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Number of CNVs detected by each tested array using standard thresholds.
Number of CNVs detected by each tested array using optimized thresholds.
Considering the absolute gene expression status, we further found that probes identified by the paired t-test in controls had a larger proportion of noninformative probes (60.5%) that had absent calls assigned by the Detection Calls algorithm in every tested array compared with those in welders (47.3%).
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The tested arrays also included combinations with unequal-diameter cylinders.
In this study, we have tested array-based sequence capture to determine the sequence of 112 genes potentially involved in MR. We show that array-based sequence capture technology is an efficient, quick and reliable method for the parallel sequencing of a range of genes of interest.
We identified a total of four pathogenic CNVs in three patients, and all tested arrays detected them.
There was a total of 332 de novo CNVs detected on any of the four tested arrays for all 21 patients (Additional file 2: Table S2).
Only five CNVs were called on all four tested arrays: the four pathogenic CNVs, and one VOUS (patient 3.2, Additional file 5: Figure S1).
The four tested arrays detected a total of 112 LCSHs larger than 5 Mb, representing 28 unique homozygous regions in five patients (Additional file 9: Table S5).
Of the 332 de novo CNVs detected on the four tested arrays, 47 were confirmed (detected on at least two arrays), and they represented 20 unique alterations (Additional file 4: Table S4).
GraphPad Prism was used to test array tomography data for normality (Kolmogorov-Smirnov test), following which parametric (t-test or ANOVA) or non-parametric (Kruskal-Wallis or Mann–Whitney) tests were performed as required.
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