Genome-wide algorithm for detecting CNV associations with diseases

SNP genotyping arrays have been developed to characterize single-nucleotide polymorphisms (SNPs) and DNA copy number variations (CNVs). The quality of the inferences about copy number can be affected by many factors including batch effects, DNA sample preparation, signal processing, and analytical approach. Nonparametric and model-based statistical algorithms have been developed to detect CNVs from SNP genotyping data. However, these algorithms lack specificity to detect small CNVs due to the high false positive rate when calling CNVs based on the intensity values. Association tests based on detected CNVs therefore lack power even if the CNVs affecting disease risk are common. In this research, by combining an existing Hidden Markov Model (HMM) and the logistic regression model, a new genome-wide logistic regression algorithm was developed to detect CNV associations with diseases. We showed that the new algorithm is more sensitive and can be more powerful in detecting CNV associations with diseases than an existing popular algorithm, especially when the CNV association signal is weak and a limited number of SNPs are located in the CNV.^

Functional data analysis approaches for genotype-phenotype association studies from next-generation sequencing

Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^

Impact of real time polymerase chain reaction technology on the therapeutic approach to treatment of staphylococcal infections

Can the early identification of the species of staphylococcus responsible for infection by the use of Real Time PCR technology influence the approach to the treatment of these infections? ^ This study was a retrospective cohort study in which two groups of patients were compared. The first group, ‘Physician Aware’ consisted of patients in whom physicians were informed of specific staphylococcal species and antibiotic sensitivity (using RT-PCR) at the time of notification of the gram stain. The second group, ‘Physician Unaware’ consisted of patients in whom treating physicians received the same information 24–72 hours later as a result of blood culture and antibiotic sensitivity determination. ^ The approach to treatment was compared between ‘Physician Aware’ and ‘Physician Unaware’ groups for three different microbiological diagnoses—namely MRSA, MSSA and no-SA (or coagulase negative Staphylococcus). ^ For a diagnosis of MRSA, the mean time interval to the initiation of Vancomycin therapy was 1.08 hours in the ‘Physician Aware’ group as compared to 5.84 hours in the ‘Physician Unaware’ group (p=0.34). ^ For a diagnosis of MSSA, the mean time interval to the initiation of specific anti-MSSA therapy with Nafcillin was 5.18 hours in the ‘Physician Aware’ group as compared to 49.8 hours in the ‘Physician Unaware’ group (p=0.007). Also, for the same diagnosis, the mean duration of empiric therapy in the ‘Physician Aware’ group was 19.68 hours as compared to 80.75 hours in the ‘Physician Unaware’ group (p=0.003) ^ For a diagnosis of no-SA or coagulase negative staphylococcus, the mean duration of empiric therapy was 35.65 hours in the ‘Physician Aware’ group as compared to 44.38 hours in the ‘Physician Unaware’ group (p=0.07). However, when treatment was considered a categorical variable and after exclusion of all cases where anti-MRS therapy was used for unrelated conditions, only 20 of 72 cases in the ‘Physician Aware’ group received treatment as compared to 48 of 106 cases in the ‘Physician Unaware’ group. ^ Conclusions. Earlier diagnosis of MRSA may not alter final treatment outcomes. However, earlier identification may lead to the earlier institution of measures to limit the spread of infection. The early diagnosis of MSSA infection, does lead to treatment with specific antibiotic therapy at an earlier stage of treatment. Also, the duration of empiric therapy is greatly reduced by early diagnosis. The early diagnosis of coagulase negative staphylococcal infection leads to a lower rate of unnecessary treatment for these infections as they are commonly considered contaminants. ^

Effect of the emergence of community acquired methicillin resistant Staphylococcus aureus on microbial resistance patterns seen during a seven year study of minocycline/rifampin catheter use

Background. Health care associated catheter related blood stream infections (CRBSI) represent a significant public health concern in the United States. Several studies have suggested that precautions such as maximum sterile barrier and use of antimicrobial catheters are efficacious at reducing CRBSI, but there is concern within the medical community that the prolonged use of antimicrobial catheters may be associated with increased bacterial resistance. Clinical studies have been done showing no association and a significant decrease in microbial resistance with prolonged minocycline/rifampin (M/R) catheter use. One explanation is the emergence of community acquired methicillin resistant Staphylococcus aureus (MRSA), which is more susceptible to antibiotics, as a cause of CRBSI.^ Methods. Data from 323 MRSA isolates cultured from cancer patients at The University of Texas MD Anderson Cancer center from 1997-2007 displaying MRSA infection were analyzed to determine whether there is a relationship between resistance to minocycline and rifampin and prolonged wide spread use of minocycline (M/R) catheters. Analysis was also conducted to determine whether there was a significant change in the prevalence community acquired MRSA (CA-MRSA) during this time period and if this emergence act as a confounder masquerading the true relationship between microbial resistance and prolonged M/R catheter use.^ Results. Our study showed that the significant (p=0.008) change in strain type over time is a confounding variable; the adjusted model showed a significant protective effect (OR 0.000281, 95% CI 1.4x10 -4-5.5x10-4) in the relationship between MRSA resistance to minocycline and prolonged M/R catheter use. The relationship between resistance to rifampin and prolonged M/R catheter use was not significant.^ Conclusion. The emergence of CA-MRSA is a confounder and in the relationship between resistance to minocycline and rifampin and prolonged M/R catheter use. However, despite the adjustment for the more susceptible CA-MRSA the widespread use of M/R catheters does not promote microbial resistance. ^

Fate and effects of drilling wastes in a shallow estuarine mesocosm

To address concerns expressed about the possible effect of drilling mud discharges on shallow, low-energy estuarine ecosystems, a 12 month study was designed to detect alterations in water quality and sediment geochemistry. Each drilling mud used in the study and sediments from the study site were analyzed in the laboratory for chemical and physical characteristics. Potential water quality impacts were simulated by the EPA-COE elutriation test procedure. Mud toxicity was measured by acute and chronic bioassays with Mysidopsis bahia, Mercenaria mercenaria, and Nereis virens.^ For the field study, a relatively pristine, shallow (1.2 m) estuary (Christmas Bay, TX) without any drilling activity for the last 30 years was chosen for the study site. After a three month baseline study, three stations were selected. Station 1 was an external control. At each treatment station (2, 3), mesocosms were constructed to enclose a 3.5 m$\sp3$ water column. Each treatment station included an internal control site also. Each in situ mesocosm, except the controls, was successively dosed at a mesocosm-specific dose (1:100; 1:1,000; or 1:10,000 v/v) with 4 field collected drilling muds (spud, nondispersed, lightly-treated, and heavily-treated lignosulfonate) in sequential order over 1.5 months. Twenty-four hours after each dose, water exchange was allowed until the next treatment. Station 3 was destroyed by a winter storm. After the last treatment, the enclosures were removed and the remaining sites monitored for 6 months. One additional site was similarly dosed (1:100 v/v) with clean dredged sediment from Christmas Bay for comparison between dredged sediments and drilling muds.^ Results of the analysis of the water samples and field measurements showed that water quality was impacted during the discharges, primarily at the highest dose (1:100 v/v), but that elevated levels of C, Cr (T,F), Cr$\sp{+3}$ (T, F), N, Pb, and Zn returned to ambient levels before the end of the 24 hour exposure period or immediately after water exchange was allowed (Al, Ba(T), Chlorophyll ABC, SS, %T). Barium, from the barite, was used as a geochemical tracer in the sediments to confirm estimated doses by mass balance calculations. Barium reached a maximum of 166x background levels at the high dose mesocosm. Barium levels returned to ambient or only slightly elevated levels at the end of the 6 month monitoring period due to sediment deposition, resuspension, and bioturbation. QA/QC results using blind samples consisting of lab standards and spiked samples for both water and sediment matrices were within acceptable coefficients of variation.^ In order to avoid impacts on water quality and sediment geochemistry in a shallow estuarine ecosystem, this study concluded that a minimal dilution of 1:1,000 (v/v) would be required in addition to existing regulatory constraints. ^

