Acute respiratory distress syndrome (ARDS) is a common, devastating clinical syndrome. In the last cycle of this project, we showed that candidate gene polymorphisms suggest a role for common genetic variation in determining host susceptibility to, and survival of ARDS in at-risk patients. Currently, the Principal Investigator o-leads an ongoing collaborative genome-wide association study of ALI/ARDS using patients and samples collected from the last cycle of this project. However, GWAS can only define disease-associated genomic loci with low to moderate effects and cannot identify causal mutations. Direct sequencing is regarded as the post-GWAS, ultimate approach to identifying causal mutations and defining disease candidate genes. The recent development of Next-Generation sequencing technologies enables population-based direct sequencing of much larger genomic regions, resulting in significant cost and time savings by bypassing most stages of fine mapping. This multidisciplinary competing renewal application will focus on rapidly advancing our knowledge of the genetic factors for ARDS development and related outcomes from our candidate gene research, as well as our recent large-scale genetic association study. We will conduct targeted sequencing of the promoter/exons/miRNA/regulatory elements within candidate genes/regions defined through analysis of whole exome sequencing data and existing genotyping data derived from the last cycle. We will then define ARDS candidate genes by investigating the aggregate information of functional genetic variations using our newly developed statistical method (SKAT), which addresses the specific issues related to the analysis of rare variations.
In Specific Aim 1, we will conduct whole exome sequencing on 100 ARDS cases and 100 matched controls to define target regions by integrating analysis of whole exome sequencing data with candidate genetic loci discovered in the previous cycle, as well as the current GWAS. With our collaborator, Dr. Mark Wurfel of University of Washington, we will also analyze available eQTL data to evaluate the functional relevance of the target regions.
In Specific Aim 2, we will design a molecular inversion probe (MIP) panel for resequencing promoter/exons/miRNA/regulatory elements within the target regions defined in Aim 1;identify all variations using MIP capture coupled with deep NextGen sequencing and define candidate genes by evaluating the associations of functional rare/common variations with ARDS susceptibility and outcomes using variation aggregation methods.
In Specific Aim 3, we will replicate the top-ranked genes by NextGen sequencing in a large collaborating external population with a similar study design. The project has the potential to have a high impact on our understanding of genetic factors for ARDS risk and survival outcomes.
Acute respiratory distress syndrome (ARDS) is a common, devastating clinical syndrome caused by several direct and indirect insults to the lung, most commonly pneumonia, sepsis, and multiple traumas. This multidisciplinary competing renewal application will focus on rapidly advancing our knowledge of the genetic factors for the development of ARDS. With the completion of this project, we expect to advance our knowledge of the risk for development of ARDS and associated outcomes (especially survival) from GWAS-defined genomic loci to causal mutations in candidate genes;results will contribute significantly to our understanding of the pathogenesis of ARDS, the identification of novel targets for therapeutic intervention, and the use of novel markers for stratification of patients at risk for ARDS and related poor outcomes such as death or prolonged mechanical ventilation.
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