New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

Physician adoption of a practice guideline: Effect on the cost of medical care for adult patients with diabetes

In the demanding environment of healthcare reform, reduction of unwanted physician practice variation is promoted, often through evidence-based guidelines. Guidelines represent innovations that direct change(s) in physician practice; however, compliance has been disappointing. Numerous studies have analyzed guideline development and dissemination, while few have evaluated the consequences of guideline adoption. The primary purpose of this study was to explore and analyze the relationship between physician adoption of the glycated hemoglobin test guideline for management of adult patients with diabetes, and the cost of medical care. The study also examined six personal and organizational characteristics of physicians and their association with innovativeness, or adoption of the guideline. ^ Cost was represented by approved charges from a managed care claims database. Total cost, and diabetes and related complications cost, first were compared for all patients of adopter physicians with those of non-adopter physicians. Then, data were analyzed controlling for disease severity based on insulin dependency, and for high cost cases. There was no statistically significant difference in any of eight cost categories analyzed. This study represented a twelve-month period, and did not reflect cost associated with future complications known to result from inadequate management of glycemia. Guideline compliance did not increase annual cost, which, combined with the future benefit of glycemic control, lends support to the cost effectiveness of the guideline in the long term. Physician adoption of the guideline was recommended to reduce the future personal and economic burden of this chronic disease. ^ Only half of physicians studied had adopted the glycated hemoglobin test guideline for at least 75% of their diabetic patients. No statistically significant relationship was found between any physician characteristic and guideline adoption. Instead, it was likely that the innovation-decision process and guideline dissemination methods were most influential. ^ A multidisciplinary, multi-faceted approach, including interventions for each stage of the innovation-decision process, was proposed to diffuse practice guidelines more effectively. Further, it was recommended that Organized Delivery Systems expand existing administrative databases to include clinical information, decision support systems, and reminder mechanisms, to promote and support physician compliance with this and other evidence-based guidelines. ^

Multiple imputation for missing continuous and dichotomous data: The effects of patterns of missingness and variable correlations on type I error with small samples

The purpose of this study is to investigate the effects of predictor variable correlations and patterns of missingness with dichotomous and/or continuous data in small samples when missing data is multiply imputed. Missing data of predictor variables is multiply imputed under three different multivariate models: the multivariate normal model for continuous data, the multinomial model for dichotomous data and the general location model for mixed dichotomous and continuous data. Subsequent to the multiple imputation process, Type I error rates of the regression coefficients obtained with logistic regression analysis are estimated under various conditions of correlation structure, sample size, type of data and patterns of missing data. The distributional properties of average mean, variance and correlations among the predictor variables are assessed after the multiple imputation process. ^ For continuous predictor data under the multivariate normal model, Type I error rates are generally within the nominal values with samples of size n = 100. Smaller samples of size n = 50 resulted in more conservative estimates (i.e., lower than the nominal value). Correlation and variance estimates of the original data are retained after multiple imputation with less than 50% missing continuous predictor data. For dichotomous predictor data under the multinomial model, Type I error rates are generally conservative, which in part is due to the sparseness of the data. The correlation structure for the predictor variables is not well retained on multiply-imputed data from small samples with more than 50% missing data with this model. For mixed continuous and dichotomous predictor data, the results are similar to those found under the multivariate normal model for continuous data and under the multinomial model for dichotomous data. With all data types, a fully-observed variable included with variables subject to missingness in the multiple imputation process and subsequent statistical analysis provided liberal (larger than nominal values) Type I error rates under a specific pattern of missing data. It is suggested that future studies focus on the effects of multiple imputation in multivariate settings with more realistic data characteristics and a variety of multivariate analyses, assessing both Type I error and power. ^

An international assessment of the comprehensibility of material safety data sheets (MSDSs)

