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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing.

ABSTRACT: BACKGROUND: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. RESULTS: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. CONCLUSIONS: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.

SUBMITTER: Danilov KA

PROVIDER: S-EPMC7488117 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing.

Danilov Kirill A KA Nikogosov Dimitri A DA Musienko Sergey V SV Baranova Ancha V AV

BMC genomics 20200910 Suppl 7

<h4>Background</h4>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.<h4>Results</h4>When compared to each other, the average precision and a ...[more]

PMID: 32912136

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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing.

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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing.

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