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In our present study, 13 variants in control group and 11 in case group were detected.
For the detection of somatic variants, a bimodal strategy was applied with tumor variants called under stringent criteria, whereas variants in control tissue were called using less stringent criteria: A minimum threshold for reads was set with variants of 15% of all reads at a given position in tumor.
The "noise" introduced by these splicing variants in control samples ensures that we are testing the variant containing samples against samples with many, distinct, splicing mutations.
However, the probability to observe 3 or more variants among 148 individuals by chance based on the frequency of SLC7A3 variants in control populations is very low (p = 0.05), supporting an excess of SLC7A3 variants in patients with ASD.
PCR amplification of clcn1 variants in control zebrafish at 48 hpf revealed two distinct splice variants, correlating with inclusion or exclusion of exons 3 and 4 in zebrafish clcn1, which was confirmed by sequencing (Fig. 4A and not shown).
We used a large number of positive control mutations to validate this capture method, and in the process uncovered a variety of genomic variants including small and large deletions, and single nucleotide variants in control patients.
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The higher representation of TNFRSF6B SNP variants in controls is in contrast to the original study and to a Canadian case/control study [13], [14].
Many malaria-related traits have been analyzed but the role of genetic variants in controlling liver infection has not been addressed.
The finding of variants in controls, particularly the finding of a nonsense mutation in a 69 years old healthy individual, clearly adds to the requirement of an extended evaluation of the pathogenicity of each variant.
The low frequency of truncating variants in controls supports PALB2 as a high-penetrance breast cancer predisposing gene.
Analysis of both panel types yielded a total of 89 variants in probands and 14 variants in controls (Supplementary Table S4 online).
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