Table 1 Comparison of strategies for rare variant association studies
From: Rare variant association studies: considerations, challenges and opportunities
Approach | Design | DNA target size | Technology | Cost/sample (US$) |
|---|---|---|---|---|
Whole-genome sequencing | 2,000 individuals at 30× (high depth) | 3.3 gigabases | For example, Illumina (DNA library and sequencing) | ~4,000a |
2,000 individuals at 5× (low depth) | 3.3 gigabases | ~800 | ||
Whole-exome sequencing | 2,000 individuals at 80× | 50 to 70 megabases | Agilent SureSelect (capture); Illumina (DNA library and sequencing) | ~750 |
Targeted sequencing of candidate genes | 2,000 individuals at 100× | 500 kilobases (exons from ~100 genes) | TruSeq Custom Amplicon Illumina (capture); Illumina (DNA library and sequencing) | ~325 |
2,000 individuals at 100× | 100 kilobases (exons from ~20 genes) | ~250 | ||
5,000 individuals at 100× | 100 kilobases (exons from ~20 genes) | ~125 | ||
Exome array | 10,000 individuals | ~250,000 coding variants | Illumina ExomeChip array | ~70 |