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Unfractionated heparin (UFH) is an anticoagulant that main works "by inactivating thrombin and activated factor X (factor Xa) through an antithrombin (AT)-dependent mechanism".

Prothrombin time (PT) is an coagulation assay that measures the "extrinsic and final common pathways of the coagulation cascade (factors VII, II (prothrombin), V, X, and fibrinogen)".

Why is PT not routinely used to measure the anticoagulation effects of heparin?

Coagulation Pathway

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Most PT assays contain polybrene, which neutralizes heparin. According to "Coagulation assays and anticoagulant monitoring":

Polybrene is a positively charged material that will neutralize UFH, and this is a component of many clot-based reagents. Polybrene is added to the majority of PT reagents (clinicians may want to confirm that the PT reagent used in their laboratory contains polybrene) and is also present in many assays used in the detection of a LA (lupus anticoagulant), such as the dilute Russell's viper venom time (dRVVT) and Staclot LA (Diagnostica Stago) kits.

Theoretically, a high enough dose of Heparin to overcome polybrene neutralizing activity can prolong PT, but this is not consistent enough to warrant monitoring with PT.

Heparin activity can instead be monitored with activated partial thromboplastin time (aPTT) or anti-factor Xa activity

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