Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

BACKGROUND: It has been reported in the quantitative trait locus (QTL) literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. RESULTS: Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. CONCLUSION: We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test

Identification of co-regulated transcripts affecting male body size in Drosophila

Factor analysis is an analytic approach that describes the covariation among a set of genes through the estimation of 'factors', which may be, for example, transcription factors, microRNAs (miRNAs), and so on, by which the genes are co-regulated. Factor analysis gives a direct mechanism by which to relate gene networks to complex traits. Using simulated data, we found that factor analysis clearly identifies the number and structure of factors and outperforms hierarchical cluster analysis. Noise genes, genes that are not correlated with any factor, can be distinguished even when factor structure is complex. Applied to body size in Drosophila simulans, an evolutionarily important complex trait, a factor was directly associated with body size

Impacts of Geographic Distance on Peritoneal Dialysis Utilization: Refining Models of Treatment Selection

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/136011/1/hesr12489.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136011/2/hesr12489-sup-0001-AuthorMatrix.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136011/3/hesr12489_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136011/4/hesr12489-sup-0002-Appendix.pd

Factors Associated with Survival of Veterans with Gastrointestinal Neuroendocrine Tumors

Background. Gastrointestinal (GI) neuroendocrine tumor (NET) incidence has been increasing; however, GI NET within the national Veterans Affairs (VA) health system has not been described. Methods. We used the VA Central Cancer Registry to identify the cohort of patients diagnosed with GI NET in 1995–2009. Cox regression models were constructed to explore factors associated with survival. Results. We included 1793 patients with NET of the stomach (9%), duodenum (10%), small intestine (24%), colon (19%) or rectum (38%). Twenty percent were diagnosed in 1995–1999, 35% in 2000–2004, and 45% in 2005–2009. Unadjusted 5-year survival rates were: stomach 56%, duodenum 66%, small intestine 52%, colon 67%, and rectum 84%. Factors associated with shorter survival were increasing age, hazard ratio (HR) 1.05 (95% CI 1.04–1.06), NET location [compared to rectum: stomach HR 2.26 (95% CI 1.68–3.05), duodenum HR 1.70 (95% CI 1.26–2.28), small intestine HR 1.85 (95% CI 1.42–2.42), and colon 1.83 (95% CI 1.41–2.39)], stage [compared to in situ/local: regional HR 1.15 (95% CI 0.90–1.47), distant HR 2.38 (95% CI 1.87–3.05)], and earlier period of diagnosis [compared to 1995–1999: 2000–2004 HR 0.70 (95% CI 0.59–0.85), 2005–2009 HR 0.43 (95% CI 0.34–0.54)]. Conclusions. The incidence of GI NET has also increased over time in the VA system with similar survival rates to those observed in non-VA settings. Worsened survival was associated with older age, tumor site, advanced stage, and earlier year of diagnosis

An electronic family health history tool to identify and manage patients at increased risk for colorectal cancer: protocol for a randomized controlled trial.

BackgroundColorectal cancer is the fourth most commonly diagnosed cancer in the United States. Approximately 3-10% of the population has an increased risk for colorectal cancer due to family history and warrants more frequent or intensive screening. Yet, < 50% of that high-risk population receives guideline-concordant care. Systematic collection of family health history and decision support may improve guideline-concordant screening for patients at increased risk of colorectal cancer. We seek to test the effectiveness of a web-based, systematic family health history collection tool and decision support platform (MeTree) to improve risk assessment and appropriate management of colorectal cancer risk among patients in the Department of Veterans Affairs primary care practices.MethodsIn this ongoing randomized controlled trial, primary care providers at the Durham Veterans Affairs Health Care System and the Madison VA Medical Center are randomized to immediate intervention or wait-list control. Veterans are eligible if assigned to enrolled providers, have an upcoming primary care appointment, and have no conditions that would place them at increased risk for colorectal cancer (such as personal history, adenomatous polyps, or inflammatory bowel disease). Those with a recent lower endoscopy (e.g. colonoscopy, sigmoidoscopy) are excluded. Immediate intervention patients put their family health history information into a web-based platform, MeTree, which provides both patient- and provider-facing decision support reports. Wait-list control patients access MeTree 12 months post-consent. The primary outcome is the risk-concordant colorectal cancer screening referral rate obtained via chart review. Secondary outcomes include patient completion of risk management recommendations (e.g. colonoscopy) and referral for genetic consultation. We will also conduct an economic analysis and an assessment of providers' experience with MeTree clinical decision support recommendations to inform future implementation efforts if the intervention is found to be effective.DiscussionThis trial will assess the feasibility and effectiveness of patient-collected family health history linked to decision support to promote risk-appropriate screening in a large healthcare system such as the Department of Veterans Affairs.Trial registrationClinicalTrials.gov, NCT02247336 . Registered on 25 September 2014

