title: Assessing the Power of Exome Chips.
abstract: Genotyping chips for rare and low-frequent variants have recently gained popularity with the introduction of exome chips, but the utility of these chips remains unclear. These chips were designed using exome sequencing data from mainly American-European individuals, enriched for a narrow set of common diseases. In addition, it is well-known that the statistical power of detecting associations with rare and low-frequent variants is much lower compared to studies exclusively involving common variants. We developed a simulation program adaptable to any exome chip design to empirically evaluate the power of the exome chips. We implemented the main properties of the Illumina HumanExome BeadChip array. The simulated data sets were used to assess the power of exome chip based studies for varying effect sizes and causal variant scenarios. We applied two widely-used statistical approaches for rare and low-frequency variants, which collapse the variants into genetic regions or genes. Under optimal conditions, we found that a sample size between 20,000 to 30,000 individuals were needed in order to detect modest effect sizes (0.5% < PAR > 1%) with 80% power. For small effect sizes (PAR <0.5%), 60,000-100,000 individuals were needed in the presence of non-causal variants. In conclusion, we found that at least tens of thousands of individuals are necessary to detect modest effects under optimal conditions. In addition, when using rare variant chips on cohorts or diseases they were not originally designed for, the identification of associated variants or genes will be even more challenging.
authors.affiliation: Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway; Department of Neurology, Oslo University Hospital, 0424, Oslo, Norway.
authors.forename: Christian Magnus
authors.initials: CM
authors.lastname: Page
authors.affiliation: Department of Neurology, University of California San Francisco, San Francisco, California, 94158, United States of America.
authors.forename: Sergio E
authors.initials: SE
authors.lastname: Baranzini
authors.affiliation: University Center for Information Technology, University of Oslo, 0316, Oslo, Norway.
authors.forename: Bjørn-Helge
authors.initials: BH
authors.lastname: Mevik
authors.affiliation: Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway; Department of Neurology, Oslo University Hospital, 0424, Oslo, Norway.
authors.forename: Steffan Daniel
authors.initials: SD
authors.lastname: Bos
authors.affiliation: Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway; Department of Neurology, Oslo University Hospital, 0424, Oslo, Norway.
authors.forename: Hanne F
authors.initials: HF
authors.lastname: Harbo
authors.affiliation: Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway; Department of Research, Cancer Registry of Norway, 0304, Oslo, Norway.
authors.forename: Bettina Kulle
authors.initials: BK
authors.lastname: Andreassen
mesh_terms: D000483:Alleles; D003198:Computer Simulation; D004867:Equipment Design; D059472:Exome / Q000235:genetics*; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques / Q000295:instrumentation*; D006801:Humans; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide