Optimizing the Use of Solid-Phase Reversible Immobilization Beads for High-Throughput Full-Length 16S rDNA Sequencing Library Construction

Solid-phase reversible immobilization (SPRI) beads are widely used for high-throughput sequencing library construction to purify and recover nucleic acids. This research was aimed at investigating the effects of SPRI bead ratio, incubation time, and elution time on nucleic acid recovery during full-length 16S rDNA high-throughput sequencing library construction. The effects of different SPRI bead ratios, incubation times, and elution times were compared for three different initial sample amounts. An L9(3 3 ) orthogonal experiment was designed to determine the optimal combination of these factors. The incubation time of three factors including SPRI beads ratio, incubation time, and elution time had a statistically significant effect on the recovery rate for the initial sample amount of 1500 ng and 3000 ng. The orthogonal experiment results indicated that incubation time had the greatest impact among the three factors. Incubation time significantly influences recovery rate in full-length 16S rDNA high-throughput sequencing library construction. The use of 0.8× SPRI beads, 15 minutes of incubation, and 10 minutes of elution resulted in the highest recovery rate. SPRI beads offer a viable method for recovering full-length 16S rDNA amplicons

Reproducibility of Middle Cerebral Artery Stenosis Measurements by DSA: Comparison of the NASCET and WASID Methods.

To evaluate the intra- and inter-observer variability of the North American Symptomatic Carotid Endarterectomy Trial (NASCET) and Warfarin-Aspirin Symptomatic Intracranial Disease (WASID) criteria for the evaluation of middle cerebral artery (MCA) stenosis using digital subtraction angiography (DSA).DSA images of 114 cases with 131 stenotic MCAs were retrospectively analyzed. Two radiologists and a researcher measured the degree of MCA stenosis independently using both NASCET and WASID methods. To determine intra-observer agreement, all the observers reevaluated the degree of MCA stenosis 4 weeks later. The linear relation and coefficient of variation (CV) between the measurements made by the two methods were assessed by correlation coefficient and multi-factor analysis of variance (ANOVA), respectively. Intra- and inter-observer variability of the two methods was evaluated by intraclass correlation coefficient (ICC), Spearman's R value, Pearson correlation coefficient and Bland-Altman plots.Despite the fact that the degree of MCA stenosis measured by NASCET was lower than measured using the WASID method, there was good linear correlation between the measurements made by the two methods (for the mean measurements of the 3 observers, NASCET% = 0.891 × WASID% - 1.89%; ICC, Spearman's R value and Pearson correlation were 0.874, 0.855, and 0.874, respectively). The CVs of both intra- and inter-observer measurements of MCA stenosis using WASID were significantly lower than that using NASCET confirmed by the multi-factor ANOVA results, which showed only the measurement methods of MCA stenosis had significant effects on the CVs both in intra- and inter-observer measurements (both P values < 0.001). Intra-observer measurements showed good or excellent agreement with respect to WASID and NASCET evaluation (ICC, 0.656 to 0.817 and 0.635 to 0.761, respectively). Good agreement for the WASID evaluation (ICC, 0.592 to 0.628) and for the NASCET evaluation (ICC, 0.529 to 0.568) was observed for inter-observer measurements. Bland-Altman plots demonstrated that the WASID method had better reproducibility and intra-observer agreement than NASCET method for evaluating MCA stenosis.Both NASCET and WASID methods have an acceptable level of agreement; however, the WASID method had better reproducibility for the evaluation of MCA stenosis, and thus the WASID method may serve as a standard for measuring the degree of MCA stenosis

Bland-Altman plots of inter-observer reproducibility of the NASCET and WASID methods.

<p>(A, C and E) WASID method for Observers 1&2, 1&3 and 2&3, respectively. (B, D and F) NASCET method for Observers 1&2, 1&3 and 2&3, respectively.</p

Scatterplots of NASCET and WASID measurements.

<p>(A) The measurements of Observer 1. (B) The measurements of Observer 2. (C) The measurements of Observer 3. (D) The mean measurements of all 3 observers.</p

Bland-Altman plots of intra-observer reproducibility of the NASCET and WASID methods.

<p>(A, C and E) WASID method for Observer 1, 2 and 3, respectively. (B, D and F) NASCET method for Observer 1, 2 and 3, respectively.</p