Table 1 Differences in omics study design for biomarker identification versus therapeutic target discovery

Ultimate goals

Differential diagnostic tool; early detection of disease; prediction of future disease; foresee disease progression; estimation of disease prognosis; follow-up of therapeutic response

Gaining insight into mechanisms of disease; identification of novel therapeutic targets

Optimal matrix

Samples closely related to the diseased organ but easily accessible (e.g. peripheral blood for multisystem diseases or alterations in immune cells; urine for renal disease; bronchoalveolar fluid for pulmonary processes; cerebrospinal fluid for cerebral illnesses)

Samples obtained from the site where the disease is taking place (e.g. kidney biopsies for renal disease; lung biopsies for pulmonary disease; heart biopsies for cardiac illness; liver biopsies for hepatic processes; peripheral blood for hematological or immunological processes; lymphoid tissue for immunological processes)

Optimal platform

Any molecule (DNA, RNA, proteins, peptides, small molecules); reproducible; cost-effective; fast; stable at room temperature or easy sample preparation

Any molecule (DNA, RNA, proteins, peptides, small molecules); integrative approaches advisable; cost-effectiveness not important; speed not important; sample preparation not important

Preferred study design

Test set–validation set approach (validation set should be independent of test set); the broader the inclusion criteria, the broader the applicability of the biomarker

Clear answers will only be obtained when clear questions are addressed with a clear study design; avoid noise from phenotypic variation; strict confounder analysis necessary when extensive phenotypic variation exists between samples