Digital Commons Network^™

Phylogenetic Search Through Partial Tree Mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith Crandall

Computational Biology Institute

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

CONCLUSIONS: The use of Partial Tree Mixing …

Examining Fatigue In Copd: Development, Validity And Reliability Of A Modified Version Of Facit-F Scale, Khaled Al-Shair, Hana Muellerova, Janelle Yorke, Stephen I. Rennard, Emiel F.M. Wouters, Nicola A. Hanania, Amir Sharafkhaneh, Jørgen Vestbo, Eclipse Investigators

Journal Articles: Pulmonary & Critical Care Med

INTRODUCTION: Fatigue is a disruptive symptom that inhibits normal functional performance of COPD patients in daily activities. The availability of a short, simple, reliable and valid scale would improve assessment of the characteristics and influence of fatigue in COPD.

METHODS: At baseline, 2107 COPD patients from the ECLIPSE cohort completed the Functional Assessment of Chronic Illness Therapy Fatigue (FACIT-F) scale. We used well-structured classic method, the principal components analysis (PCA) and Rasch analysis for structurally examining the 13-item FACIT-F.

RESULTS: Four items were less able to capture fatigue characteristics in COPD and were deleted. PCA was applied to the remaining …

Discriminating Famous From Fictional Names Based On Lifetime Experience: Evidence In Support Of A Signal-Detection Model Based On Finite Mixture Distributions., Ben Bowles, Iain M Harlow, Melissa M Meeking, Stefan Köhler

Brain and Mind Institute Researchers' Publications

It is widely accepted that signal-detection mechanisms contribute to item-recognition memory decisions that involve discriminations between targets and lures based on a controlled laboratory study episode. Here, the authors employed mathematical modeling of receiver operating characteristics (ROC) to determine whether and how a signal-detection mechanism contributes to discriminations between moderately famous and fictional names based on lifetime experience. Unique to fame judgments is a lack of control over participants' previous exposure to the stimuli deemed "targets" by the experimenter; specifically, if they pertain to moderately famous individuals, participants may have had no prior exposure to a substantial proportion of the …

Dimerization And Heme Binding Are Conserved In Amphibian And Starfish Homologues Of The Microrna Processing Protein Dgcr8., Rachel Senturia, Arthur Laganowsky, Ian Barr, Brooke D. Scheidemantle, Feng Guo

Natural Sciences and Mathematics | Faculty Scholarship

Human DiGeorge Critical Region 8 (DGCR8) is an essential microRNA (miRNA) processing factor that is activated via direct interaction with Fe(III) heme. In order for DGCR8 to bind heme, it must dimerize using a dimerization domain embedded within its heme-binding domain (HBD). We previously reported a crystal structure of the dimerization domain from human DGCR8, which demonstrated how dimerization results in the formation of a surface important for association with heme. Here, in an attempt to crystallize the HBD, we search for DGCR8 homologues and show that DGCR8 from Patiria miniata (bat star) also binds heme. The extinction coefficients (ε) …

Intense Physical Activity Is Associated With Cognitive Performance In The Elderly, Belinda Brown, Jeremiah Peiffer, Hamid Sohrabi, Alinda Mondal, Veer Bala Gupta, Stephanie Rainey-Smith, Kevin Taddei, S Burnham, K Ellis, C Szoeke, C L Masters, D Ames, C Rowe, Ralph Martins

Research outputs 2012

Numerous studies have reported positive impacts of physical activity on cognitive function. However, the majority of these studies have utilised physical activity questionnaires or surveys, thus results may have been influenced by reporting biases. Through the objective measurement of routine levels of physical activity via actigraphy, we report a significant association between intensity, but not volume, of physical activity and cognitive functioning. A cohort of 217 participants (aged 60-89 years) wore an actigraphy unit for 7 consecutive days and underwent comprehensive neuropsychological assessment. The cohort was stratified into tertiles based on physical activity intensity. Compared with individuals in the lowest …

Nutrition, Inflammation, And Infectious Disease, Helieh S. Oz, Sung-Ling Yeh

Physiology Faculty Publications

No abstract provided.

