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Table 3 Summary of validation experiments performed

From: Analytical validation of whole exome and whole genome sequencing for clinical applications

Experiment Action
Concordance with SNP Array Measure concordance with high-density SNP arrays
Concordance with integrated NGS-derived variants Measure concordance with Genome In A Bottle (GIAB) NA12878 callset
Calling variants from targeted NGS panel Measure concordance with calls from a targeted NGS panel (all calls previously validated either by in-house Sanger assays or the presence of the variant in the sample in Hapmap, 1000G, etc.)
Intra-run reproducibility Measure concordance for the same sample sequenced in the same run with:
A) Different sample preparations across the same flow cell, or
B) The same sample preparation across different flow cells
Inter-run reproducibility Measure concordance for the same sample on the same machine with:
A) The same sample preparation different runs, or
B) Different sample preparation across different runs
Inter-machine reproducibility Measure concordance for the same sample with the same sample preparation on different machines of the same model in the same run cycle
Inter-mode reproducibility Measure concordance between high-throughput and rapid run Illumina modes