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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing
Kirill A Danilov1,2, Dimitri A Nikogosov3, Sergey V Musienko3
1Atlas Biomed Group Limited, Tintagel House, 92 Albert Embankment, Lambeth, London, SE1 7TY, UK. danilov@atlasbiomed.com.
BMC Genomics
|September 11, 2020
Summary
Whole Genome Sequencing (WGS) and BeadChip genotyping show high precision (>0.99) in large-scale DNA analysis. WGS demonstrated superior precision for discordant variants, though further validation is needed.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Comparing genotyping techniques like BeadChip and Whole Genome Sequencing (WGS) for precision is complex.
- Sanger sequencing is impractical for validating large-scale genotyping data.
Purpose of the Study:
- To perform a cross-validation analysis of genotyping calls between Illumina GSA BeadChip and WGS techniques.
- To assess the precision and accuracy of these high-throughput genotyping methods.
Main Methods:
- Cross-validation analysis comparing BeadChip and WGS genotyping data.
- Utilized a sliding window approach to identify regions with discordant variants.
- Sanger sequencing for targeted validation of specific discordant genotypes.
Main Results:
- Average precision and accuracy for both BeadChip and WGS exceeded 0.991 and 0.997, respectively.
- An average of 0.639% of variants were discordant between the two platforms.
- Sanger sequencing validation of discordant variants indicated higher precision for WGS (0.81) compared to BeadChip (0.5).
Conclusions:
- Whole Genome Sequencing (WGS) genotype calling demonstrates higher overall precision among discordantly genotyped variants.
- The number of validated discordant variants was insufficient to draw definitive conclusions on all discrepancies.
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