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Incomplete hippocampal inversion (IHI), also called hippocampal malrotation, is an atypical presentation of the hippocampus present in about 20% of healthy individuals. Here we conducted the first genome-wide association study (GWAS) in IHI to elucidate the genetic underpinnings that may contribute to the incomplete inversion during brain development. A total of 1381 subjects contributed to the discovery cohort obtained from the IMAGEN database. The incidence rate of IHI was 26.1%. Loci with P<1e-5 were followed up in a validation cohort comprising 161 subjects from the PING study. Summary statistics from the discovery cohort were used to compute IHI heritability as well as genetic correlations with other traits. A locus on 18q11.2 (rs9952569; OR = 1.999; Z = 5.502; P = 3.755e-8) showed a significant association with the presence of IHI. A functional annotation of the locus implicated genes AQP4 and KCTD1. However, neither this locus nor the other 16 suggestive loci reached a significant p-value in the validation cohort. The h2 estimate was 0.54 (sd: 0.30) and was significant (Z = 1.8; P = 0.036). The top three genetic correlations of IHI were with traits representing either intelligence or education attainment and reached nominal P< = 0.013.
Pubmed ID: 31990937 RIS Download
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A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method.
View all literature mentionsOpen source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
View all literature mentionsOpen and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.
View all literature mentionsA large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.
View all literature mentionsSoftware application designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about How did you make the figures in your talk? or How did you make the figures for your GWAS paper? (entry from Genetic Analysis Software)
View all literature mentionsPlatform that can be used to annotate, prioritize, visualize and interpret GWAS results. To submit your own GWAS, login is required for security reason. You can browse public results of FUMA from Browse Public Results without registration or login.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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