Pegylated Arginine Deiminase Downregulates Colitis In Murine Models, Helieh S. Oz, Jian Zhong, Willem J. S. De Villiers

Physiology Faculty Publications

Arginine deiminase (ADI), an arginine-metabolizing enzyme involved in cell signaling, is dysregulated in multiple inflammatory diseases and cancers. We hypothesized that pegylated ADI (ADI-PEG) provide protection against colitis.

METHODS: Dextran sodium sulfate colitis was induced in IL-10-deficient and BALB/c (WT) mice. ADI-PEG was administered i.p., and inflammatory mediators and pathology were evaluated.

RESULTS: Acute colitis in mice was manifested by increases in inflammatory biomarkers, such as serum amyloid A (SAA, P < 0.001), IL-12 p40, and disease index (3-Fold). In contrast, ADI-PEG significantly decreased clinical disease index, SAA levels, and inflammatory cytokines in blood as well as in colonic explants. Animals developed moderate (2.2 ± 0.3 WT) to severe (3.6 ± 0.5 IL-10 deficient) colonic pathology; and ADI-PEG treatment significantly improved the severity of colitis (P < 0.05). Marked infiltration of CD68+ macrophages and iNOS expression were detected in colonic submucosa in colitic animals but not detected in ADI-PEG-treated animals.

CONCLUSION: ADI-PEG attenuated inflammatory responses by suppression of macrophage infiltration and iNOS expression in colitic animals. ADI-PEG can serve as a potential therapeutic value in IBD.

Associations Of Cardiorespiratory Fitness And Fatness With Metabolic Syndrome In Rural Women With Prehypertension., Patricia A. Hageman, Carol H. Pullen, Melody A. Hertzog, Linda S. Boeckner, Susan Noble Walker

Journal Articles: Physical Therapy

BACKGROUND: This study investigated the associations of fitness and fatness with metabolic syndrome in rural women, part of a recognized US health disparities group.

METHODS: Fitness, percentage body fat, BMI, and metabolic syndrome criteria were assessed at baseline in 289 rural women with prehypertension, ages 40-69, enrolled in a healthy eating and activity community-based clinical trial for reducing blood pressure.

RESULTS: Ninety (31%) women had metabolic syndrome, of which 70% were obese by BMI (≥30 kg/m²), 100% by percentage body fat (≥30%), and 100% by revised BMI standards (≥25 kg/m²) cited in current literature. Hierarchical logistic regression models, adjusted for …

Genes Adopt Non-Optimal Codon Usage To Generate Cell Cycle-Dependent Oscillations In Protein Levels., Milana Frenkel-Morgenstern, Tamar Danon, Thomas Christian, Takao Igarashi, Lydia Cohen, Ya-Ming Hou, Lars Juhl Jensen

Department of Biochemistry and Molecular Biology Faculty Papers

The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle at the protein level exhibit non-optimal codon preferences. Remarkably, cell cycle-regulated genes expressed in different phases display different codon preferences. Here, we show empirically that transfer RNA (tRNA) expression is indeed highest in the G2 phase of the cell cycle, consistent with the non-optimal codon usage of genes expressed at this time, and lowest …

Use Of A Clay Modeling Task To Reduce Chocolate Craving., Jackie Andrade, Sally Pears, Jon May, David J. Kavanagh

School of Psychology

Elaborated Intrusion theory (EI theory; Kavanagh, Andrade, & May, 2005) posits two main cognitive components in craving: associative processes that lead to intrusive thoughts about the craved substance or activity, and elaborative processes supporting mental imagery of the substance or activity. We used a novel visuospatial task to test the hypothesis that visual imagery plays a key role in craving. Experiment 1 showed that spending 10 min constructing shapes from modeling clay (plasticine) reduced participants' craving for chocolate compared with spending 10 min 'letting your mind wander'. Increasing the load on verbal working memory using a mental arithmetic task (counting …

Emergence Of Bimodal Cell Population Responses From The Interplay Between Analog Single-Cell Signaling And Protein Expression Noise., Marc R Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzyński, Jan B. Hoek, Walter Kolch, Babatunde A Ogunnaike, Boris N Kholodenko

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Cell-to-cell variability in protein expression can be large, and its propagation through signaling networks affects biological outcomes. Here, we apply deterministic and probabilistic models and biochemical measurements to study how network topologies and cell-to-cell protein abundance variations interact to shape signaling responses.

