Head-to-head comparison of BeadChip and WGS/WES genotyping techniques for their precision is far from straightforward. A tool for validation of high-throughput genotyping calls such as Sanger sequencing is neither scalable nor practical for large-scale DNA processing. Here we report a cross-validation analysis of genotyping calls obtained via Illumina GSA BeadChip and WGS (Illumina HiSeq X Ten) techniques. When compared to each other, the average precision and accuracy of BeadChip and WGS genotyping techniques exceeded 0.991 and 0.997, respectively. The average fraction of discordant variants for both platforms was found to be 0.639%. A sliding window approach was utilized to explore genomic regions not exceeding 500 bp encompassing a maximal amount of discordant variants for further validation by Sanger sequencing. Notably, 12 variants out of 26 located within eight identified regions were consistently discordant in related calls made by WGS and BeadChip. When Sanger sequenced, a total of 16 of these genotypes were successfully resolved, indicating that a precision of WGS and BeadChip genotyping for this genotype subset was at 0.81 and 0.5, respectively, with accuracy values of 0.87 and 0.61. We conclude that WGS genotype calling exhibits higher overall precision within the selected variety of discordantly genotyped variants, though the amount of validated variants remained insufficient.

中文翻译：

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使用Sanger测序进行部分验证的BeadChip和WGS基因分型输出的比较。

BeadChip和WGS / WES基因分型技术在精度上的直接对比远非直截了当。用于验证高通量基因分型调用的工具（如Sanger测序）既不可扩展，也不适合大规模DNA处理。在这里，我们报告了通过Illumina GSA BeadChip和WGS（Illumina HiSeq X十）技术获得的基因分型调用的交叉验证分析。相互比较时，BeadChip和WGS基因分型技术的平均精度和准确度分别超过了0.991和0.997。发现两个平台的不一致变体的平均比例为0.639％。利用滑动窗口方法探索不超过500 bp的基因组区域，其中包含最大数量的不一致变体，以通过Sanger测序进一步验证。值得注意的是 位于八个已确定区域内的26个中的12个变体在WGS和BeadChip进行的相关调用中始终不一致。当对Sanger进行测序时，成功解析了16种基因型，这表明该基因型子集的WGS和BeadChip基因分型的精度分别为0.81和0.5，准确度值为0.87和0.61。我们得出的结论是，尽管经过验证的变体数量仍然不足，但WGS基因型调用在选定的各种不一致的基因型变体中显示出更高的整体精度。表明该基因型子集的WGS和BeadChip基因分型的精度分别为0.81和0.5，准确度值为0.87和0.61。我们得出的结论是，尽管经过验证的变体数量仍然不足，但WGS基因型调用在选定的各种不一致的基因型变体中显示出更高的整体精度。表明该基因型子集的WGS和BeadChip基因分型的精度分别为0.81和0.5，准确度值为0.87和0.61。我们得出的结论是，尽管经过验证的变体数量仍然不足，但WGS基因型调用在选定的各种不一致的基因型变体中显示出更高的整体精度。