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Resulting VCFs were tested for concordance against benchmark whole-genome VCFs from the Genome in a Bottle Consortium [ 21].
In this fashion, we are able to make genome-wide comparisons and test for concordance against an extensive library of more than 3200 physical and pharmacological stressors [ 13].
The remaining 499 SNV positions (45,908 total) had at least one minor allele called by either the array or SPLINTER and were used to determine sequencing SNV concordance against the array.
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In the training set, TRC test showed 100% sensitivity, specificity and concordance rates against the permanent histopathology test.
The WES and WGS replicates used in different experiments are listed in Table 4, with all replicates used for concordance testing against alternate technologies and curated variant sets.
The GRS model trained on the European GWA SNPs together with SNP2HLA imputed markers ('GRS-imputed'), improved the AUC over GRS14 by +0.007 (AUC = 0.838, CI 0.816-0.860, P <10−6 value for paired concordance test against the GRS14) (Fig. 1).
Approximately 99.5% concordance was observed against respective HapMap data across the 117 samples and 52 Mendelian inconsistencies were observed in 25 HapMap trios (Table S2).
In summary, we found high levels of concordance between antibody reactivity against the recombinant domains and reactivity against the native protein in serum from rabbits and mice, but less so in serum from rats.
κ coefficient 0.33 (95% confidence interval 0.06 to 0.59) for concordance of primary outcome against SF-36.
The ranking concordance values were plotted against the selection thresholds, with independent response curves generated for up-regulated and down-regulated probesets.
Genotype concordance was also compared against the Genome in the Bottle Consortium (www.genomeinabottle.org) benchmark whole-genome genotype calls dataset designed to minimizes bias from any one method by integrating 14 datasets from five sequencing technologies, seven read mappers and three variant callers [ 21].
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