RESULTS: We observe bimodal distributions of extracellular signal-regulated kinase (ERK) responses to epidermal growth factor (EGF) stimulation, which are generally thought to indicate bistable or ultrasensitive signaling behavior in single cells. Surprisingly, we find that a simple MAPK/ERK-cascade model with negative feedback that displays graded, analog ERK responses at a single cell level can explain the experimentally …

Partition Decoupling For Multi-Gene Analysis Of Gene Expression Profiling Data, Rosemary Braun, Gregory Leibon, Scott Pauls, Daniel Rockmore

Dartmouth Scholarship

Background:

Multi-gene interactions likely play an important role in the development of complex phenotypes, and relationships between interacting genes pose a challenging statistical problem in microarray analysis, since the genes involved in these interactions may not exhibit marginal differential expression. As a result, it is necessary to develop tools that can identify sets of interacting genes that discriminate phenotypes without requiring that the classification boundary between phenotypes be convex.

Results:

We describe an extension and application of a new unsupervised statistical learning technique, known as the Partition Decoupling Method (PDM), to gene expression microarray data. This method may be used …

A Perceptual Metric For Photo Retouching, Eric Kee, Hany Farid

Dartmouth Scholarship

In recent years, advertisers and magazine editors have been widely criticized for taking digital photo retouching to an extreme. Impossibly thin, tall, and wrinkle- and blemish-free models are routinely splashed onto billboards, advertisements, and magazine covers. The ubiquity of these unrealistic and highly idealized images has been linked to eating disorders and body image dissatisfaction in men, women, and children. In response, several countries have considered legislating the labeling of retouched photos. We describe a quantitative and perceptually meaningful metric of photo retouching. Photographs are rated on the degree to which they have been digitally altered by explicitly modeling and …

Switches, Excitable Responses And Oscillations In The Ring1b/Bmi1 Ubiquitination System., Lan K Nguyen, Javier Muñoz-García, Helene Maccario, Aaron Ciechanover, Walter Kolch, Boris N Kholodenko

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

In an active, self-ubiquitinated state, the Ring1B ligase monoubiquitinates histone H2A playing a critical role in Polycomb-mediated gene silencing. Following ubiquitination by external ligases, Ring1B is targeted for proteosomal degradation. Using biochemical data and computational modeling, we show that the Ring1B ligase can exhibit abrupt switches, overshoot transitions and self-perpetuating oscillations between its distinct ubiquitination and activity states. These different Ring1B states display canonical or multiply branched, atypical polyubiquitin chains and involve association with the Polycomb-group protein Bmi1. Bistable switches and oscillations may lead to all-or-none histone H2A monoubiquitination rates and result in discrete periods of gene (in)activity. Switches, overshoots …

Non-Geometric Echocardiographic Indices Of Ventricular Function In Patients With A Fontan Circulation., Jonathan Rhodes, Renee Margossian, Lynn A. Sleeper, Piers Barker, Timothy J. Bradley, Minmin Lu, Mark Fogel, Matthew A. Harris, Wyman W. Lai, Andrew J. Powell, Michael D. Puchalski, Girish S. Shirali, Steven D. Colan, Pediatric Heart Network Investigators

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Complex anatomy and limited windows complicate echocardiographic assessments of ventricular function in Fontan patients. For the Pediatric Heart Network Fontan Cross-Sectional Study, data were acquired from which mean ventricular pressure change during isovolumetric contraction (dP/dt(ic)), Tei index, and maximal systolic annular velocity (S') could be measured. The purpose of this study was to compare these nongeometric indices of ventricular function to cardiac magnetic resonance (CMR) measurements of ventricular ejection fraction (EF).