Material Safety Data Sheets (MSDSs) are an integral component of occupational hazard communication systems. These documents are used to disseminate hazard information to workers on chemical substances. The primary purpose of this study was to investigate the comprehensibility of MSDSs by workers at an international level. ^ A total of 117 employees of a multi-national petrochemical company participated; thirty-nine (39) each in the United States, Canada and the United Kingdom. Overall participation rate of those approached to participate was 82%. These countries were selected as they each utilize one of the three major existing hazard communication systems for fixed workplaces. The systems are comprised of the Occupational Safety and Health Administration's Hazard Communication Standard in the United States, the Workplace Hazardous Materials Information System (WHMIS) in Canada, and the compilation of several European Union directives addressing classification, labeling of substances and preparations, and MSDSs in Europe. ^ A pretest posttest randomized study design was used, with the posttest being comparable to an open book test. The results of this research indicated that only about two-thirds of the information on the MSDSs was comprehended by the workers with a significant difference identified among study participants based on country comparisons. This data was fairly consistent with the results of previous MSDS comprehensibility studies conducted in the United States. There was no significant difference in the comprehension level among study participants when taking into account the international hazard communication standard that the MSDS complied with. Marginally, age, education level and experience level did not have a significant impact on the comprehension level. ^ Participants did find MSDSs to be satisfactory in providing the information needed to protect them regardless of their views on the readability and formatting of MSDSs. The health-related information was the least comprehended as less than half of it was comprehended on the basis of the responses. The findings from this research suggest that there is much work needed yet to make MSDSs more comprehensible on a global basis, particularly regarding health-related information. ^

Bayesian joint modeling of longitudinal and survival data

The joint modeling of longitudinal and survival data is a new approach to many applications such as HIV, cancer vaccine trials and quality of life studies. There are recent developments of the methodologies with respect to each of the components of the joint model as well as statistical processes that link them together. Among these, second order polynomial random effect models and linear mixed effects models are the most commonly used for the longitudinal trajectory function. In this study, we first relax the parametric constraints for polynomial random effect models by using Dirichlet process priors, then three longitudinal markers rather than only one marker are considered in one joint model. Second, we use a linear mixed effect model for the longitudinal process in a joint model analyzing the three markers. In this research these methods were applied to the Primary Biliary Cirrhosis sequential data, which were collected from a clinical trial of primary biliary cirrhosis (PBC) of the liver. This trial was conducted between 1974 and 1984 at the Mayo Clinic. The effects of three longitudinal markers (1) Total Serum Bilirubin, (2) Serum Albumin and (3) Serum Glutamic-Oxaloacetic transaminase (SGOT) on patients' survival were investigated. Proportion of treatment effect will also be studied using the proposed joint modeling approaches. ^ Based on the results, we conclude that the proposed modeling approaches yield better fit to the data and give less biased parameter estimates for these trajectory functions than previous methods. Model fit is also improved after considering three longitudinal markers instead of one marker only. The results from analysis of proportion of treatment effects from these joint models indicate same conclusion as that from the final model of Fleming and Harrington (1991), which is Bilirubin and Albumin together has stronger impact in predicting patients' survival and as a surrogate endpoints for treatment. ^

Risk factors for Clostridium difficile nosocomial diarrhea in patients at the Michael E. Debakey Veterans Affairs Medical Center, Houston, Texas

