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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
  1. We provide cost estimates for next-generation DNA sequencing or genotyping experiments using different study designs.
  2. aWith the recently developed Illumina HiSeq X Ten platform, whole-genome sequencing at high coverage is 60 to 70% cheaper. We do not recommend or endorse any specific companies or products. Cost estimates do not include bioinformatics processing.