Efficiency clustering for low-density microarrays and its application to QPCR

Background

Pathway-targeted or low-density arrays are used more and more frequently in biomedical research, particularly those arrays that are based on quantitative real-time PCR. Typical QPCR arrays contain 96-1024 primer pairs or probes, and they bring with it the promise of being able to reliably measure differences in target levels without the need to establish absolute standard curves for each and every target. To achieve reliable quantification all primer pairs or array probes must perform with the same efficiency.

Results

Our results indicate that QPCR primer-pairs differ significantly both in reliability and efficiency. They can only be used in an array format if the raw data (so called CT values for real-time QPCR) are transformed to take these differences into account. We developed a novel method to obtain efficiency-adjusted CT values. We introduce transformed confidence intervals as a novel measure to identify unreliable primers. We introduce a robust clustering algorithm to combine efficiencies of groups of probes, and our results indicate that using n < 10 cluster-based mean efficiencies is comparable to using individually determined efficiency adjustments for each primer pair (N = 96-1024).

Conclusions

Careful estimation of primer efficiency is necessary to avoid significant measurement inaccuracies. Transformed confidence intervals are a novel method to assess and interprete the reliability of an efficiency estimate in a high throughput format. Efficiency clustering as developed here serves as a compromise between the imprecision in assuming uniform efficiency, and the computational complexity and danger of over-fitting when using individually determined efficiencies.

Exploratory analysis of exercise adherence patterns with sedentary pregnant women

BACKGROUND

It is not well understood how sedentary women who wish to engage in regular exercise adhere to interventions during pregnancy and what factors may influence adherence over time.

OBJECTIVE

The aim of this study was to examine longitudinal patterns of pregnant women's adherence to exercise.

METHODS

Exploratory secondary data analyses were carried out with 124 previously sedentary pregnant women (ages 31 +/- 5 years; 85% non-Hispanic White) from a randomized controlled trial. Daily exercise logs (n = 92) from 18 through 35 weeks of gestation were explored using linear regression, functional data, and principal component analyses.

RESULTS

Adherence decreased as gestation week increased (p < .001). The top adherers maintained levels of adherence, and the bottom adherers decreased levels of adherence. And adherence pattern was influenced by types of exercise throughout the study period.

DISCUSSION

Exercise behavior patterns were explored in a randomized controlled trial study, using chronometric data on exercise attendance. A new analytic approach revealed that sedentary pregnant women may adopt exercise habits differently from other populations.