. 2015 Feb 10;10:16. doi: 10.1186/s13023-014-0195-4

Table 3.

Biomarker example types organized by biological level and compared for pathophysiologic level

Biomarker Type	Pathophysiologic Process or Stage	General Examples	Specific Examples	Pros	Cons
Genetic marker	1° Cause	Presence of a gene mutation	CF mutations	Measure presence of gene	Not a function
RNA/gene expression	1° pathophysiologic	Expression of aberrant RNA	Friedrich’s ataxia	Direct impact on gene expression	Unclear about downstream effect
		RNA splicing error	Fragile X
		Presence of new gene expression	Fragile X
Enzyme or protein level	1° pathophysiologic	Enzyme activity in tissue	Alpha-1-antitrypsin	Direct measure of active compound	Difficult to verify tissue effect
Enzyme or protein level	1° pathophysiologic	Protein in circulation	Alpha-1-antitrypsin	Direct measure of active compound	Difficult to verify tissue effect
Biochemical	1° pathophysiologic	Blood level of an accumulating metabolite due to a 1° block	Phenylalanine in PKU	Directly toxic compound or active compound	Not a measure of tissue effect
Biochemical	1° pathophysiologic	Decrease in level of critical needed biochemical	BH4 in BH4 deficiency	Directly toxic compound or active compound	Not a measure of tissue effect
Secondary Biochemical	2° pathophysiologic	Increase in secondary metabolite that is toxic or part of pathophysiology but not from original defect	Succinyl-lactone in tyrosinemia I	Directly measure of toxic effector	Cannot always measure downstream toxicity
Secondary Biochemical	2° pathophysiologic		Homogentisic acid in alkaptonuria	Directly measure of toxic effector	Cannot always measure downstream toxicity
Biopsy	2° pathophysiologic	Presence of abnormal cells or marker	GL3 granules in Fabry	Direct measure of disease or absence of protein	Variability of biopsies, representative sampling, variable assay methods
Biopsy	2° pathophysiologic	Pathological change in structure	Dystrophin in Duchenne	Direct measure of disease or absence of protein
Ex vivo explant	2° pathophysiologic	Evaluate a cell removed from the patient for a phenotype or function	CGD/y-interferon	None	Failed : questionable validity of an ex vivo assessment
X-ray/Imaging	2° pathophysiologic	Bone structure	X-ray ricket score	Bone structure is nature of disease	X-ray does not show function exactly
		Presence of abnormal lesions
		Change in size
		Visual appearance like fundoscopy
Clinical Physiology tests	1° clinical effect	Tests used in clinical evaluations of clinical conditions dependent primarily on a single tissue/organ	FVC in CF	Measure of a physical function that is directly relevant	Not strictly a clinical outcome and hard to gauge size of effect with clinical outcome
Clinical Physiology tests	1° clinical effect	EMG, EKG, NCV, BAER, hand held dynamometry	Muscle strength in DMD or HIBM	Measure of a physical function that is directly relevant
Clinical function	2° clinical effect or intermediate clinical measure	Tests that study integrated multiple body systems/organs, Pulmonary function tests, sleep apnea, muscle function	6 min walk test	Measure of a patient’s function	Need to interpret magnitude of change for relevance to patient
Clinical function	2° clinical effect or intermediate clinical measure		Walking speed	Measure of a patient’s function

The table provides examples of different types of specimens that might be obtained from a patient or featured measured in a patient and relates these examples to their pathophysiologic stage. The goal is to highlight the type of measures and relate these measures to the cause of disease and those steps that are further downstream. Examples for the endpoint measure in patients with specific diseases are provided to highlight the pros and cons of different types of biomarkers.