METHODS: Echocardiographic and CMR studies were performed prospectively using standardized protocols; measurements were completed by core laboratories. Data from both modalities were available from 137 patients.

RESULTS: A …

An Engineered Approach To Stem Cell Culture: Automating The Decision Process For Real-Time Adaptive Subculture Of Stem Cells, Dai Fei Elmer Ker, Lee E. Weiss, Silvina N. Junkers, Mei Chen, Zhaozheng Yin, Mike F. Sandbothe, Seungil Huh, Sungeun Eom, Ryoma Bise, Elvira Osuna-Highley, Takeo Kanade, Phil Gordon Campbell

Computer Science Faculty Research & Creative Works

Current cell culture practices are dependent upon human operators and remain laborious and highly subjective, resulting in large variations and inconsistent outcomes, especially when using visual assessments of cell confluency to determine the appropriate time to subculture cells. Although efforts to automate cell culture with robotic systems are underway, the majority of such systems still require human intervention to determine when to subculture. Thus, it is necessary to accurately and objectively determine the appropriate time for cell passaging. Optimal stem cell culturing that maintains cell pluripotency while maximizing cell yields will be especially important for efficient, cost-effective stem cell-based therapies. …

Combined Fluorescence And Reflectance Spectroscopy For In Vivo Quantification Of Cancer Biomarkers In Low- And High-Grade Glioma Surgery, Pablo A. ValdéS, Anthony Kim, Keith D. Paulsen, Frederic Leblond, Olga M. Conde, Brent T. Harris, David W. Roberts

Dartmouth Scholarship

Biomarkers are indicators of biological processes and hold promise for the diagnosis and treatment of disease. Gliomas represent a heterogeneous group of brain tumors with marked intra- and inter-tumor variability. The extent of surgical resection is a significant factor influencing post-surgical recurrence and prognosis. Here, we used fluorescence and reflectance spectral signatures for in vivo quantification of multiple biomarkers during glioma surgery, with fluorescence contrast provided by exogenously-induced protoporphyrin IX (PpIX) following administration of 5-aminolevulinic acid. We performed light-transport modeling to quantify multiple biomarkers indicative of tumor biological processes, including the local concentration of PpIX and associated photoproducts, total hemoglobin …

Microarray-Based Cancer Prediction Using Single Genes., Xiaosheng Wang, Richard Simon

Journal Articles: Genetics, Cell Biology & Anatomy

BACKGROUND: Although numerous methods of using microarray data analysis for cancer classification have been proposed, most utilize many genes to achieve accurate classification. This can hamper interpretability of the models and ease of translation to other assay platforms. We explored the use of single genes to construct classification models. We first identified the genes with the most powerful univariate class discrimination ability and then constructed simple classification rules for class prediction using the single genes.

RESULTS: We applied our model development algorithm to eleven cancer gene expression datasets and compared classification accuracy to that for standard methods including Diagonal Linear …

Rna Oxidation Adducts 8-Ohg And 8-Oha Change With Aβ42 Levels In Late-Stage Alzheimer's Disease, Adam M. Weidner, Melissa A. Bradley, Tina L. Beckett, Dana M. Niedowicz, Amy L.S. Dowling, Sergey V. Matveev, Harry Levine, Mark A. Lovell, M. Paul Murphy

Sanders-Brown Center on Aging Faculty Publications

While research supports amyloid-β (Aβ) as the etiologic agent of Alzheimer's disease (AD), the mechanism of action remains unclear. Evidence indicates that adducts of RNA caused by oxidation also represent an early phenomenon in AD. It is currently unknown what type of influence these two observations have on each other, if any. We quantified five RNA adducts by gas chromatography/mass spectroscopy across five brain regions from AD cases and age-matched controls. We then used a reductive directed analysis to compare the RNA adducts to common indices of AD neuropathology and various pools of Aβ. Using data from four disease-affected brain …

