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Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

ABSTRACT: BACKGROUND: Microarray-based comparative genomic hybridization (aCGH) is used for rapid comparison of genomes of different bacterial strains. The purpose is to evaluate the distribution of genes from sequenced bacterial strains (control) among unsequenced strains (test). We previously compared the use of single strain versus multiple strain control with arrays covering multiple genomes. The conclusion was that a multiple strain control promoted a better separation of signals between present and absent genes. FINDINGS: We now extend our previous study by applying the Expectation-Maximization (EM) algorithm to fit a mixture model to the signal distribution in order to classify each gene as present or absent and by comparing different methods for analyzing aCGH data, using combinations of different control strain choices, two different statistical mixture models, with or without normalization, with or without logarithm transformation and with test-over-control or inverse signal ratio calculation. We also assessed the impact of replication on classification accuracy. Higher values of accuracy have been achieved using the ratio of control-over-test intensities, without logarithmic transformation and with a strain mix control. Normalization and the type of mixture model fitted by the EM algorithm did not have a significant impact on classification accuracy. Similarly, using the average of replicate arrays to perform the classification does not significantly improve the results. CONCLUSIONS: Our work provides a guiding benchmark comparison of alternative methods to analyze aCGH results that can impact on the analysis of currently ongoing comparative genomic projects or in the re-analysis of published studies.

SUBMITTER: Cardoso LS

PROVIDER: S-EPMC3995598 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

Cardoso Liliana Sofia LS Suissas Cláudia Elvas CE Ramirez Mário M Antunes Marília M Pinto Francisco Rodrigues FR

BMC research notes 20140314

<h4>Background</h4>Microarray-based comparative genomic hybridization (aCGH) is used for rapid comparison of genomes of different bacterial strains. The purpose is to evaluate the distribution of genes from sequenced bacterial strains (control) among unsequenced strains (test). We previously compared the use of single strain versus multiple strain control with arrays covering multiple genomes. The conclusion was that a multiple strain control promoted a better separation of signals between prese ...[more]

PMID: 24629208

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Project description:The disinfection of commercial hatching eggs before incubation is a common strategy to reduce potential vertical transmission of bacterial and fungal infections from the eggshell to one-day-old chicks that may prevail in poultry products and eventually reach the end consumer. The present investigation focuses on the parallel testing and application of four different disinfection methods (conventional and alternative) under commercial hatchery conditions against natural eggshell bacterial contamination. Hatching eggs from two ROSS 308 broiler breeder flocks were selected and divided into six different groups: two groups were not disinfected and served as negative controls, and four were independently disinfected following product specifications and protocols. From each group, a sample of 100 hatching eggs was selected for bacterial re-isolation, utilizing a modified shell rinse method. Colony-forming units (cfu) from the shell rinse suspensions were determined and analyzed to establish cfu values for each tested egg. These values were analyzed to determine the bacterial disinfection capacity of the four disinfection methods under commercial hatchery conditions. The tested methods were hydrogen peroxide + alcohol, peracetic acid, low energy electron beam, and the gold standard in practice: formaldehyde. Among these methods, formaldehyde, peracetic acid, and low energy electron beam showed a significant difference when compared to the non-disinfected groups whereas hydrogen peroxide + alcohol did not. The bacterial disinfection capacity of the tested methods was compared as well to the gold standard method formaldehyde fumigation and only low energy electron beam achieved similar disinfection levels as formaldehyde. According to our data, three methods significantly reduce the bacterial load on the eggshell of hatching eggs under commercial hatching conditions, including potential alternative methods such as low energy electron beam that perform similar to the gold standard in practice.

Dataset Information

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

Publications

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.

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