Background. Clostridium difficile is the leading cause of hospital associated infectious diarrhea and colitis. About 3 million cases of Clostridium difficile diarrhea occur each year with an annual cost of $1 billion. ^ About 20% of patients acquire C. difficile during hospitalization. Infection with Clostridium difficile can result in serious complications, posing a threat to the patient's life. ^ Purpose. The aim of this research was to demonstrate the uniqueness in the characteristics of C. difficile positive nosocomial diarrhea cases compared with C. difficile negative nosocomial diarrhea controls admitted to a local hospital. ^ Methods. One hundred and ninety patients with a positive test and one hundred and ninety with a negative test for Clostridium difficile nosocomial diarrhea, selected from patients tested between January 1, 2002 and December 31, 2003, comprised the study population. Demographic and clinical data were collected from medical records. Logistic regression analyses were conducted to determine the associated odds between selected variables and the outcome of Clostridium difficile nosocomial diarrhea. ^ Results. For the antibiotic classes, cephalosporins (OR, 1.87; CI 95, 1.23 to 2.85), penicillins (OR, 1.57; CI 95, 1.04 to 2.37), fluoroquinolones (OR, 1.65; CI 95, 1.09 to 2.48) and antifungals (OR, 2.17; CI 95, 1.20 to 3.94), were significantly associated with Clostridium difficile nosocomial diarrhea Ceftazidime (OR, 1.95; CI 95, 1.25 to 3.03, p=0.003), gatifloxacin (OR, 1.97; CI 95, 1.31 to 2.97, p=0.001), clindamycin (OR, 3.13; CI 95, 1.99 to 4.93, p<0.001) and vancomycin (OR, 1.77; CI 95, 1.18 to 2.66, p=0.006, were also significantly associated with the disease. Vancomycin was not statistically significant when analyzed in a multivariable model. Other significantly associated drugs were, antacids, laxatives, narcotics and ranitidine. Prolong use of antibiotics and an increased number of comorbid conditions were also associated with C. difficile nosocomial diarrhea. ^ Conclusion. The etiology for C. difficile diarrhea is multifactorial. Exposure to antibiotics and other drugs, prolonged antibiotic usage, the presence and severity of comorbid conditions and prolonged hospital stay were shown to contribute to the development of the disease. It is imperative that any attempt to prevent the disease, or contain its spread, be done on several fronts. ^

Physician's adherence to the standard protocol for diabetes treatment in Brooke Army Medical Center (BAMC)

The level of compliance with clinical practice guidelines for patients with Type II Diabetes Mellitus was evaluated in 157 patients treated at BAMC from 1 January 2006 to 1 January 2007. This retrospective analysis was conducted reviewing data from medical records and following the VA/DOD protocols that health care providers are expected to follow at this facility. Data collected included patient’s age and gender, presence or absence of complications of diabetes, physical examination findings, glycemic and lipid control, eye care, foot care, kidney function, and self-management and education. Subjects were selected performing systematic random sampling, and included both male and female patients, from a variety of ages and ethnic groups. The Diabetes complications screened for included glycemic and lipid complications, retinopathy, cardiovascular complications, peripheral circulation complications, and nephropathy. The results revealed that 19.10% had no complications and that the most common complications were: cardiovascular (49.68%), glycemic and lipid control (10.82%), retinopathy and peripheral circulation (8.28% each), and nephropathy (2.54%). Only 2.54% of the records reviewed did not include information on complications. Strictly following the Department of Defense guidelines, six treatment modules were evaluated independently and together to get a final percentage of adherence to the clinical practice guidelines. It was established that the level of adherence was going to be graded as follows: Extremely deficient: 0-15%; very poor: 16-30%; Poor and in need of improvement: 31-45%. Acceptable: 46-60%; Good: 61-80%, and Excellent: 81-100%. The results indicated that the percentage of physicians' adherence to each protocol was as follows: 88.31%, 89.93%, 90.63%, 89.42%, 89.42% and 89.64%. When the results were pooled, the level of adherence to the clinical practice guidelines was 89.55%, proving my hypothesis that Brooke Army Medical Center physicians have excellent adherence to the standard protocols for Diabetes Type II to treat their patients. ^

Trends in health information seeking among cancer and non-cancer adults between 2003 and 2005: A descriptive analysis of Health Information National Trends Survey (HINTS) data

