The effect of algorithms on copy number variant detection

Background

The detection of copy number variants (CNVs) and the results of CNV-disease association studies rely on how CNVs are defined, and because array-based technologies can only infer CNVs, CNV-calling algorithms can produce vastly different findings. Several authors have noted the large-scale variability between CNV-detection methods, as well as the substantial false positive and false negative rates associated with those methods. In this study, we use variations of four common algorithms for CNV detection (PennCNV, QuantiSNP, HMMSeg, and cnvPartition) and two definitions of overlap (any overlap and an overlap of at least 40% of the smaller CNV) to illustrate the effects of varying algorithms and definitions of overlap on CNV discovery.

Methodology and Principal Findings

We used a 56 K Illumina genotyping array enriched for CNV regions to generate hybridization intensities and allele frequencies for 48 Caucasian schizophrenia cases and 48 age-, ethnicity-, and gender-matched control subjects. No algorithm found a difference in CNV burden between the two groups. However, the total number of CNVs called ranged from 102 to 3,765 across algorithms. The mean CNV size ranged from 46 kb to 787 kb, and the average number of CNVs per subject ranged from 1 to 39. The number of novel CNVs not previously reported in normal subjects ranged from 0 to 212.

Conclusions and Significance

Motivated by the availability of multiple publicly available genome-wide SNP arrays, investigators are conducting numerous analyses to identify putative additional CNVs in complex genetic disorders. However, the number of CNVs identified in array-based studies, and whether these CNVs are novel or valid, will depend on the algorithm(s) used. Thus, given the variety of methods used, there will be many false positives and false negatives. Both guidelines for the identification of CNVs inferred from high-density arrays and the establishment of a gold standard for validation of CNVs are needed.     

Engineering Antigen-Specific T Cells from Genetically Modified Human Hematopoietic Stem Cells in Immunodeficient Mice

There is a desperate need for effective therapies to fight chronic viral infections. The immune response is normally fastidious at controlling the majority of viral infections and a therapeutic strategy aimed at reestablishing immune control represents a potentially powerful approach towards treating persistent viral infections. We examined the potential of genetically programming human hematopoietic stem cells to generate mature CD8+ cytotoxic T lymphocytes that express a molecularly cloned, “transgenic” human anti-HIV T cell receptor (TCR). Anti-HIV TCR transduction of human hematopoietic stem cells directed the maturation of a large population of polyfunctional, HIV-specific CD8+ cells capable of recognizing and killing viral antigen-presenting cells. Thus, through this proof-of-concept we propose that genetic engineering of human hematopoietic stem cells will allow the tailoring of effector T cell responses to fight HIV infection or other diseases that are characterized by the loss of immune control.     

Pro-inflammatory Genes as Biomarkers and Therapeutic Targets in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is a major health problem worldwide, and patients have a particularly poor 5-year survival rate. Thus, identification of the molecular targets in OSCC and subsequent innovative therapies are greatly needed. Prolonged exposure to alcohol, tobacco, and pathogenic agents are known risk factors and have suggested that chronic inflammation may represent a potential common denominator in the development of OSCC. Microarray analysis of gene expression in OSCC cell lines with high basal NF-κB activity and OSCC patient samples identified dysregulation of many genes involved in inflammation, wound healing, angiogenesis, and growth regulation. In particular IL-8, CCL5, STAT1, and VEGF gene expression was up-regulated in OSCC. Moreover, IL-8 protein levels were significantly higher in OSCC cell lines as compared with normal human oral keratinocytes. Targeting IL-8 expression by siRNA significantly reduced the survival of OSCC cells, indicating that it plays an important role in OSCC development and/or progression. Inhibiting the inflammatory pathway by aspirin and the proteasome/NF-κB pathway by bortezomib resulted in marked reduction in cell viability in OSCC lines. Taken together our studies indicate a strong link between inflammation and OSCC development and reveal IL-8 as a potential mediator. Treatment based on prevention of general inflammation and/or the NF-κB pathway shows promise in OSCCs.     

Algebraic connectivity may explain the evolution of gene regulatory networks

Gene expression is a result of the interplay between the structure, type, kinetics, and specificity of gene regulatory interactions, whose diversity gives rise to the variety of life forms. As the dynamic behavior of gene regulatory networks depends on their structure, here we attempt to determine structural reasons which, despite the similarities in global network properties, may explain the large differences in organismal complexity. We demonstrate that the algebraic connectivity, the smallest non-trivial eigenvalue of the Laplacian, of the directed gene regulatory networks decreases with the increase of organismal complexity, and may therefore explain the difference between the variety of analyzed regulatory networks. In addition, our results point out that, for the species considered in this study, evolution favours decreasing concentration of strategically positioned feed forward loops, so that the network as a whole can increase the specificity towards changing environments. Moreover, contrary to the existing results, we show that the average degree, the length of the longest cascade, and the average cascade length of gene regulatory networks cannot recover the evolutionary relationships between organisms. Whereas the dynamical properties of special subnetworks are relatively well understood, there is still limited knowledge about the evolutionary reasons for the already identified design principles pertaining to these special subnetworks, underlying the global quantitative features of gene regulatory networks of different organisms. The behavior of the algebraic connectivity, which we show valid on gene regulatory networks extracted from curated databases, can serve as an additional evolutionary principle of organism-specific regulatory networks.     

Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase

The neurotoxin fasciculin-2 (FAS2) is a picomolar inhibitor of synaptic acetylcholinesterase (AChE). The dynamics of binding between FAS2 and AChE is influenced by conformational fluctuations both before and after protein encounter. Submicrosecond molecular dynamics trajectories of apo forms of fasciculin, corresponding to different conformational substates, are reported here with reference to the conformational changes of loop I of this three-fingered toxin. This highly flexible loop exhibits an ensemble of conformations within each substate corresponding to its functions. The high energy barrier found between the two major substates leads to transitions that are slow on the timescale of the diffusional encounter of noninteracting FAS2 and AChE. The more stable of the two apo substates may not be the one observed in the complex with AChE. It seems likely that the more stable apo form binds rapidly to AChE and conformational readjustments then occur in the resulting encounter complex.     

Purification, functional characterization, cloning, and identification of mutants of a seed-specific arabinan hydrolase in Arabidopsis

This work describes the purification and characterization of an enzyme that exhibits arabinan hydrolase activity in seeds of Arabidopsis thaliana. The enzyme, designated XYL3, had an apparent molecular mass of 80 kDa when purified to homogeneity, and was identified using MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) as a putative beta-D-xylosidase that belongs to family 3 of glycoside hydrolases encoded by gene At5g09730. XYL3 hydrolysed synthetic substrates such as p-nitrophenyl-alpha-L-arabinofuranoside and p-nitrophenyl-beta-D-xyloside with similar catalytic efficiency. XYL3 released L-arabinose from (1-->5)-alpha-L-arabinofuranobiose, arabinoxylan, sugar beet arabinan, and debranched arabinan. The enzyme hydrolysed both arabinosyl-substituted side group residues and terminal arabinofuranosyl residues (1-->5)-alpha-linked to the arabinan backbone. This indicates that XYL3 is able to degrade all terminal arabinosyl residues and suggests that it participates in the in-vivo hydrolysis of arabinan. Analysis of gene expression patterns by semi-quantitative RT-PCR, in-situ hybridization and a promoter-GUS fusion demonstrated that AtBX3 was specifically expressed in the seed endosperm at the globular stage of the embryo. Immunolocalization using LM6 anti-arabinan antisera found that arabinan, the XYL3 substrate, was also present in this seed tissue. T-DNA null mutants for AtBX3 were identified. The mutant plants lacked the alpha-L-arabinofuranosidase and beta-D-xylosidase activities corresponding to XYL3. Mutants showed reduced seed size and are delayed in seedling germination compared with the wild type.     

Ethnic Differences in Correlates of Obesity between Latin‐American and Black Women

Objective: To date, no studies have examined dietary intake, physical activity, and body image in a large sample of Latin‐American and black women recruited using the same methodology. The aim of this study was to examine three potential correlates of obesity (dietary intake, body image, and physical activity) in a large sample of Latin‐American and black women across the weight spectrum. Research Methods and Procedures: Participants were black (n = 271) and Latin‐American (n = 234) adult women who completed a 24‐hour dietary recall and physical activity and body image questionnaires. Results: After controlling for BMI, education, marital status, and number of children, black women consumed more kilocalories, dietary fat (grams), and percent calories from fat than Latin‐American women, who consumed more carbohydrates (grams) and dietary fiber (total and soluble). Black women engaged in more sedentary behavior than Latin‐American women. Although Latin‐American women weighed less than black women, they perceived their current body image as heavier and reported greater body image dissatisfaction than black women. Black women also reported a higher ideal body image than Latin‐American women. Discussion: The combined effect of a diet higher in calories and fat, increased sedentary behavior, and more accepting body image could account for higher rates of obesity among black women. Future studies should further explore cultural attitudes and beliefs related to weight that could provide information for the development of culturally competent obesity interventions.     

Transglucosylation of hydroquinone catalysed by α-glucosidase from baker's yeast

Hydroquinone α-isomaltoside and hydroquinone α-glucoside were synthesized by transglucosylation in an aqueous system with baker's yeast α-glucosidase from hydroquinone and maltose as a glucosyl donor. Only one phenolic group was glucosylated, with α-selectivity, and the nature of the reaction products was governed by the concentration of hydroquinone. The optimal conditions for synthesis of glycosides were 9 mM hydroquinone and 1.5 M maltose in a 100 mM sodium citrate/phosphate buffer at pH 5.0 and 30 °C for 20 h. Under these conditions both hydroquinone α-glycosides were obtained in nearly equimolar amounts with a total molar yield of 28% with respect to hydroquinone and a total glycoside concentration of 1 mg/mL in the reaction mixture.