A GENETIC MARKER STUDY OF NON - INSULIN DEPENDENT DIABETICS IN THE MEXICAN-AMERICAN COMMUNITY FROM STARR COUNTY, TEXAS (PLASMA GLUCOSE, HEMOGLOBIN ANALYSIS)

Diabetes mellitus occurs in two forms, insulin-dependent (IDDM, formerly called juvenile type) and non-insulin dependent (NIDDM, formerly called adult type). Prevalence figures from around the world for NIDDM, show that all societies and all races are affected; although uncommon in some populations (.4%), it is common (10%) or very common (40%) in others (Tables 1 and 2).^ In Mexican-Americans in particular, the prevalence rates (7-10%) are intermediate to those in Caucasians (1-2%) and Amerindians (35%). Information about the distribution of the disease and identification of high risk groups for developing glucose intolerance or its vascular manifestations by the study of genetic markers will help to clarify and solve some of the problems from the public health and the genetic point of view.^ This research was designed to examine two general areas in relation to NIDDM. The first aims to determine the prevalence of polymorphic genetic markers in two groups distinguished by the presence or absence of diabetes and to observe if there are any genetic marker-disease association (univariate analysis using two by two tables and logistic regression to study the individual and joint effects of the different variables). The second deals with the effect of genetic differences on the variation in fasting plasma glucose and percent glycosylated hemoglobin (HbAl) (analysis of Covariance for each marker, using age and sex as covariates).^ The results from the first analysis were not statistically significant at the corrected p value of 0.003 given the number of tests that were performed. From the analysis of covariance of all the markers studied, only Duffy and Phosphoglucomutase were statistically significant but poor predictors, given that the amount they explain in terms of variation in glycosylated hemoglobin is very small.^ Trying to determine the polygenic component of chronic disease is not an easy task. This study confirms the fact that a larger and random or representative sample is needed to be able to detect differences in the prevalence of a marker for association studies and in the genetic contribution to the variation in glucose and glycosylated hemoglobin. The importance that ethnic homogeneity in the groups studied and standardization in the methodology will have on the results has been stressed. ^

TRANSOVARIAL TRANSMISSION OF YELLOW FEVER VIRUS BY A SYLVATIC VECTOR, HAEMAGOGUS EQUINUS (THEOBALD)

The potential of a sylvatic vector to act as reservoir of yellow fever virus was assessed in Haemagogus equinus (Theobald). Mosquitoes from the Maje'75 laboratory colony and a Panamanian human isolated strain of yellow fever virus were used. Female mosquitoes infected with yellow fever virus had a minimum transovarial transmission rate of 1:5745. This is the first time transovarial transmission of yellow fever virus has been demonstrated in a New World sylvatic vector. Transovarial transmission of yellow fever virus in this sylvatic mosquito species may be an alternative mechanism for biological survival of the virus during adverse periods or in the absence of susceptible vertebrate hosts. ^

The incidence of necrotizing changes in adults with pneumococcal pneumonia

Background. Necrotizing pneumonia is generally considered a rare complication of pneumococcal pneumonia in adults. We systematically studied the incidence of necrotizing changes in adult patients with pneumococcal pneumonia, and examined the severity of infection, the role of causative serotype and the association with bacteremia. ^ Methods. We used a data base of all pneumococcal infections identified at our medical center between 2000 and 2010. Original readings of chest X-rays (CXR) and computerized tomography (CT) were noted. All images were then reread independently by 2 radiologists. The severity of disease was assessed using the SMART-COP scoring system. ^ Results. There were 351 cases of pneumococcal pneumonia. Necrosis was reported in no original CXR readings and 6 of 136 (4.4%) CTs. With re-reading, 8 of 351 (2.3%) CXR and 15 of 136 (11.0%) CT had necrotizing changes. Overall, these changes were found in 23 of 351 (6.6%, 95% CI 4.0 - 9.1) patients. The incidence of bacteremia and the admitting SMART-COP scores were similar in patients with and without necrosis (P=1.00 and P=0.32, respectively). Type 3 pneumococcus was more commonly isolated from patients with than from patients without necrotizing pneumonia (P=0.05), but a total of 10 serotypes were identified among 16 cases in which the organism was available for typing. ^ Conclusions. Necrotizing changes in the lungs were seen in 6.6% (95% CI 4.0 - 9.1) of a large series of adults with pneumococcal pneumonia. Patients with necrosis were not more likely to have bacteremia or more severe disease. Type 3 pneumococcus was commonly implicated, but 9 other serotypes were also identified.^