No Evidence Of Association Between Hiv-1 And Malaria In Populations With Low Hiv-1 Prevalence, Diego F. Cuadros, Adam J. Branscum, Gisela García-Ramos

Biology Faculty Publications

BACKGROUND: The geographic overlap between HIV-1 and malaria has generated much interest in their potential interactions. A variety of studies have evidenced a complex HIV-malaria interaction within individuals and populations that may have dramatic effects, but the causes and implications of this co-infection at the population level are still unclear. In a previous publication, we showed that the prevalence of malaria caused by the parasite Plasmodium falciparum is associated with HIV infection in eastern sub-Saharan Africa. To complement our knowledge of the HIV-malaria co-infection, the objective of this work was to assess the relationship between malaria and HIV prevalence in …

Effect Of Variable Transmission Rate On The Dynamics Of Hiv In Sub-Saharan Africa, Diego F. Cuadros, Phillip H. Crowley, Ben Augustine, Sarah L. Stewart, Gisela García-Ramos

Biology Faculty Publications

BACKGROUND: The cause of the high HIV prevalence in sub-Saharan Africa is incompletely understood, with heterosexual penile-vaginal transmission proposed as the main mechanism. Heterosexual HIV transmission has been estimated to have a very low probability; but effects of cofactors that vary in space and time may substantially alter this pattern.

METHODS: To test the effect of individual variation in the HIV infectiousness generated by co-infection, we developed and analyzed a mathematical sexual network model that simulates the behavioral components of a population from Malawi, as well as the dynamics of HIV and the co-infection effect caused by other infectious diseases, …

Assessing Medicare Beneficiaries’ Strength‐Of‐Preference Scores For Health Care Options: How Engaging Does The Elicitation Technique Need To Be?, Trafford Crump, Hilary A. Llewellyn-Thomas

Dartmouth Scholarship

The objective was to determine if participants’ strength‐of‐preference scores for elective health care interventions at the end‐of‐life (EOL) elicited using a non‐engaging technique are affected by their prior use of an engaging elicitation technique.

Identification Of Factors Associated With Good Response To Growth Hormone Therapy In Children With Short Stature: Results From The Answer Program®., Peter A Lee, John Germak, Robert Gut, Naum Khutoryansky, Judith Ross

Department of Pediatrics Faculty Papers

UNLABELLED: ABSTRACT:

OBJECTIVE: To identify factors associated with growth in children on growth hormone (GH) therapy using data from the American Norditropin Studies: Web-enabled Research (ANSWER) Program® registry.

METHODS: GH-naïve children with GH deficiency, multiple pituitary hormone deficiency, idiopathic short stature, Turner syndrome, or a history of small for gestational age were eligible (N = 1,002). Using a longitudinal statistical approach, predictive factors were identified in patients with GHD for change from baseline in height standard deviation score (ΔHSDS) following 2 years of treatment.

RESULTS: Gradual increases in ΔHSDS over time were observed for all diagnostic categories. Significant predictive factors …

Digeorge Critical Region 8 (Dgcr8) Is A Double-Cysteine-Ligated Heme Protein., Ian Barr, Aaron T. Smith, Rachel Senturia, Yanqiu Chen, Brooke D. Scheidemantle, Judith N. Burstyn, Feng Guo

Natural Sciences and Mathematics | Faculty Scholarship

All known heme-thiolate proteins ligate the heme iron using one cysteine side chain. We previously found that DiGeorge Critical Region 8 (DGCR8), an essential microRNA processing factor, associates with heme of unknown redox state when overexpressed in Escherichia coli. On the basis of the similarity of the 450-nm Soret absorption peak of the DGCR8-heme complex to that of cytochrome P450 containing ferrous heme with CO bound, we identified cysteine 352 as a probable axial ligand in DGCR8. Here we further characterize the DGCR8-heme interaction using biochemical and spectroscopic methods. The DGCR8-heme complex is highly stable, with a half-life exceeding 4 …

Gene Expression In Cardiac Tissues From Infants With Idiopathic Conotruncal Defects., Douglas C. Bittel, Merlin G. Butler, Nataliya Kibiryeva, Jennifer A. Marshall, Jie Chen, Gary K. Lofland, James E. O'Brien

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Tetralogy of Fallot (TOF) is the most commonly observed conotruncal congenital heart defect. Treatment of these patients has evolved dramatically in the last few decades, yet a genetic explanation is lacking for the failure of cardiac development for the majority of children with TOF. Our goal was to perform genome wide analyses and characterize expression patterns in cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) obtained at the time of reconstructive surgery from 19 children with tetralogy of Fallot.