Cancer is the second leading cause of death in the United States. With the advent of new technologies, changes in health care delivery, and multiplicity of provider types that patients must see, cancer care management has become increasingly complex. The availability of cancer health information has been shown to help cancer patients cope with the management and effects of their cancers. As a result, more cancer patients are using the internet to find resources that can aid in decision-making and recovery. ^ The Health Information National Trends Survey (HINTS) is a nationally representative survey designed to collect information about the experiences of cancer and non-cancer adults with health information sources. The HINTS survey focused on both conventional sources as well as newer technologies, particularly the internet. This study is a descriptive analysis of the HINTS 2003 and HINTS 2005 survey data. The purpose of the research is to explore the general trends in health information seeking and use by US adults, and especially by cancer patients. ^ From 2003 to 2005, internet use for various health-related activities appears to have increased among adults with and without cancer. Differences were found between the groups in the general trust in information media, particularly the internet. Non-cancer respondents tended to have greater trust in information media than cancer respondents. ^ The latter portion of this work examined characteristics of HINTS respondents that were thought to be relevant to how much trust individuals placed in the internet as a source of health information. Trust in health information from the internet was significantly greater among younger adults, higher-earning households, internet users, online seekers of health or cancer information, and those who found online cancer information useful. ^

The relationship between risk perception and ethnicity as an explanation for late stage skin cancer diagnosis in Black and Hispanic populations: An analysis using data from the 2005 Health Information and National Trends Survey

Objective. The purpose of this study was to determine the relationship between ethnicity and skin cancer risk perception while controlling for other risk factors: education, gender, age, access to healthcare, family history of skin cancer, fear, and worry. ^ Methods. This study utilized the Health Information National Trends Survey (HINTS) dataset, a nationally representative sample of 5,586 individuals 18 years of age or older. One third of the respondents were chosen at random and asked questions involving skin cancer. Analysis was based on questions that identified skin cancer risk perception, fear of finding skin cancer, and frequency of worry about skin cancer and a variety of sociodemographic factors. ^ Results. Ethnicity had a significant impact on risk perception scores while controlling for other risk factors. Other risk factors that also had a significant impact on risk perception scores included family history of skin cancer, age, and worry. ^

Estimating parameters in Markov models for longitudinal studies with missing data or surrogate outcomes

The discrete-time Markov chain is commonly used in describing changes of health states for chronic diseases in a longitudinal study. Statistical inferences on comparing treatment effects or on finding determinants of disease progression usually require estimation of transition probabilities. In many situations when the outcome data have some missing observations or the variable of interest (called a latent variable) can not be measured directly, the estimation of transition probabilities becomes more complicated. In the latter case, a surrogate variable that is easier to access and can gauge the characteristics of the latent one is usually used for data analysis. ^ This dissertation research proposes methods to analyze longitudinal data (1) that have categorical outcome with missing observations or (2) that use complete or incomplete surrogate observations to analyze the categorical latent outcome. For (1), different missing mechanisms were considered for empirical studies using methods that include EM algorithm, Monte Carlo EM and a procedure that is not a data augmentation method. For (2), the hidden Markov model with the forward-backward procedure was applied for parameter estimation. This method was also extended to cover the computation of standard errors. The proposed methods were demonstrated by the Schizophrenia example. The relevance of public health, the strength and limitations, and possible future research were also discussed. ^

Outcome-based adaptive randomization for binary data in clinical trials---Compare and contrast

Monte Carlo simulation has been conducted to investigate parameter estimation and hypothesis testing in some well known adaptive randomization procedures. The four urn models studied are Randomized Play-the-Winner (RPW), Randomized Pôlya Urn (RPU), Birth and Death Urn with Immigration (BDUI), and Drop-the-Loses Urn (DL). Two sequential estimation methods, the sequential maximum likelihood estimation (SMLE) and the doubly adaptive biased coin design (DABC), are simulated at three optimal allocation targets that minimize the expected number of failures under the assumption of constant variance of simple difference (RSIHR), relative risk (ORR), and odds ratio (OOR) respectively. Log likelihood ratio test and three Wald-type tests (simple difference, log of relative risk, log of odds ratio) are compared in different adaptive procedures. ^ Simulation results indicates that although RPW is slightly better in assigning more patients to the superior treatment, the DL method is considerably less variable and the test statistics have better normality. When compared with SMLE, DABC has slightly higher overall response rate with lower variance, but has larger bias and variance in parameter estimation. Additionally, the test statistics in SMLE have better normality and lower type I error rate, and the power of hypothesis testing is more comparable with the equal randomization. Usually, RSIHR has the highest power among the 3 optimal allocation ratios. However, the ORR allocation has better power and lower type I error rate when the log of relative risk is the test statistics. The number of expected failures in ORR is smaller than RSIHR. It is also shown that the simple difference of response rates has the worst normality among all 4 test statistics. The power of hypothesis test is always inflated when simple difference is used. On the other hand, the normality of the log likelihood ratio test statistics is robust against the change of adaptive randomization procedures. ^