Biomarker circadian rhythm profiles in critically ill mechanically ventilated patients

Objective: To explore the natural trajectory of core body temperature (CBT) and cortisol (CORT) circadian rhythms in mechanically ventilated intensive care unit (MV ICU) patients. ^ Design: Prospective, observational, time-series pilot study. ^ Setting: Medical-surgical and pulmonary ICUs in a tertiary care hospital. ^ Sample: Nine (F = 3, M = 6) adults who were mechanically ventilated within 12 hrs of ICU admission with mean ± SD age of 65.2 ± 14 years old. ^ Measurements: Core body temperature and environmental measures of light, sound, temperature, and relative humidity were logged in 1-min intervals. Hourly urine specimens and 2-hr interval blood specimens were collected for up to 7 consecutive days for CORT assay. Mechanical ventilation days, ICU length of stay, and ICU mortality were documented. Acute Physiology and Chronic Health Evaluation (APACHE) II scores were computed for each study day. The data of each biologic and environmental variable were analyzed using single cosinor analysis of 24-hr serial segments. One patient did not complete the study because mortality occurred within 8 hrs of enrollment. Nine ICU patients completed the study in 1.6 to 7.0 days. ^ Results: No normal circadian rhythm pattern was found when the cosinor-derived parameters of amplitude (one-half the peak-trough variability) and acrophase (peak time) were compared with cosinor-derived parameter reference ranges of healthy, diurnally active humans, although 83% of patient-day CBT segments showed statistically significant (p ≤ .05) and biologically meaningful (R2≥ 0.30) 24-hr rhythms with abnormal cosinor parameters. Cosinor parameters of the environmental temporal profiles showed 27% of light, 76% of ambient temperature, and 78% of relative humidity serial segments had a significant and meaningful 24-hr diurnal pattern. Average daily light intensity varied from 34 to 187 lx with a maximum light exposure of 1877 lx. No sound measurement segment had a statistically significant cosine pattern, and numerous 1-minute interval peaks ≥ 60 dB occurred around the clock. Average daily ambient temperature and relative humidity varied from 19 to 24°C and from 25% to 61%, respectively. There was no statistically significant association between CBT or clinical outcomes and cosinor-derived parameters of the environmental variables. Circadian rhythms of urine and plasma CORT were deferred for later analysis. ^ Conclusions: The natural trajectory of the CBT circadian rhythm in MV ICU patients demonstrated persistent cosinor parameter alteration, even when a significant and meaningful 24-hr rhythm was present. The ICU environmental measures showed erratic light and sound exposures. Room temperature and relative humidity data produced the highest rate of significant and meaningful diurnal 24-hr patterns. Additional research is needed to clarify relations among the CBT biomarker of the circadian clock and environmental variables of MV ICU patients. ^

Seroprevalence of Chagas' disease in Texas among shelter dogs in Houston and the Rio Grande Valley region and its implication for human infection