Group Versus Individual Physical Therapy for Veterans With Knee Osteoarthritis: Randomized Clinical Trial

BACKGROUND: Efficient approaches are needed for delivering nonpharmacological interventions for management of knee osteoarthritis (OA). OBJECTIVE: This trial compared group-based versus individual physical therapy interventions for management of knee OA. DESIGN AND METHODS: Three hundred twenty patients with knee OA at the VA Medical Center in Durham, North Carolina, (mean age=60 years, 88% male, 58% nonwhite) were randomly assigned to receive either the group intervention (group physical therapy; six 1-hour sessions, typically 8 participants per group) or the individual intervention (individual physical therapy; two 1-hour sessions). Both programs included instruction in home exercise, joint protection techniques, and individual physical therapist evaluation. The primary outcome measure was the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC; range=0-96, higher scores indicate worse symptoms), measured at baseline, 12 weeks, and 24 weeks. The secondary outcome measure was the Short Physical Performance Battery (SPPB; range=0-12, higher scores indicate better performance), measured at baseline and 12 weeks. Linear mixed models assessed the difference in WOMAC scores between arms. RESULTS: At 12 weeks, WOMAC scores were 2.7 points lower in the group physical therapy arm compared with the individual physical therapy arm (95% confidence interval [CI]-5.9, 0.5; P=.10), indicating no between-group difference. At 24 weeks, WOMAC scores were 1.3 points lower in the group physical therapy arm compared with the individual physical therapy arm (95% CI-4.6, 2.0; P=.44), indicating no significant between-group difference. At 12 weeks, SPPB scores were 0.1 points lower in the group physical therapy arm compared with the individual physical therapy arm (95% CI-0.5, 0.2; P=.53), indicating no difference between groups. LIMITATIONS: This study was conducted in one VA medical center. Outcome assessors were blinded, but participants and physical therapists were not blinded. CONCLUSIONS: Group physical therapy was not more effective than individual physical therapy for primary and secondary study outcomes. Either group physical therapy or individual physical therapy may be a reasonable delivery model for health care systems to consider

Open-label randomized trial of titrated disease management for patients with hypertension: Study design and baseline sample characteristics

Despite the availability of efficacious treatments, only half of patients with hypertension achieve adequate blood pressure (BP) control. This paper describes the protocol and baseline subject characteristics of a 2-arm, 18-month randomized clinical trial of titrated disease management (TDM) for patients with pharmaceutically-treated hypertension for whom systolic blood pressure (SBP) is not controlled (≥140mmHg for non-diabetic or ≥130mmHg for diabetic patients). The trial is being conducted among patients of four clinic locations associated with a Veterans Affairs Medical Center. An intervention arm has a TDM strategy in which patients' hypertension control at baseline, 6, and 12 months determines the resource intensity of disease management. Intensity levels include: a low-intensity strategy utilizing a licensed practical nurse to provide bi-monthly, non-tailored behavioral support calls to patients whose SBP comes under control; medium-intensity strategy utilizing a registered nurse to provide monthly tailored behavioral support telephone calls plus home BP monitoring; and high-intensity strategy utilizing a pharmacist to provide monthly tailored behavioral support telephone calls, home BP monitoring, and pharmacist-directed medication management. Control arm patients receive the low-intensity strategy regardless of BP control. The primary outcome is SBP. There are 385 randomized (192 intervention; 193 control) veterans that are predominately older (mean age 63.5 years) men (92.5%). 61.8% are African American, and the mean baseline SBP for all subjects is 143.6mmHg. This trial will determine if a disease management program that is titrated by matching the intensity of resources to patients' BP control leads to superior outcomes compared to a low-intensity management strategy

A feasibility study to develop and test a Spanish patient and provider intervention for managing osteoarthritis in Hispanic/Latino adults (PRIMO-Latino)

Abstract Background Arthritis affects approximately 50 million adults in the USA. Hispanics/Latinos have a higher prevalence of arthritis-attributed activity limitations primarily related to osteoarthritis (OA). Hispanic/Latinos are less likely to receive hip replacement independent of health care access, and they are less likely to receive knee replacement. There have been few interventions to improve OA treatment among the Hispanic/Latino population in the USA. In our study, we aimed to develop and test a telephone delivered culturally appropriate Spanish behavioral intervention for the management of OA in Hispanic/Latino adults. Methods We conducted a feasibility study in an academic health center and local community in Durham, North Carolina. We enrolled self-identified Spanish speaking overweight/obese adults (≥ 18) with OA of the knee and/or hip under the care of a primary health care provider. The 12-month patient intervention focused on physical activity, weight management, and cognitive behavioral pain management skills. The patient intervention was delivered via telephone with calls scheduled twice per month for the first 6 months, then monthly for the last 6 months (18 sessions). The one-time provider intervention included delivery of patient-specific OA treatment recommendations, based on patients’ baseline data and published guidelines. The primary measures were metrics of feasibility, including recruitment and intervention delivery. We also assessed pain, stiffness, and function using the Spanish-Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Results A total of 1879 participants were identified for potential enrollment. Of those, 1864 did not meet inclusion criteria, were not able to be reached or refused. Fifteen participants enrolled in the intervention. The mean number of phone calls completed was 14.7. Eighty percent completed more than 16 calls. The mean WOMAC baseline score (SD) was 39 (20); mean improvement in WOMAC scores between baseline and 12 months, among 11 participants who completed the study, was − 13.27 [95% CI, − 25.09 to − 1.46] points. Conclusion Recruitment of Hispanics/Latinos, continues to be a major challenge. A Spanish-based telephone delivering lifestyle intervention for OA management in Hispanic/Latino adults is feasible to deliver and may lead to improved OA symptoms. Future research is needed to further test the feasibility and effectiveness of this type of intervention in this segment of the population. Trial registration NCT0178241

The association of comorbid conditions with patient-reported outcomes in Veterans with hip and knee osteoarthritis

There is limited understanding of how comorbid health conditions affect osteoarthritis (OA)-related outcomes. This study examined associations of different comorbidity measures with baseline OA-related patient-reported outcomes (PROs) among patients with hip and knee OA. Data were from patients (N=300, 9 % female, mean age = 61.1; SD=9.2) enrolled in a randomized control trial at the Durham Veterans Affairs Medical Center. Separate multivariable regression models, adjusted for demographic and clinical characteristics, examined the association of each comorbidity measure with baseline PROs: pain, physical function, depressive symptoms, fatigue, and insomnia. Comorbidity measures included the Self-Administered Comorbidity Questionnaire (SACQ), conditions reported as activity-limiting (SACQ-AL), and indicators of depression, diabetes, hypertension, and back pain. Mean (SD) numbers of comorbid conditions and activity-limiting conditions were 3.4 (1.8) and 1.6 (1.4), respectively. Comorbidity scores (SACQ overall and SACQ-AL) and individual comorbidity conditions were each associated with worse OA-related PROs adjusting for demographic and clinical factors. Worse SACQ overall and SACQ-AL scores were associated with worse mean scores for pain, depressive symptoms, fatigue, and insomnia (p values <0.01). Additionally, increasing SACQ-AL scores were associated with worse mean scores for function (p<0.01). Depression was associated with worse pain (p=0.03), fatigue, and insomnia (p values <0.01). Diabetes was associated with worse fatigue (p=0.01), depressive symptoms (p=0.02), and insomnia (p=0.03). Back pain was associated with worse pain scores (p=0.02). Results provide evidence that comorbidity burden, particularly activity-limiting conditions, is associated with worse OA-related PROs. Interventions for patients with OA need to address comorbid conditions and their impact on key outcomes