Diagnosis of sexually transmitted infections in developing nations using syndromic management: Is it working?

Sexually transmitted infections (STIs) are a major public health problem, and controlling their spread is a priority. According to the World Health Organization (WHO), there are 340 million new cases of treatable STIs among 15–49 year olds that occur yearly around the world (1). Infection with STIs can lead to several complications such as pelvic inflammatory disorder (PID), cervical cancer, infertility, ectopic pregnancy, and even death (1). Additionally, STIs and associated complications are among the top disease types for which healthcare is sought in developing nations (1), and according to the UNAIDS report, there is a strong connection between STIs and the sexual spread of HIV infection (2). In fact, it is estimated that the presence of an untreated STI can increase the likelihood of contracting and spreading HIV by a factor up to 10 (2). In addition, developing countries are poorer in resources and lack inexpensive and precise diagnostic laboratory tests for STIs, thereby exacerbating the problem. Thus, the WHO recommends syndromic management of STIs for delivering care where lab testing is scarce or unattainable (1). This approach utilizes the use of an easy to use algorithm to help healthcare workers recognize symptoms/signs so as to provide treatment for the likely cause of the syndrome. Furthermore, according to the WHO, syndromic management offers instant and legitimate treatment compared to clinical diagnosis, and that it is also more cost-effective for some syndromes over the use of laboratory testing (1). In addition, even though it has been shown that the vaginal discharge syndrome has low specificity for gonorrhea and Chlamydia and can lead to over treatment (1), this is the recommended way to manage STIs in developing nations. Thus, the purpose of this paper is to specifically address the following questions: is syndromic management working to lower the STI burden in developing nations? How effective is it, and should it still be recommended? To answer these questions, a systematic literature review was conducted to evaluate the current effectiveness of syndromic management in developing nations. This review examined published articles over the past 5 years that compared syndromic management to laboratory testing and had published sensitivity, specificity, and positive predicative value data. Focusing mainly on vaginal discharge, urethral discharge, and genital ulcer algorithms, it was seen that though syndromic management is more effective in diagnosing and treating urethral and genial ulcer syndromes in men, there still remains an urgent need to revise the WHO recommendations for managing STIs in developing nations. Current studies have continued to show decreased specificity, sensitivity and positive predicative values for the vaginal discharge syndrome, and high rates of asymptomatic infections and healthcare workers neglecting to follow guidelines limit the usefulness of syndromic management. Furthermore, though advocate d as cost-effective by the WHO, there is a cost incurred from treating uninfected people. Instead of improving this system, it is recommended that better and less expensive point of care and the development of rapid test diagnosis kits be the focus and method of diagnosis and treatment in developing nations for STI management. ^

Disparities in medical expenditure and utilization among hypertensive men and women in the U.S.: Cross-section and lifetime analysis

