PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-6 (6)
 

Clipboard (0)
None

Select a Filter Below

Journals
Year of Publication
Document Types
1.  A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record 
Purpose
Genome-scale clinical sequencing is being adopted more broadly in medical practice. The National Institutes of Health developed the Clinical Sequencing Exploratory Research (CSER) program to guide implementation and dissemination of best practices for the integration of sequencing into clinical care. This study describes and compares the state of the art of incorporating whole-exome and whole-genome sequencing results into the electronic health record, including approaches to decision support across the six current CSER sites.
Methods
The CSER Medical Record Working Group collaboratively developed and completed an in-depth survey to assess the communication of genome-scale data into the electronic health record. We summarized commonalities and divergent approaches.
Results
Despite common sequencing platform (Illumina) adoptions, there is a great diversity of approaches to annotation tools and workflow, as well as to report generation. At all sites, reports are human-readable structured documents available as passive decision support in the electronic health record. Active decision support is in early implementation at two sites.
Conclusion
The parallel efforts across CSER sites in the creation of systems for report generation and integration of reports into the electronic health record, as well as the lack of standardized approaches to interfacing with variant databases to create active clinical decision support, create opportunities for cross-site and vendor collaborations.
doi:10.1038/gim.2013.120
PMCID: PMC3951437  PMID: 24071794
clinical decision support; clinical sequencing; decision support rules; electronic health record; electronic medical record; next-generation sequencing
3.  The Implementation and Acceptability of an HPV Vaccination Decision Support System Directed at Both Clinicians and Families 
We developed an electronic medical record (EMR)-based HPV vaccine decision support intervention targeting clinicians, (immunization alerts, education, and feedback) and families (phone reminders and referral to an educational website). Through telephone surveys completed by 162 parents of adolescent girls, we assessed the acceptability of the family-focused intervention and its effect on information-seeking behavior, communication, and HPV vaccine decision-making. The intervention was acceptable to parents and 46% remembered receiving the reminder call. Parents reported that the call prompted them to seek out information regarding the HPV vaccine, discuss the vaccine with friends and family, and reach a decision. Parents whose adolescent girls attended practices receiving the clinician-focused intervention were more likely to report that their clinician discussed the HPV vaccine at preventive visits. The results of this study demonstrate the acceptability and potential impact on clinical care of a comprehensive decision support system directed at both clinicians and families.
PMCID: PMC3540460  PMID: 23304334
4.  Blood Cultures in the Emergency Department Evaluation of Childhood Pneumonia 
Background
Blood cultures are frequently obtained in the emergency department (ED) evaluation of children with community-acquired pneumonia (CAP).
Objectives
To determine the prevalence of bacteremia in children presenting to the ED with CAP, identify subgroups at increased risk for bacteremia, and quantify the impact of positive blood cultures on management.
Methods
This case-control study was nested within a cohort of children followed at 35 pediatric practices. Patients from this cohort who were ≤18 years of age, evaluated in the ED in 2006–2007, and diagnosed with CAP were eligible. Cases were those with bacteremia. Controls included those with negative blood cultures and those without blood cultures performed.
Results
877 (9.6%) of 9,099 children with CAP were evaluated in the ED. The mean age was 3.6 years; 53% were male. Blood cultures were obtained in 291 children (33.2%). Overall, the prevalence of bacteremia was 2.1% (95% confidence interval [CI]: 0.8%–4.4%). Bacteremia occurred in 2.6% (95% CI: 1.0%–5.6%) with an infiltrate on chest radiograph and in 13.0% (95% CI: 2.8%–33.6%) with complicated pneumonia. Streptococcus pneumoniae accounted for 4 of the 6 cases of bacteremia. Blood culture results altered management in 5 of the 6 bacteremic patients; 1 had an appropriate broadening and 4 had an appropriate narrowing of coverage. The contamination rate was 1.0% (95% CI: 0.2%–3.0%).
Conclusion
Children presenting to the ED for evaluation of CAP are at low risk for bacteremia. Although positive blood cultures frequently altered clinical management, the overall impact was small given the low prevalence of bacteremia.
doi:10.1097/INF.0b013e31820a5adb
PMCID: PMC3097278  PMID: 21206393
child; pneumonia; bacteremia; Streptococcus pneumoniae; epidemiology
5.  Research Subject Enrollment by Primary Care Pediatricians Using an Electronic Health Record 
Clinical research relies on enrollment of appropriate subjects. Individuals who hear about research from their clinician are more likely to participate. We developed two strategies for research subject enrollment using the EHR and its underlying data: pop-up alerts for clinicians, and patient lists for on-site research assistants. Eleven studies used clinician alerts and most referred an adequate volume of potential subjects (range 17 to 1,162; median 324). Only a small portion of these potential subjects consented to participate (range 3% to 25%; median 11%). Two of the three studies that used EHR derived patient lists and on-site research assistants reached their enrollment goals. All three principal investigators were satisfied with this approach. These results demonstrate that EHR alerts and patient lists can facilitate research subject enrollment in primary care pediatrics. Future work will identify methods to improve the clinician EHR alert when on-site enrollment by research assistants is not feasible.
PMCID: PMC2655899  PMID: 18693844
6.  Follow-Up Analysis of Genome-Wide Association Data Identifies Novel Loci for Type 1 Diabetes 
Diabetes  2009;58(1):290-295.
OBJECTIVE—Two recent genome-wide association (GWA) studies have revealed novel loci for type 1 diabetes, a common multifactorial disease with a strong genetic component. To fully utilize the GWA data that we had obtained by genotyping 563 type 1 diabetes probands and 1,146 control subjects, as well as 483 case subject–parent trios, using the Illumina HumanHap550 BeadChip, we designed a full stage 2 study to capture other possible association signals.
RESEARCH DESIGN AND METHODS—From our existing datasets, we selected 982 markers with P < 0.05 in both GWA cohorts. Genotyping these in an independent set of 636 nuclear families with 974 affected offspring revealed 75 markers that also had P < 0.05 in this third cohort. Among these, six single nucleotide polymorphisms in five novel loci also had P < 0.05 in the Wellcome Trust Case-Control Consortium dataset and were further tested in 1,303 type 1 diabetes probands from the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) plus 1,673 control subjects.
RESULTS—Two markers (rs9976767 and rs3757247) remained significant after adjusting for the number of tests in this last cohort; they reside in UBASH3A (OR 1.16; combined P = 2.33 × 10−8) and BACH2 (1.13; combined P = 1.25 × 10−6).
CONCLUSIONS—Evaluation of a large number of statistical GWA candidates in several independent cohorts has revealed additional loci that are associated with type 1 diabetes. The two genes at these respective loci, UBASH3A and BACH2, are both biologically relevant to autoimmunity.
doi:10.2337/db08-1022
PMCID: PMC2606889  PMID: 18840781

Results 1-6 (6)