Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome.

PREMISE: An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda). METHODS: High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population. RESULTS: The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions. DISCUSSION: The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.

The prevalence of psychiatric diagnoses and associated mortality in hospitalized US trauma patients.

BACKGROUND: We hypothesized that psychiatric diagnoses would be common in hospitalized trauma patients in the United States and when present, would be associated with worse outcomes. MATERIALS AND METHODS: The Nationwide Inpatient Sample (NIS, 2012) was used to determine national estimates for the number of patients admitted with an injury. Psychiatric diagnoses were identified using diagnosis codes according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition. RESULTS: A total of 36.5 million patients were admitted to hospitals in the United States in 2012. Of these, 1.3 million (4%) were due to trauma. Psychiatric conditions were more common in patients admitted for trauma versus those admitted for other reasons (44% versus 34%, P < 0.001). Trauma patients who had a psychiatric diagnosis compared to trauma patients without a psychiatric diagnosis were older (mean age: 61 versus 56 y, P < 0.001), more often female (52% versus 50%, P < 0.001), and more often white (73% versus 68%, P < 0.001). For ages 18-64, drug and alcohol abuse predominated (41%), whereas dementia and related disorders (48%) were the most common in adults ≥65 y. Mortality was lower for trauma patients with a psychiatric diagnosis compared to those who did not in both unadjusted and adjusted analysis (1.9% versus 2.8%; odds ratio: 0.56, P < 0.001). CONCLUSIONS: Psychiatric conditions are present in almost half of all hospitalized trauma patients in the United States; however, the types of conditions varied with age. The frequency of psychiatric conditions in the trauma population suggests efforts should be made to address this component of patient health.