Objectives. To investigate procedural gender equity by assessing predisposing, enabling and need predictors of gender differences in annual medical expenditures and utilization among hypertensive individuals in the U.S. Also, to estimate and compare lifetime medical expenditures among hypertensive men and women in the U.S. ^ Data source. 2001-2004 the Medical Expenditure Panel Survey (MEPS);1986-2000 National Health Interview Survey (NHIS) and National Health Interview Survey linked to mortality in the National Death Index through 2002 (2002 NHIS-NDI). ^ Study design. We estimated total medical expenditure using four equations regression model, specific medical expenditures using two equations regression model and utilization using negative binomial regression model. Procedural equity was assessed by applying the Aday et al. theoretical framework. Expenditures were estimated in 2004 dollars. We estimated hypertension-attributable medical expenditure and utilization among men and women. ^ To estimate lifetime expenditures from ages 20 to 85+, we estimated medical expenditures with cross-sectional data and survival with prospective data. The four equations regression model were used to estimate average annual medical expenditures defined as sum of inpatient stay, emergency room visits, outpatient visits, office based visits, and prescription drugs expenditures. Life tables were used to estimate the distribution of life time medical expenditures for hypertensive men and women at different age and factors such as disease incidence, medical technology and health care cost were assumed to be fixed. Both total and hypertension attributable expenditures among men and women were estimated. ^ Data collection. We used the 2001-2004 MEPS household component and medical condition files; the NHIS person and condition files from 1986-1996 and 1997-2000 sample adult files were used; and the 1986-2000 NHIS that were linked to mortality in the 2002 NHIS-NDI. ^ Principal findings. Hypertensive men had significantly less utilization for most measures after controlling predisposing, enabling and need factors than hypertensive women. Similarly, hypertensive men had less prescription drug (-9.3%), office based (-7.2%) and total medical (-4.5%) expenditures than hypertensive women. However, men had more hypertension-attributable medical expenditures and utilization than women. ^ Expected total lifetime expenditure for average life table individuals at age 20, was $188,300 for hypertensive men and $254,910 for hypertensive women. But the lifetime expenditure that could be attributed to hypertension was $88,033 for men and $40,960 for women. ^ Conclusion. Hypertensive women had more utilization and expenditure for most measures than hypertensive men, possibly indicating procedural inequity. However, relatively higher hypertension-attributable health care of men shows more utilization of resources to treat hypertension related diseases among men than women. Similar results were reported in lifetime analyses.^ Key words: gender, medical expenditures, utilization, hypertension-attributable, lifetime expenditure ^

Evaluation of therapist and client language in Motivational Interviewing (MI) sessions: A secondary analysis of data from the Southern Methodist Alcohol Research Trial (SMART) study

In the United States, “binge” drinking among college students is an emerging public health concern due to the significant physical and psychological effects on young adults. The focus is on identifying interventions that can help decrease high-risk drinking behavior among this group of drinkers. One such intervention is Motivational interviewing (MI), a client-centered therapy that aims at resolving client ambivalence by developing discrepancy and engaging the client in change talk. Of late, there is a growing interest in determining the active ingredients that influence the alliance between the therapist and the client. This study is a secondary analysis of the data obtained from the Southern Methodist Alcohol Research Trial (SMART) project, a dismantling trial of MI and feedback among heavy drinking college students. The present project examines the relationship between therapist and client language in MI sessions on a sample of “binge” drinking college students. Of the 126 SMART tapes, 30 tapes (‘MI with feedback’ group = 15, ‘MI only’ group = 15) were randomly selected for this study. MISC 2.1, a mutually exclusive and exhaustive coding system, was used to code the audio/videotaped MI sessions. Therapist and client language were analyzed for communication characteristics. Overall, therapists adopted a MI consistent style and clients were found to engage in change talk. Counselor acceptance, empathy, spirit, and complex reflections were all significantly related to client change talk (p-values ranged from 0.001 to 0.047). Additionally, therapist ‘advice without permission’ and MI Inconsistent therapist behaviors were strongly correlated with client sustain talk (p-values ranged from 0.006 to 0.048). Simple linear regression models showed a significant correlation between MI consistent (MICO) therapist language (independent variable) and change talk (dependent variable) and MI inconsistent (MIIN) therapist language (independent variable) and sustain talk (dependent variable). The study has several limitations such as small sample size, self-selection bias, poor inter-rater reliability for the global scales and the lack of a temporal measure of therapist and client language. Future studies might consider a larger sample size to obtain more statistical power. In addition the correlation between therapist language, client language and drinking outcome needs to be explored.^

Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^