Chagas’ disease, also called American Trypanosomiasis, is a vector-borne disease caused by the protozoan parasite Trypanosoma cruzi. T. cruzi is spread by triatomine insects, commonly referred to as ‘kissing bugs.’ After the insect takes a blood meal from its animal or human host, it usually defecates near the bite wound. The parasite is present in the feces, and when rubbed into the bite wound or mucous membranes by the host, infection ensues. Chagas’ disease is highly endemic in Central and South America where it originated. Many people in these endemic areas live in poor conditions surrounded by animals, mainly dogs, that can serve as a possible link to human infection. In Chagas’ endemic countries, dogs can be used as a sentinel to infer risk for human infection. In Texas, the prevalence of Chagas’ and risk for human infection is largely unknown. This study aimed to determine the prevalence of Chagas’ disease in shelter dogs in Houston, Texas and the Rio Grande Valley region by using an immunochromatographic assay (Chagas’ Stat-Pak) to test for the presence of T. cruzi antibodies. Of the 822 samples tested, 26 were found to be positive (3.2%). In both locations, Chagas’ prevalence increased over time. This study found that dogs, especially strays, can serve as sentinels for disease activity. Public health authorities can implement this strategy to understand the level of Chagas’ activity in a defined geographic area and prevent human infection.^

An outbreak of Multi-Drug Resistant Acinetobacter in the burn intensive care unit of a large tertiary care center

Risk factors for Multi-Drug Resistant Acinetobacter (MDRA) acquisition were studied in patients in a burn intensive care unit (ICU) where there was an outbreak of MDRA. Forty cases were matched with eighty controls based on length of stay in the Burn ICU and statistical analysis was performed on data for several different variables. Matched analysis showed that mechanical ventilation, transport ventilation, number of intubations, number of bronchoscopy procedures, total body surface area burn, and prior Methicillin Resistant Staphylococcus aureus colonization were all significant risk factors for MDRA acquisition. ^ MDRA remains a significant threat to the burn population. Treatment for burn patients with MDRA is challenging as resistance to antibiotics continues to increase. This study underlined the need to closely monitor the most critically ill ventilated patients during an outbreak of MDRA as they are the most at risk for MDRA acquisition.^

The relationship of obesity and cardiovascular disease

Aim. To review published literature on the relationship of obesity and cardiovascular disease.^ Methods. To look at all the studies published on the topic from 2005.^ Results. In the studies done prior to 2011, body mass index and in particular waist to hip ratio (51.57) was found to be associated with coronary heart disease. But, this relationship was challenged by the latest Lancet 2011meta-analysis 1 which concluded that singly or in combination, body-mass index, waist circumference, and waist-to-hip ratio did not importantly improve prediction of first-onset cardiovascular disease when additional information exists on blood pressure, history of diabetes, and cholesterol measures were available. Furthermore, they also found long-term reproducibility of BMI to be superior to that of waist-to-hip ratio (or waist circumference). Interestingly, body mass index in later childhood and early adult life showed positive association with coronary heart disease later in life 2. In US female health professionals 3 increasing body mass index was found to be associated with increased coronary heart disease risk. Overall 4, physical activity was found to be independently associated with fewer risk factors, less coronary artery disease, and fewer adverse events in women. Finally, obesity was found to be associated with increased overall cardiovascular mortality and coronary heart disease mortality 5.^ Conclusions. There is insufficient data to draw guidelines regarding parameters of obesity affecting cardiovascular disease. But there is data to support that lower body mass index would lead to decreased cardiovascular disease mortality. And physical activity has a direct association with less coronary artery disease in women.^

Biomedical informatics applications for epilepsy management: A systematic review

Epilepsy is a very complex disease which can have a variety of etiologies, co-morbidities, and a long list of psychosocial factors4. Clinical management of epilepsy patients typically includes serological tests, EEG's, and imaging studies to determine the single best antiepileptic drug (AED). Self-management is a vital component of achieving optimal health when living with a chronic disease. For patients with epilepsy self-management includes any necessary actions to control seizures and cope with any subsequent effects of the condition9; including aspects of treatment, seizure, and lifestyle. The use of computer-based applications can allow for more effective use of clinic visits and ultimately enhance the patient-provider relationship through focused discussion of determinants affecting self-management. ^ The purpose of this study is to conduct a systematic literature review on informatics application in epilepsy self-management in an effort to describe current evidence for informatics applications and decision support as an adjunct to successful clinical management of epilepsy. Each publication was analyzed for the type of study design utilized. ^ A total of 68 publications were included and categorized by the study design used, development stage, and clinical domain. Descriptive study designs comprised of three-fourths of the publications and indicate an underwhelming use of prospective studies. The vast majority of prospective studies also focused on clinician use to increase knowledge in treating patients with epilepsy. ^ Due to the chronic nature of epilepsy and the difficulty that both clinicians and patients can experience in managing epilepsy, more prospective studies are needed to evaluate applications that can effectively increase management activities. Within the last two decades of epilepsy research, management studies have employed the use of biomedical informatics applications. While the use of computer applications to manage epilepsy has increased, more progress is needed.^