METHODS: We employed genome wide gene expression microarrays to characterize cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) …

Animal Models For Periodontal Disease, Helieh S. Oz, David A. Puleo

Center for Oral Health Research Faculty Publications

Animal models and cell cultures have contributed new knowledge in biological sciences, including periodontology. Although cultured cells can be used to study physiological processes that occur during the pathogenesis of periodontitis, the complex host response fundamentally responsible for this disease cannot be reproduced in vitro. Among the animal kingdom, rodents, rabbits, pigs, dogs, and nonhuman primates have been used to model human periodontitis, each with advantages and disadvantages. Periodontitis commonly has been induced by placing a bacterial plaque retentive ligature in the gingival sulcus around the molar teeth. In addition, alveolar bone loss has been induced by inoculation or …

Determinants Of Multimethod Contraceptive Use In A Sample Of Adolescent Women Diagnosed With Psychological Disorders, Delia L. Lang, Jessica M. Sales, Laura F. Salazar, Ralph J. Diclemente, Richard A. Crosby, Larry K. Brown, Geri R. Donenberg

Health, Behavior & Society Faculty Publications

OBJECTIVE: Despite recommendations for concurrent use of contraceptives and condoms to prevent unintended pregnancy and STIs, multimethod contraceptive use among women is poor. This study examined individual-, interpersonal-, and environmental-level factors that predict multimethod use among sexually active adolescent women diagnosed with psychological disorders.

METHODS: This multisite study analyzed data from 288 sexually active adolescent women who provided sociodemographic, psychosocial, and behavioral data related to birth control and condom use.

RESULTS: 34.7% of the participants reported multimethod use in the past three months. Controlling for empirically and theoretically relevant covariates, a multivariable logistic regression identified self-efficacy, multiple partners, pregnancy history, …

The Cardiac Atlas Project--An Imaging Database For Computational Modeling And Statistical Atlases Of The Heart, Carissa G. Fonseca, Michael Backhaus, David A. Bluemke, Randall D. Britten, Jae Do Chung, Brett R. Cowan, Alan H. Kadish

Office of the President Publications and Research

MOTIVATION: Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape …

Capturing Changes In Gene Expression Dynamics By Gene Set Differential Coordination Analysis, Tianwei Yu, Yun Bai

PCOM Scholarly Works

Analyzing gene expression data at the gene set level greatly improves feature extraction and data interpretation. Currently most efforts in gene set analysis are focused on differential expression analysis - finding gene sets whose genes show first-order relationship with the clinical outcome. However the regulation of the biological system is complex, and much of the change in gene expression dynamics do not manifest in the form of differential expression. At the gene set level, capturing the change in expression dynamics is difficult due to the complexity and heterogeneity of the gene sets. Here we report a systematic approach to detect …

Mitochondrial Genome Sequence Analysis: A Custom Bioinformatics Pipeline Substantially Improves Affymetrix Mitochip V2.0 Call Rate And Accuracy., Hongbo M Xie, Juan C Perin, Theodore G Schurr, Matthew C Dulik, Sergey I Zhadanov, Joseph A Baur, Michael P King, Emily Place, Colleen Clarke, Michael Grauer, Jonathan Schug, Avni Santani, Anthony Albano, Cecilia Kim, Vincent Procaccio, Hakon Hakonarson, Xiaowu Gai, Marni J Falk

Department of Biochemistry and Molecular Biology Faculty Papers

BACKGROUND: Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate …