A systematic assessment of normalization approaches for the Infinium 450K methylation platform

The Illumina Infinium HumanMethylation450 BeadChip has emerged as one of the most popular platforms for genome wide profiling of DNA methylation. While the technology is wide-spread, systematic technical biases are believed to be present in the data. For example, this array incorporates two different chemical assays, i.e., Type I and Type II probes, which exhibit different technical characteristics and potentially complicate the computational and statistical analysis. Several normalization methods have been introduced recently to adjust for possible biases. However, there is considerable debate within the field on which normalization procedure should be used and indeed whether normalization is even necessary. Yet despite the importance of the question, there has been little comprehensive comparison of normalization methods. We sought to systematically compare several popular normalization approaches using the Norwegian Mother and Child Cohort Study (MoBa) methylation data set and the technical replicates analyzed with it as a case study. We assessed both the reproducibility between technical replicates following normalization and the effect of normalization on association analysis. Results indicate that the raw data are already highly reproducible, some normalization approaches can slightly improve reproducibility, but other normalization approaches may introduce more variability into the data. Results also suggest that differences in association analysis after applying different normalizations are not large when the signal is strong, but when the signal is more modest, different normalizations can yield very different numbers of findings that meet a weaker statistical significance threshold. Overall, our work provides useful, objective assessment of the effectiveness of key normalization methods.     

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

DNA methylation plays an important role in disease etiology. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a widely used platform in large-scale epidemiologic studies. This platform can efficiently and simultaneously measure methylation levels at ∼480,000 CpG sites in the human genome in multiple study samples. Due to the intrinsic chip design of 2 types of chemistry probes, data normalization or preprocessing is a critical step to consider before data analysis. To date, numerous methods and pipelines have been developed for this purpose, and some studies have been conducted to evaluate different methods. However, validation studies have often been limited to a small number of CpG sites to reduce the variability in technical replicates. In this study, we measured methylation on a set of samples using both whole-genome bisulfite sequencing (WGBS) and 450K chips. We used WGBS data as a gold standard of true methylation states in cells to compare the performances of 8 normalization methods for 450K data on a genome-wide scale. Analyses on our dataset indicate that the most effective methods are peak-based correction (PBC) and quantile normalization plus β-mixture quantile normalization (QN.BMIQ). To our knowledge, this is the first study to systematically compare existing normalization methods for Illumina 450K data using novel WGBS data. Our results provide a benchmark reference for the analysis of DNA methylation chip data, particularly in white blood cells.     

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; (2) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); (3) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive data set suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays.     

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethylation450 Methylation array.     

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethylation450 Methylation array.     

Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

Analysis of epigenetic mechanisms, particularly DNA methylation, is of increasing interest for epidemiologic studies examining disease etiology and impacts of environmental exposures. The Infinium HumanMethylation450 BeadChip^® (450K), which interrogates over 480?000 CpG sites and is relatively cost effective, has become a popular tool to characterize the DNA methylome. For large-scale studies, minimizing technical variability and potential bias is paramount. The goal of this paper was to evaluate the performance of several existing and novel color channel normalizations designed to reduce technical variability and batch effects in 450K analysis from a large population study. Comparative assessment of 10 normalization procedures included the GenomeStudio^® Illumina procedure, the lumi smooth quantile approach, and the newly proposed All Sample Mean Normalization (ASMN). We also examined the performance of normalizations in combination with correction for the two types of Infinium chemistry utilized on the 450K array. We observed that the performance of the GenomeStudio^® normalization procedure was highly variable and dependent on the quality of the first sample analyzed in an experiment, which is used as a reference in this procedure. While the lumi normalization was able to decrease batch variability, it increased variation among technical replicates, potentially reducing biologically meaningful findings. The proposed ASMN procedure performed consistently well, both at reducing batch effects and improving replicate comparability. In summary, the ASMN procedure can improve existing color channel normalization, especially for large epidemiologic studies, and can be successfully implemented to enhance a 450K DNA methylation data pipeline.     

PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions

The software tool PBEAM provides a parallel implementation of the BEAM, which is the first algorithm for large scale epistatic interaction mapping, including genome-wide studies with hundreds of thousands of markers. BEAM describes markers and their interactions with a Bayesian partitioning model and computes the posterior probability of each marker sets via Markov Chain Monte Carlo (MCMC). PBEAM takes the advantage of simulating multiple Markov chains simultaneously. This design can efficiently reduce ~n-fold execution time in the circumstance of n CPUs. The implementation of PBEAM is based on MPI libraries.

Availability

PBEAM is available for download at http://bioinfo.au.tsinghua.edu.cn/pbeam/     

cDNA芯片阳性对照的制备及在芯片敏感性分析中的应用

cDNA芯片是一种高通量基因表达谱分析技术,在生理病理条件下细胞基因表达谱分析,新基因发现和功能研究等方面具有广阔应用前景。CDNA芯片阳性对照的选取以及CDNA芯片检测敏感性是芯片成功应用的关键问题之一。以在系统发育上与人类基因同源性小的荧火虫荧光素酶基因材料,制备了用于人类和其他动物基因表达谱CDNA芯片的通用型阳性对照探针和相应的mRNA参照物,经反转录对mRNA参照物进行Cy3荧光标记并与DNA芯片杂交后发现,mRNA参照物能特异性地与荧光酶基因cDNA片断杂交,而与人β-肌动蛋白基因,人G3PDH基因以及λDNA/HINDⅢ无杂交反应。把mRNA参照物以不同比例加入HepG2总RNA中,以反转录荧光标记后与CDNA芯片杂交,结果发现当总RNA中的MRNA含量为1/10^4稀释（即mRNA分子个数约为10^8个）时,CDNA芯片基本检测不出mRNA标记产物的杂交信号。而且,cDNA芯片检测的信号强度与芯片上固定的探针浓度密切相关,当探针浓度为2g/L时,杂交信号最强,随着探针浓度下降芯片的杂交信号趋于减弱。CDNA芯片通用型阳性参照物的制备以及应用于CDNA芯片检测敏感性研究为CDNA芯片应用于人和其他动物基因表达谱高通量分析和新基因功能研究提供了技术基础和理论依据。     

A genome-wide association study for quantitative trait loci of show-jumping in Hanoverian warmblood horses

Show-jumping is an economically important breeding goal in Hanoverian warmblood horses. The aim of this study was a genome-wide association study (GWAS) for quantitative trait loci (QTL) for show-jumping in Hanoverian warmblood horses, employing the Illumina equine SNP50 Beadchip. For our analyses, we genotyped 115 stallions of the National State stud of Lower Saxony. The show-jumping talent of a horse includes style and ability in free-jumping. To control spurious associations based on population stratification, two different mixed linear animal model (MLM) approaches were employed, besides linear models with fixed effects only and adaptive permutations for correcting multiple testing. Population stratification was explained best in the MLM considering Hanoverian, Thoroughbred, Trakehner and Holsteiner genes and the marker identity-by-state relationship matrix. We identified six QTL for show-jumping on horse chromosomes (ECA) 1, 8, 9 and 26 (-log(10) P-value >5) and further putative QTL with -log(10) P-values of 3-5 on ECA1, 3, 11, 17 and 21. Within six QTL regions, we identified human performance-related genes including PAPSS2 on ECA1, MYL2 on ECA8, TRHR on ECA9 and GABPA on ECA26 and within the putative QTL regions NRAP on ECA1, and TBX4 on ECA11. The results of our GWAS suggest that genes involved in muscle structure, development and metabolism are crucial for elite show-jumping performance. Further studies are required to validate these QTL in larger data sets and further horse populations.     

Non-target organism risk assessment of MIR604 maize expressing mCry3A for control of corn rootworm

Abstract:  Event MIR604 maize expresses a modified Cry3A protein (mCry3A), for control of corn rootworm. As part of the environmental safety assessment of MIR604 maize, risks to non-target organisms of mCry3A were assessed. The potential exposure of non-target organisms to mCry3A following cultivation of MIR604 maize was determined, and the hypothesis that such exposure is not harmful was tested. The hypothesis was tested rigorously by making worst-case or highly conservative assumptions about exposure, along with laboratory testing for hazards using species taxonomically related to the target pest and species expected to have high exposure to mCry3A, or both. Further rigour was introduced by study designs incorporating long exposures and measurements of sensitive endpoints. No adverse effects were observed in any study, and in most cases exposure to mCry3A in the study was higher than the worst-case expected exposure. In all cases, exposure in the study was higher than realistic, but still conservative, estimates of exposure. These results indicate minimal risk of MIR604 maize to non-target organisms.     

Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma

Metastatic melanoma is a deadly treatment-resistant form of skin cancer whose global incidence is on the rise. During melanocyte transformation and melanoma progression the expression profile of many genes changes. Among these, a gene implicated in several steps of melanocyte development, TFAP2A, is frequently silenced; however, the molecular mechanism of TFAP2A silencing in human melanoma remains unknown. In this study, we measured TFAP2A mRNA expression in primary human melanocytes compared to 11 human melanoma samples by quantitative real-time RT-PCR. In addition, we assessed CpG DNA methylation of the TFAP2A promoter in these samples using bisulfite sequencing. Compared to primary melanocytes, which showed high TFAP2A mRNA expression and no promoter methylation, human melanoma samples showed decreased TFAP2A mRNA expression and increased promoter methylation. We further show that increased CpG methylation correlates with decreased TFAP2A mRNA expression. Using The Cancer Genome Atlas, we further identified TFAP2A as a gene displaying among the most decreased expression in stage 4 melanomas vs. non-stage 4 melanomas, and whose CpG methylation was frequently associated with lack of mRNA expression. Based on our data, we conclude that TFAP2A expression in human melanomas can be silenced by aberrant CpG methylation of the TFAP2A promoter. We have identified aberrant CpG DNA methylation as an epigenetic mark associated with TFAP2A silencing in human melanoma that could have significant implications for the therapy of human melanoma using epigenetic modifying drugs.     

Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma

Metastatic melanoma is a deadly treatment-resistant form of skin cancer whose global incidence is on the rise. During melanocyte transformation and melanoma progression the expression profile of many genes changes. Among these, a gene implicated in several steps of melanocyte development, TFAP2A, is frequently silenced; however, the molecular mechanism of TFAP2A silencing in human melanoma remains unknown. In this study, we measured TFAP2A mRNA expression in primary human melanocytes compared to 11 human melanoma samples by quantitative real-time RT-PCR. In addition, we assessed CpG DNA methylation of the TFAP2A promoter in these samples using bisulfite sequencing. Compared to primary melanocytes, which showed high TFAP2A mRNA expression and no promoter methylation, human melanoma samples showed decreased TFAP2A mRNA expression and increased promoter methylation. We further show that increased CpG methylation correlates with decreased TFAP2A mRNA expression. Using The Cancer Genome Atlas, we further identified TFAP2A as a gene displaying among the most decreased expression in stage 4 melanomas vs. non-stage 4 melanomas, and whose CpG methylation was frequently associated with lack of mRNA expression. Based on our data, we conclude that TFAP2A expression in human melanomas can be silenced by aberrant CpG methylation of the TFAP2A promoter. We have identified aberrant CpG DNA methylation as an epigenetic mark associated with TFAP2A silencing in human melanoma that could have significant implications for the therapy of human melanoma using epigenetic modifying drugs.     

A cell culture platform for Cryptosporidium that enables long-term cultivation and new tools for the systematic investigation of its biology

Cryptosporidium parasites are a major cause of diarrhoea that pose a particular threat to children in developing areas and immunocompromised individuals. Curative therapies and vaccines are lacking, mainly due to lack of a long-term culturing system of this parasite. Here, we show that COLO-680N cells infected with two different Cryptosporidium parvum strains produce sufficient infectious oocysts to infect subsequent cultures, showing a substantial fold increase in production, depending on the experiment, over the most optimistic HCT-8 models. Oocyst identity was confirmed using a variety of microscopic- and molecular-based methods. This culturing system will accelerate research on Cryptosporidium and the development of anti-Cryptosporidium drugs.     

A comparison of health assessment approaches for evaluating the effects of contaminant-related stress on fish populations

Various methods are available for investigating the effects of environmental conditions or stress on fish ranging from assessments at the individual level to the population and community level. Each method, however, has limitations and advantages, and the type of method used influences the interpretation of stressor effects on fish health. We compared and evaluated three methods for investigating the effects of contaminants on fish health for populations in a stream receiving a variety of industrial effluents including PCBs, heavy metals (primarily mercury), and chlorine. These methods are: (1) individual bioindicator variables including measurements of biochemical, physiological, histopathological, and organismal-level responses, (2) statistically based integrative indices based on multivariate responses, and (3) integrative ecologically relevant measurements such as population and community-level responses. Many of the individual-level measurements reflect biochemical and physiological conditions and are therefore short-term response indicators of stress. Use of several individual variables in multivariate discriminant analysis allows a more integrative approach for evaluating response of fish to stressors. Community- and population-level measurements integrate the responses to a variety of environmental conditions and therefore may be less reflective of contaminant-induced stress. The three methods used together provide the best strategy for evaluating fish health in order that environmentally sound decisions can be made regarding the implications of contaminant-related stress on aquatic ecosystems.Managed by Martin Marietta Energy Systems, Inc., under contract DE-AC05-840R21400 with the U.S. Department of Energy.     

A comparison of national approaches to setting ecological status boundaries in phytobenthos assessment for the European Water Framework Directive: results of an intercalibration exercise

The European Union (EU)’s Water Framework Directive (WFD) requires that all Member States participate in intercalibration exercises in order to ensure that ecological status concepts and assessment levels are consistent across the EU. This paper describes one such exercise, performed by the countries in the Central/Baltic Geographical Intercalibration Group stretching from Ireland in the west to Estonia in the east and from the southern parts of Scandinavia to the northern regions of Spain and Italy (but excluding alpine regions, which were intercalibrated separately). In this exercise, methods used to measure ecological status of rivers using benthic diatoms were compared. Ecological status is estimated as the ratio between the observed value of a biological element and the value expected in the absence of significant human impact. Approaches to defining the ‘reference sites’, from which these ‘expected’ values were derived, varied from country to country. Minimum criteria were established as part of the exercise but there was still considerable variation between national reference values, reflecting typological differences that could not be resolved during the exercise. A simple multimetric index was developed to compare boundary values using two widely used diatom metrics. Boundary values for high/good status and good/moderate status set by each participant were converted to their equivalent values of this intercalibration metric using linear regression. Variation of ±0.05 EQR units around the median value was considered to be acceptable and the exercise provided a means for those Member States who fell significantly above or below this line to review their approaches and, if necessary, adjust their boundaries. Handling editor: J. Padisak     

A review of pain assessment techniques and pharmacological approaches to pain relief after bovine castration: Practical implications for cattle production within the United States

Castration of male calves destined for beef production is a common livestock management practice in the United States amounting to approximately 7 million procedures per year. Recently there has been renewed interest in identifying methods to reduce pain associated with dehorning and castration. Although several studies have reported that analgesic drug administration prior to castration attenuates plasma cortisol response, there are currently no compounds specifically approved for pain relief in livestock in the U.S. Validated pain assessment tools are needed to support regulatory approval of analgesic compounds. This may include use of accelerometers, videography, heart rate variability determination, electroencephalography, thermography and plasma neuropeptide measurement to assess behavioral, physiological and neuroendocrine changes associated with a pain response. Extra-label drug use (ELDU) for pain relief is regulated under the Animal Medicinal Drug Use Clarification Act (AMDUCA) and requires that drugs be administered by or under the supervision of a veterinarian. Agents that may provide preemptive analgesia include local anesthetics, nonsteroidal anti-inflammatory drugs (NSAIDs), opioids, α2-agonists, and N-methyl d-aspartate (NMDA) receptor antagonists. A review of the published literature suggests that a significant decrease in plasma cortisol concentration after castration was associated with preemptive administration of a NSAID and local anesthesia. Local anesthesia alone tended to decrease peak plasma cortisol concentrations more than NSAIDs. However NSAIDs alone tended to decrease the area under the plasma cortisol-time curve more than local anesthesia alone. These findings suggest that multimodal analgesic regimens that extend into the post-operative period are more effective at mitigating pain and distress associated with castration than a single drug modality. Regulatory approval of safe and cost effective analgesic compounds with convenient routes of administration is needed for routine use of pain relieving drugs to be considered as standard practice at the time of castration.     

Extractionless method for the simultaneous high-performance liquid chromatographic determination of urinary caffeine metabolites for N-acetyltransferase 2, cytochrome P450 1A2 and xanthine oxidase activity assessment

Urinary metabolic ratios of caffeine are used in humans to assess the enzymatic activities of cytochrome P450 isoenzyme 1A2 (CYP1A2), xanthine oxidase (XO) and for phenotyping individuals for the bimodal N-acetyltransferase 2 (NAT2), all of them involved in the activation or detoxification of various xenobiotic compounds. Most reported analytical procedures for the measurement of the urinary metabolites of caffeine include a liquid–liquid extraction of urine samples prior to their analysis by reversed-phase HPLC. At neutral to basic pH however, 5-acetylamino-6-formylamino-3-methyluracil (AFMU), a metabolite of caffeine, spontaneously decomposes to 5-acetylamino-6-amino-3-methyluracil (AAMU). Since AAMU is not extracted in most organic solvents, the extent of AFMU decomposition cannot be precisely assessed. Although the decomposition reaction can be minimized by immediate acidification of the urine, accurate results can only be obtained when both AAMU and AFMU are monitored, or alternatively, if AAMU is measured after complete transformation of AFMU into AAMU in basic conditions. We report a liquid chromatographic method for the simultaneous quantitative analysis of the five urinary metabolites of caffeine used for the CYP1A2, XO and NAT2 phenotyping studies: AAMU, AFMU, 1-methylxanthine, 1-methyluric acid and 1,7-dimethyluric acid. These metabolites are satisfactory separated from all other known caffeine metabolites as well as endogenous urinary constituents. Sample treatment does not require any liquid–liquid extraction procedure. Urine samples are diluted and centrifuged before being injected (10 μl) onto a YMC-Pack Polyamine II (250×4.6 mm) column. A step-wise gradient elution program is applied using acetonitrile–0.75% (v/v) formic acid: (91:9) at 0 min→(75:25) at 25 min→(65:35) at 35 min→(65:35) at 45 min, followed by a re-equilibration step to the initial solvent composition. The flow-rate is 1.0 ml/min and the separations are monitored by UV absorbance at 260 and 280 nm. The procedure described here represents a substantial improvement over previous methods: a single analysis and a minimal urine sample treatment enables the simultaneous quantitation of five caffeine metabolites, notably AFMU and AAMU, used for the determination of CYP450 1A2, XO and NAT2 enzyme activity. Importantly enough, phenotyping individuals for the bimodal NAT2 is made possible without the uncertainty associated with the deformylation of AFMU, which is likely to happen at all steps prior to the analysis, during sample storage and even in the bladder of the subjects.