The dystrophin gene and cognitive function in the general population

Computational cognitive modeling and validation of Dp140 induced alteration of working memory in Duchenne Muscular Dystrophy

Duchenne Muscular Dystrophy has emerged as a model to assess cognitive domains. The DMD gene variant location and its association with variable degrees of cognitive impairment necessitate identification of a common denominator. Computer architectures provide a framework to delineate the mechanisms involved in the cognitive functioning of the human brain. Copy number variations in the 79 exons of DMD gene were screened in 84 DMD subjects by Multiplex Ligation-dependent Probe Amplification (MLPA). DMD subjects were categorized based on the presence or absence of DP140 isoform. The cognitive and neuropsychological assessments were carried out as per inclusion criteria using standard scales. Instance-based learning theory (IBLT) based on the partial matching process was developed to mimic Stroop Color and Word Task (SCWT) performance on Adaptive Control of Thought-Rational (ACT-R) cognitive architecture based on IBLT. Genotype-phenotype correlation was conducted based on the mutation location in DMD gene. Assessment of specific cognitive domains in DP140 - ve group corresponded to the involvement of multiple brain lobes including temporal (verbal and visual learning and memory), parietal (visuo-conceptual and visuo-constructive abilities) and frontal (sustained and focused attention, verbal fluency, cognitive control). Working memory axis was found to be the central domain through tasks including RAVLT trial 1, recency effect, digit span backward, working memory index, arithmetic subtests in the Dp140 - ve group. IBLT validated the non-reliance of DMD subjects on recency indicating affected working memory domain. Modeling strategy revealed altered working memory processes in DMD cases with affected Dp140 isoform. DMD brain was observed to rely on primacy than the recency suggesting alterations in working memory capacity. Modeling revealed lowered activation of DMD brain with Dp140 - ve in order to retrieve the instances.

Genetic effects and gene-by-education interactions on episodic memory performance and decline in an aging population

Both social and genetic factors contribute to cognitive impairment and decline, yet genetic factors identified through genome-wide association studies (GWAS) explain only a small portion of trait variability. This "missing heritability" may be due to rare, potentially functional, genetic variants not assessed by GWAS, as well as gene-by-social factor interactions not explicitly modeled. Gene-by-social factor interactions may also operate differently across race/ethnic groups. We selected 39 genes that had significant, replicated associations with cognition, dementia, and related traits in published GWAS. Using gene-based analysis (SKAT/iSKAT), we tested whether common and/or rare variants were associated with episodic memory performance and decline either alone or through interaction with education in >10,000 European ancestry (EA) and >2200 African ancestry (AA) respondents from the Health and Retirement Study (HRS). Nine genes in EA and five genes in AA were associated with memory performance or decline (p < 0.05), and these effects did not attenuate after adjusting for education. Interaction between education and CLPTM1 on memory performance was significant in AA (p = 0.003; FDR-adjusted p = 0.038) and nominally significant in EA (p = 0.026). In both ethnicities, low memory performance was associated with CLPTM1 genotype (rs10416261) only for those with less than high school education, and effects persisted after adjusting for APOE ε4. For over 70% of gene-by-education interactions across the genome that were at least nominally significant in either ethnic group (p < 0.05), genetic effects were only observed for those with less than high school education. These results suggest that genetic effects on memory identified in this study are not mediated by education, but there may be important gene-by-education interactions across the genome, including in the broader APOE genomic region, which operate independently of APOE ε4. This work illustrates the importance of developing theoretical frameworks and methodological approaches for integrating social and genomic data to study cognition across ethnic groups.

Variants in TTC25 affect autistic trait in patients with autism spectrum disorder and general population

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder with a complex genetic architecture. To identify genetic variants underlying ASD, we performed single-variant and gene-based genome-wide association studies using a dense genotyping array containing over 2.3 million single-nucleotide variants in a discovery sample of 160 families with at least one child affected with non-syndromic ASD using a binary (ASD yes/no) phenotype and a quantitative autistic trait. Replication of the top findings was performed in Psychiatric Genomics Consortium and Erasmus Rucphen Family (ERF) cohort study. Significant association of quantitative autistic trait was observed with the TTC25 gene at 17q21.2 (effect size=10.2, P-value=3.4 × 10^-7) in the gene-based analysis. The gene also showed nominally significant association in the cohort-based ERF study (effect=1.75, P-value=0.05). Meta-analysis of discovery and replication improved the association signal (P-value_meta=1.5 × 10^-8). No genome-wide significant signal was observed in the single-variant analysis of either the binary ASD phenotype or the quantitative autistic trait. Our study has identified a novel gene TTC25 to be associated with quantitative autistic trait in patients with ASD. The replication of association in a cohort-based study and the effect estimate suggest that variants in TTC25 may also be relevant for broader ASD phenotype in the general population. TTC25 is overexpressed in frontal cortex and testis and is known to be involved in cilium movement and thus an interesting candidate gene for autistic trait.