title: A comparison of whole genome sequencing with exome sequencing for family-based association studies.
abstract: As the cost of DNA sequencing decreases, association studies based on whole genome sequencing are now becoming feasible. It is still unclear, however, how much more we could gain from whole genome sequencing compared to exome sequencing, which has been widely used to study a variety of diseases. In this project, we performed a comparison between whole genome sequencing and exome sequencing for family-based association analysis using data from Genetic Analysis Workshop 18. Whole genome sequencing was able to identify several significant hits within intergenic regions. However, the increased cost of multiple testing counteracted the benefits and resulted in a higher false discovery rate. Our results suggest that exome sequencing is a cost-effective way to identify disease-related variants. With the decreasing sequencing cost and accumulating knowledge of the human genome, whole genome sequencing has the potential to identify important variants in regulatory regions typically inaccessible for exome sequencing.
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue 3rd Floor, Boston, MA 02118, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Lacey
authors.affiliation: Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
authors.forename: Jae Yoon
authors.initials: JY
authors.lastname: Chung
authors.affiliation: Department of Medicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA.
authors.forename: Honghuang
authors.initials: H
authors.lastname: Lin