | OTC Deficiency | CPS1 Deficiency | Organic Acidemia |
|---|---|---|---|
| Ammonia | ↑↑ | ↑↑ | ↑ (moderate) |
| Orotic acid | ↑↑↑ | Normal/Low | Normal |
| Plasma amino acids | ↓Arginine, ↑Glutamine, ↓Citrulline | ↓Arginine, ↑Glutamine, ↓Citrulline | Variable |
| Urine organic acids | Orotic acid only | Normal | Specific organic acids (MMA, PA, etc.) |
| Anion gap | Normal | Normal | High |
| Inheritance | X-linked | AR | AR |
| Problem | Key Definition | Critical DDx | First Clue | Urgent Action |
|---|---|---|---|---|
| Neonatal cholestasis | Direct/conjugated bilirubin > 17 µmol/L | Biliary atresia vs medical causes | Pale stool + dark urine + persistent jaundice | Fractionate bilirubin and exclude biliary atresia urgently |
| Hyperlactatemia | Lactate > 2 mmol/L | Type A (hypoxia) vs Type B (no hypoxia) | Acidosis + raised lactate | Treat underlying cause; check L:P ratio if genetic cause suspected |
| Hyperammonemia | Above the age/lab-specific range | UCD vs organic acidemia vs liver failure | Encephalopathy + ↑NH₃ ± low urea | Urgent metabolic consultation; reverse catabolism and use scavengers/RRT per protocol |
| Hypoglycemia | Age/context-specific operational threshold | Ketotic vs hypoketotic | Low glucose + altered consciousness | Treat immediately; obtain critical sample first only if this causes no delay |
High Yield Summary
- Children are not small adults: reference intervals, differential diagnoses, tests, sample handling and treatment all differ.
- Neonatal cholestasis: always pathological; fractionate bilirubin and exclude biliary atresia urgently—do not wait for a day-60 threshold.
- Hyperlactataemia: distinguish Type A (with tissue hypoxia) from Type B, but first exclude collection/processing artefact; use L:P only with a genuine, correctly handled elevation.
- Hyperammonaemia: consider UCD urgently; OTC classically combines hyperammonaemia, low citrulline and orotic aciduria, but values can normalise between crises.
- Hypoglycaemia: treat first; collect a critical sample without delay when feasible. Quantitative BOHB/FFA are more informative than urine ketones or insulin alone.
- IEM: individually rare and collectively important; many—but not all—are autosomal recessive and may mimic sepsis.
- Clinical heuristic: intoxication, energy deficiency and complex-molecule disease are useful bedside groups, distinct from current ICIMD taxonomy.
- Major metabolic investigations: interpret PAA, UOA and PAC as patterns shaped by illness timing, diet and treatment; add phenotype-directed genetics.
- Newborn screening: programme- and date-specific; it identifies risk rather than making a diagnosis, and a normal screen does not exclude every IEM.
- Primary CoQ10 deficiency: potentially treatable, but dose and response are genotype/formulation dependent and specialist supervised.
Active Recall - Paediatric Chemical Pathology
[1] Lecture slides: GC 157. Paediatric Chemical Pathology.pdf [2] Lecture slides: GC 154. Biochemical Screening for Early Detection of Diseases.pdf [3] Lecture slides: Chemical Pathology Seminar_Inherited metabolic disease 2025.pdf [4] Lecture slides: Chemical Pathology Data interpretation.pdf [5] Lecture slides: GC 078. Polyuria and polydipsia glucose metabolism, diabetes mellitus, diabetic ketoacidosis [Update 2025].pdf [6] Lecture slides: MBBS IV Electrolytes_2024.pdf [11] NASPGHAN/ESPGHAN. Guideline for the Evaluation of Cholestatic Jaundice in Infants. J Pediatr Gastroenterol Nutr. 2017;64:154–168. [12] Pediatric Endocrine Society. Recommendations for Evaluation and Management of Persistent Hypoglycemia in Neonates, Infants, and Children. J Pediatr. 2015. [13] De Leon DD, et al. International Guidelines for the Diagnosis and Management of Hyperinsulinism. Horm Res Paediatr. 2024. [14] Morizono H, et al. Ornithine Transcarbamylase Deficiency. GeneReviews. Revised 2022. [15] Ferreira CR, et al. An International Classification of Inherited Metabolic Disorders (ICIMD). J Inherit Metab Dis. 2021. [16] HKSAR Government. LCQ7: Pilot Study on Newborn Screening for Inborn Errors of Metabolism. 3 June 2026. [17] Chinsky JM, et al. Tyrosinemia Type I. GeneReviews. Updated 2025. [18] Salviati L, et al. Primary Coenzyme Q10 Deficiency Overview. GeneReviews. Updated 2023. [19] Leslie ND, et al. Very Long-Chain Acyl-Coenzyme A Dehydrogenase Deficiency. GeneReviews. Updated 2025.
GC156 Many Of My Family Members Have Cancers Cancer Genetics And Cytogenetics (notes)
Cancer genetics and cytogenetics is the study of hereditary gene mutations, chromosomal abnormalities, and familial cancer syndromes that predispose individuals and their relatives to an increased risk of developing various malignancies.
GC158 Point-of-care Testing (POCT)
Point-of-care testing is diagnostic testing performed at or near the site of patient care, outside the central laboratory, to provide rapid results that facilitate immediate clinical decision-making.