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Upper limb function is commonly impaired after stroke, and recovery of UL function is important for regaining independence in daily living activities1. Stroke rehabilitation trials are often aimed at improving UL recovery and outcomes after stroke. The majority of stroke rehabilitation research is conducted with patients at the chronic stage (>6 months poststroke), yet most rehabilitation occurs early after stroke2,3. More research needs to be conducted with patients soon after a stroke to build an evidence base for rehabilitation practice.
One of the greatest challenges when conducting research soon after the stroke is detecting the effects of the intervention against the background of recovery occurring during the initial weeks and months after the stroke. High intersubject variability in clinical presentation and recovery creates noise that can obscure the beneficial effects of interventions. Intervention and control groups are typically balanced on clinical measures of initial neurological impairment. However, these measures are often poor predictors of the patient's potential for subsequent recovery, particularly those with severe initial impairment4,5. This means that groups can be matched for baseline clinical measures and not matched for their recovery potential, which makes it more difficult to ascertain the intervention's effects. Biomarkers can address this challenge by identifying an individual patient's potential for motor recovery, so that groups can be accurately matched and stratified6,7,8. Biomarkers can also be used to select patients who are most likely to respond to the intervention's known or hypothesized mechanisms of action6.
The functional integrity of the corticospinal tract (CST) is a key biomarker that predicts recovery of UL function after stroke5,8,9,10,11,12. The CST conveys descending motor output from the primary motor cortex to the spinal cord and is essential for coordination and fine motor control. Patients with a functional CST after stroke are more likely to regain strength, coordination, and dexterity than patients without. A clinical assessment can be sufficient to confirm that the CST is functional in mildly impaired patients13,14,15. However, patients with more severe initial impairment may or may not have a functional CST, and a neurophysiological assessment using transcranial magnetic stimulation (TMS) is needed9,10,11,16,17.
TMS is a noninvasive and painless technique that can be used to test CST function18. The TMS coil delivers a magnetic stimulus over the primary motor cortex that generates a descending volley in the CST, eliciting a motor-evoked potential (MEP) in the muscles of the contralateral limb19. The presence of a MEP in the paretic arm or hand (MEP+) indicates a functional CST and is associated with greater potential for recovery of UL function. Patients who are MEP- are most likely to have worse UL recovery, with no return of coordinated and dexterous hand function4,6,9,12,16.
Testing all patients with TMS is impractical and unnecessary, as those with mild initial impairment most likely have a functional CST17. Therefore, a hierarchical approach is needed so that TMS is only used for patients with more severe initial impairment. The PREP2 algorithm was developed using a combination of clinical measures and TMS to evaluate CST function and predict likely UL outcome at 3 months poststroke (Figure 1)17. PREP2 starts at day 3 poststroke by testing the strength of shoulder abduction and finger extension in the paretic arm (SAFE score), using Medical Research Council grades. If the sum of these grades is 5 or more out of 10, it is "safe" to assume the patient is MEP+. These patients are expected to have a good or excellent UL outcome by 3 months poststroke, depending on their age17. These patients do not need TMS to determine MEP status, minimizing cost and unnecessary testing for the patient.
Patients with a SAFE score of less than 5 on day 3 poststroke require TMS to determine the functional integrity of their CST. If a MEP can be elicited from the paretic extensor carpi radialis (ECR) or first dorsal interosseus (FDI) muscles, the patient is MEP+ and is expected to recover fine motor control of the hand by 3 months poststroke. Approximately half of patients with a SAFE score less than 5 on day 3 poststroke are MEP+. Importantly, patients can have a SAFE score as low as zero and be MEP+. This illustrates the need for TMS in this subgroup of patients, as clinical assessment alone cannot distinguish between patients with and without a functional CST. Patients who are MEP- have significant CST damage. These patients are expected to have a limited or poor UL functional outcome depending on their overall stroke severity, measured with the National Institute of Health Stroke Scale (NIHSS) (Figure 1)17. These MEP- patients are not expected to regain coordinated and dexterous finger control and can be grouped together for research purposes.

Figure 1: The PREP2 algorithm. SAFE = Shoulder Abduction, Finger Extension score, which is the sum of the Medical Research Council grades for each of these movements out of 5, for a total SAFE score out of 10. MEP+ = Motor Evoked Potentials can be elicited from the paretic extensor carpi radialis (ECR) and/or first dorsal interosseous (FDI) muscles of the paretic UL using transcranial magnetic stimulation. NIHSS = National Institutes of Health Stroke Scale. The algorithm predicts one of four possible UL functional outcomes at 3 months poststroke. Each prediction category is associated with a rehabilitation focus that can be used to tailor UL therapy2. The colored dots represent, proportionally, PREP2 algorithm accuracy. The dots are color-coded based on the outcome category actually achieved 3 months poststroke (Green = Excellent; Blue = Good; Orange = Limited; Red = Poor). Figure reproduced from Stinear et al.17. Please click here to view a larger version of this figure.
In clinical practice, PREP2 predicts one of four outcome categories that can be used to tailor rehabilitation for individual patients and help patients and families to understand what they can expect for their UL recovery. To date, PREP2 is the only externally validated UL prediction tool that combines clinical assessment and biomarker information in a decision tree17. It is also the only UL prediction tool with research on the effects of implementation in clinical practice20,21. PREP2 predictions are accurate for about 75% of patients, too optimistic for 17% and too pessimistic for 8% of patients at 3 months poststroke17. Accuracy is highest for MEP- patients (accurate for 90% of MEP- patients), highlighting the value of using TMS to identify these patients with severe damage to the descending motor pathways17. PREP2 remains correct for around 80% of patients at 2 years poststroke22. This supports the use of PREP2 to predict UL functional motor outcomes at 3 months and longer term. Information about delivering PREP2 predictions and using them in clinical practice is outside the scope of this methods paper, but detailed resources are available online23.
PREP2 provides researchers with a tool to select and stratify patients for clinical trials. This allows patients to be grouped not only according to baseline clinical characteristics, but also their neurobiological potential for UL recovery. Despite the mounting evidence for the use of TMS as a prognostic biomarker for UL recovery, lack of familiarity with TMS protocols in hospital settings with subacute stroke patients may be a barrier to its use in research. Therefore, this protocol aims to demonstrate how to use the SAFE score and TMS to evaluate CST function in patients in a hospital setting early after stroke.