NCBI's Database of Genotypes and Phenotypes: dbGaP.

The Database of Genotypes and Phenotypes (dbGap, http://www.ncbi.nlm.nih.gov/gap) is a National Institutes of Health-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents. Publicly accessible metadata about submitted studies, summary level data, and documents related to studies can be accessed freely on the dbGaP website. Individual-level data are accessible via Controlled Access application to scientists across the globe.

A new method for evaluating radial neck fractures based on Judet classification.

Aims: To propose a new method for evaluating paediatric radial neck fractures and improve the accuracy of fracture angulation measurement, particularly in younger children, and thereby facilitate planning treatment in this population. Methods: Clinical data of 117 children with radial neck fractures in our hospital from August 2014 to March 2023 were collected. A total of 50 children (26 males, 24 females, mean age 7.6 years (2 to 13)) met the inclusion criteria and were analyzed. Cases were excluded for the following reasons: Judet grade I and Judet grade IVb (> 85° angulation) classification; poor radiograph image quality; incomplete clinical information; sagittal plane angulation; severe displacement of the ulna fracture; and Monteggia fractures. For each patient, standard elbow anteroposterior (AP) view radiographs and corresponding CT images were acquired. On radiographs, Angle P (complementary to the angle between the long axis of the radial head and the line perpendicular to the physis), Angle S (complementary to the angle between the long axis of the radial head and the midline through the proximal radial shaft), and Angle U (between the long axis of the radial head and the straight line from the distal tip of the capitellum to the coronoid process) were identified as candidates approximating the true coronal plane angulation of radial neck fractures. On the coronal plane of the CT scan, the angulation of radial neck fractures (CTa) was measured and served as the reference standard for measurement. Inter- and intraobserver reliabilities were assessed by Kappa statistics and intraclass correlation coefficient (ICC). Results: Angle U showed the strongest correlation with CTa (p < 0.001). In the analysis of inter- and intraobserver reliability, Kappa values were significantly higher for Angles S and U compared with Angle P. ICC values were excellent among the three groups. Conclusion: Angle U on AP view was the best substitute for CTa when evaluating radial neck fractures in children. Further studies are required to validate this method.

The Framingham Heart Study 100K SNP genome-wide association study resource: overview of 17 phenotype working group reports.

BACKGROUND: The Framingham Heart Study (FHS), founded in 1948 to examine the epidemiology of cardiovascular disease, is among the most comprehensively characterized multi-generational studies in the world. Many collected phenotypes have substantial genetic contributors; yet most genetic determinants remain to be identified. Using single nucleotide polymorphisms (SNPs) from a 100K genome-wide scan, we examine the associations of common polymorphisms with phenotypic variation in this community-based cohort and provide a full-disclosure, web-based resource of results for future replication studies. METHODS: Adult participants (n = 1345) of the largest 310 pedigrees in the FHS, many biologically related, were genotyped with the 100K Affymetrix GeneChip. These genotypes were used to assess their contribution to 987 phenotypes collected in FHS over 56 years of follow up, including: cardiovascular risk factors and biomarkers; subclinical and clinical cardiovascular disease; cancer and longevity traits; and traits in pulmonary, sleep, neurology, renal, and bone domains. We conducted genome-wide variance components linkage and population-based and family-based association tests. RESULTS: The participants were white of European descent and from the FHS Original and Offspring Cohorts (examination 1 Offspring mean age 32 +/- 9 years, 54% women). This overview summarizes the methods, selected findings and limitations of the results presented in the accompanying series of 17 manuscripts. The presented association results are based on 70,897 autosomal SNPs meeting the following criteria: minor allele frequency > or + 10%, genotype call rate > or = 80%, Hardy-Weinberg equilibrium p-value > or = 0.001, and satisfying Mendelian consistency. Linkage analyses are based on 11,200 SNPs and short-tandem repeats. Results of phenotype-genotype linkages and associations for all autosomal SNPs are posted on the NCBI dbGaP website at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. CONCLUSION: We have created a full-disclosure resource of results, posted on the dbGaP website, from a genome-wide association study in the FHS. Because we used three analytical approaches to examine the association and linkage of 987 phenotypes with thousands of SNPs, our results must be considered hypothesis-generating and need to be replicated. Results from the FHS 100K project with NCBI web posting provides a resource for investigators to identify high priority findings for replication.

The NCBI dbGaP database of genotypes and phenotypes.

The National Center for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.