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<b>Background:</b> The least significant change (LSC) method should be introduced and considered a proper method to define the smallest clinically important difference between two consecutive measurements. <b>Methods:</b> The LSC was calculated based on 150 patients, with a total 25-hydroxyvitamin D [25(OH)D] IDS-iSYS assay performed in triplicate. The LSC was determined by multiplying the calculated root mean square precision error by a factor of 2.77. The study group was additionally divided into subgroups according to gender, age, serum 25(OH)D concentration, and date of assays. <b>Results:</b> The LSC was 4.0 ng/mL (13.2%) for the entire group (n = 150; 450 assays) and was not dependent on gender, age of patients, or the date of assays (<i>p</i> > 0.05). The LSC value depended only on the 25(OH)D concentration value. In the subgroup with vitamin D deficiency (<20 ng/mL), the obtained LSC value was 2.2 ng/mL (14.7%), which was lower compared to all other groups (<i>p</i> < 0.05 for insufficiency, and <i>p</i> < 0.0001 for the optimal concentration value). In the subgroup with 25(OH)D concentrations >50 ng/mL (n = 4; 12 assays), the calculated LSC was 11.8 ng/mL (16.9%) and differed statistically only from the subgroup with vitamin D deficiency (<i>p</i> < 0.005). <b>Conclusions:</b> An absolute LSC of 4.0 ng/mL was calculated for the IDS-iSYS assay used in our study and should be considered when two (or more) assay results of 25(OH)D performed for a single patient are compared.