Phase | Primary objectives | Sample set | # Samples | Sample type | DNA input (ng) | 1052-Amplicon sequencing platform | Confirmation sequencing platform and panel |
---|---|---|---|---|---|---|---|
Workflow Optimization And Platform Evaluation | Evaluate analytical performance of the panel | Reference DNA mixtures with known genotypes (based on 1000 Genomes Project) | 6 (Samples), 6 (Mixtures) | Intact | 250-2000 | GAIIx | PGM AmpliSeq |
Determine the impact of DNA input quantity | |||||||
Catalog systematic variants based on Hardy-Weinberg equilibrium. | Intact disease free lymphocyte samples | 29 | Intact | 500 | GAIIx | N/A | |
Evaluate intact- and FFPE-DNA samples | NA12878 and 2 CRC blocks | 1 (Intact), 2 (FFPE) | Intact, FFPE | 250-1000 | GAIIx | N/A | |
Demonstrate the impact of input DNA mass on variance | |||||||
Investigate GC > AT background | CRC blocks | 8 | FFPE | 250 | GAIIx | GAIIx 35-amplicon | |
Platform Evaluation Using Clinical Specimens | Assess performance on clinically relevant FFPE samples | Clinical CRC samples | 46 | FFPE | 250 | GAIIx | PGM 1-amplicon |
Assess performance on clinically relevant FFPE samples stratified by QFI | Clinical thyroid-cancer samples | 72 | FFPE | 500, 1000 | HiSeq | Luminex liquid bead array |