Identification of genetic variants using bar-coded multiplexed sequencing.

We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8-90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.

Candidate Agtr2 influenced genes and pathways identified by expression profiling in the developing brain of Agtr2(-/y) mice.

Intellectual disability (ID) is a common developmental disability observed in 1 to 3% of the human population. A possible role for the Angiotensin II type 2 receptor (AGTR2) in brain function, affecting learning, memory, and behavior, has been suggested in humans and rodents. Mice lacking the Agtr2 gene (Agtr2(-/y)) showed significant impairment in their spatial memory and exhibited abnormal dendritic spine morphology. To identify Agtr2 influenced genes and pathways, we performed whole genome microarray analysis on RNA isolated from brains of Agtr2(-/y) and control male mice at embryonic day 15 (E15) and postnatal day one (P1). The gene expression profiles of the Agtr2(-/y) brain samples were significantly different when compared to profiles of the age-matched control brains. We identified 62 differently expressed genes (p< or =0.005) at E15 and in P1 brains of the Agtr2(-/y) mice. We verified the differential expression of several of these genes in brain samples using quantitative RT-PCR. Differentially expressed genes encode molecules involved in multiple cellular processes including microtubule functions associated with dendritic spine morphology. This study provides insight into Agtr2 influenced candidate genes and suggests that expression dysregulation of these genes may modulate Agtr2 actions in the brain that influences learning and memory.

Identification of a common variant affecting human episodic memory performance using a pooled genome-wide association approach: a case study of disease gene identification.

Genome-wide association studies (GWAS) are an important tool for discovering novel genes associated with disease or traits. Careful design of case-control groups greatly facilitates the efficacy of these studies. Here we describe a pooled GWAS study undertaken to find novel genes associated with human episodic memory performance. A genomic locus for the WW and C2 domain-containing 1 protein, KIBRA (also known as WWC1), was found to be associated with memory performance in three cognitively normal cohorts from Switzerland and the USA. This result was further supported by correlation of KIBRA genotype and differences in hippocampal activation as measured by functional magnetic resonance imaging (fMRI). These findings provide an excellent example of the application of GWAS using a pooled genomic DNA approach to successfully identify a locus with strong effects on human memory.

Hippocampal gene expression changes during age-related cognitive decline.

As humans age, cognitive performance decreases differentially across individuals. This age-related decline in otherwise healthy individuals is likely due to the interaction of multiple factors including genetics and environment. We hypothesized that altered spatial memory performance in genetically similar mice could be in part due to differential gene expression patterns in the hippocampus. To investigate this we utilized Morris water maze (MWM) testing in a group of young (3 months) and aged (24 months) C57BL/J male mice. Two sub-groups were identified in the aged animals; one in which MWM performance was not significantly different when compared to the young animals (aged-unimpaired; "AU") and one in which performance was significantly different by 1.5 standard deviations from the mean (aged-impaired; "AI"). One week after testing was completed the entire hippocampus was collected from six each of AU, AI and young mice and their gene expression profiles were compared using Affymetrix microarrays. Benjamini and Hochberg FDR correction at p<0.05 identified 18 genes differentially expressed between the AI and AU mice. The correlation between behavioral deficits and gene expression patterning allows a better understanding of how altered gene expression in the hippocampus contributes to accelerated age-related cognitive decline and delineates between gene expression changes associated with normal aging vs. memory performance.