Evaluation of elevator shafts as a pathway for fungal spores and particles to enter a hospital housing immuno-compromised patients

Background. It is estimated that hospitals spend between 28 and 33 billion dollars per year as a result of hospital-acquired infections. (Scott, 2009) The costs continue to rise despite the guidance and controls provided by hospital infection control staff to reduce patient exposures to fungal spores and other infectious agents. With all processes and controls in place, the vented elevator shaft represents an unprotected opening from the top of the building to the lower floors. The hypothesis for this prospective study is that there is a positive correlation between the number of Penicillium/Aspergillus-like spores, Cladosporium, ascospores, basidiospores in spores/m3 as individual spore categories found in the hoistway vent of an elevator shaft and the levels of the same spores, sampled near-simultaneously in the outdoor intake of the elevator shaft. Specific aims of this study include determining if external Penicillium/Aspergillus-like spores are entering the healthcare facility via the elevator shaft and hoistway vents. Additional aims include determining levels of Penicillium/Aspergillus-like spores outdoors, in the elevator shafts, and indoors in areas possibly affected by elevator shaft air; and, finally, to evaluate whether any effect is observed due to the installation of a hoistway vent damper, installed serendipitously during this study. ^ Methods. Between April 2010 and September 2010, a total of 3,521 air samples were collected, including 363 spore trap samples analyzed microscopically for seven spore types, and polymerase chain reaction analyses on 254 air samples. 2178 particle count measurements, 363 temperature readings and 363 relative humidity readings were also obtained from 7 different locations potentially related to the path of air travel inside and near a centrally-located and representative elevator shaft. ^ Results. Mean Penicillium/Aspergillus-like spore values were higher outside the building (530 spores/m3 of air) than inside the hoistway (22.8 spores/m3) during the six month study. Mean values inside the hospital were lower than outside throughout the study, ranging from 15 to 73 spores/m3 of air. Mean Penicillium/Aspergillus-like spore counts inside the hoistway decreased from 40.1 spores/m3 of air to 9 spores/m3 of air following the installation of a back draft damper between the outside air and the elevator shaft. Comparison of samples collected outside the building and inside the hoistway vent prior to installing the damper indicated a strong positive correlation (Spearman's Rho=0.8008, p=0.0001). The similar comparison following the damper installation indicated a moderate non-significant inverse correlation (Spearman's rho = −0.2795, p=0.1347). ^ Conclusion. Elevator shafts are one pathway for mold spores to enter a healthcare facility. A significant correlation was detected between spores and particle counts inside the hoistway and outside prior to changes in the ventilation system. The insertion of the back draft damper appeared to lower the spore counts inside the hoistway and inside the building. The mold spore counts in air outside the study building were higher in the period following the damper installation while the levels inside the hoistway and hospital decreased. Cladosporium and Penicillium/Aspergillus -like spores provided a method for evaluating indoor air quality as a natural tracer from outside the building to inside the building. Ascospores and basidiospores were not a valuable tracer due to low levels of detection during this study. ^ Installation of a back draft damper provides additional protection for the indoor environment of a hospital or healthcare facility, including in particular patients who may be immunocompromised. Current design standards and references do not require the installation of a back draft damper, but evaluation of adding language to relevant building codes should be considered. The data indicate a reduction in levels of Penicillium/Aspergillus -like spores, particle counts and a reduction in relative humidity inside of the elevator shaft after damper installation.^