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 |