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Maximizing signal-to-noise ratio in the random mutation capture assay.

ABSTRACT: The 'Random Mutation Capture' assay allows for the sensitive quantitation of DNA mutations at extremely low mutation frequencies. This method is based on PCR detection of mutations that render the mutated target sequence resistant to restriction enzyme digestion. The original protocol prescribes an end-point dilution to about 0.1 mutant DNA molecules per PCR well, such that the mutation burden can be simply calculated by counting the number of amplified PCR wells. However, the statistical aspects associated with the single molecular nature of this protocol and several other molecular approaches relying on binary (on/off) output can significantly affect the quantification accuracy, and this issue has so far been ignored. The present work proposes a design of experiment (DoE) using statistical modeling and Monte Carlo simulations to obtain a statistically optimal sampling protocol, one that minimizes the coefficient of variance in the measurement estimates. Here, the DoE prescribed a dilution factor at about 1.6 mutant molecules per well. Theoretical results and experimental validation revealed an up to 10-fold improvement in the information obtained per PCR well, i.e. the optimal protocol achieves the same coefficient of variation using one-tenth the number of wells used in the original assay. Additionally, this optimization equally applies to any method that relies on binary detection of a small number of templates.

SUBMITTER: Poovathingal SK

PROVIDER: S-EPMC3300001 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature

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Maximizing signal-to-noise ratio in the random mutation capture assay.

Poovathingal Suresh Kumar SK Gruber Jan J Ng Li Fang LF Halliwell Barry B Gunawan Rudiyanto R

Nucleic acids research 20111217 5

The 'Random Mutation Capture' assay allows for the sensitive quantitation of DNA mutations at extremely low mutation frequencies. This method is based on PCR detection of mutations that render the mutated target sequence resistant to restriction enzyme digestion. The original protocol prescribes an end-point dilution to about 0.1 mutant DNA molecules per PCR well, such that the mutation burden can be simply calculated by counting the number of amplified PCR wells. However, the statistical aspect ...[more]

PMID: 22180539

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Project description:BACKGROUND:Routine PET exams are increasingly performed with reduced injected activities, leading to the use of different image reconstruction parameters than the NEMA parameters, in order to prevent from any deleterious decrease in signal-to-noise ratio (SNR) and thus, in lesion detectability. This study aimed to provide a global head-to-head comparison between digital (Vereos, Philips®) and analog (Ingenuity TF, Philips®) PET cameras of the trade-off between SNR and contrast through a wide-ranging number of reconstruction iterations, and with a further reconstruction optimization based on the SNR of small lesions. METHODS:Image quality parameters were compared between the two cameras on human and phantom images for a number of OSEM reconstruction iterations ranging from 1 to 10, the number of subsets being fixed at 10, and with the further identification of reconstruction parameters maximizing the SNR of spheres and adenopathies nearing 10 mm in diameter. These reconstructions were additionally obtained with and without time-of-flight (TOF) information (TOF and noTOF images, respectively) for further comparisons. RESULTS:On both human and phantom TOF images, the compromise between SNR and contrast was consistently more advantageous for digital than analog PET, with the difference being particularly pronounced for the lowest numbers of iterations and the smallest spheres. SNR was maximized with 1 and 2 OSEM iterations for the TOF images from digital and analog PET, respectively, whereas 4 OSEM iterations were required for the corresponding noTOF images from both cameras. On the TOF images obtained with this SNR optimization, digital PET exhibited a 37% to 44% higher SNR as compared with analog PET, depending on sphere size. These relative differences were however much lower for the noTOF images optimized for SNR (- 4 to + 18%), as well as for images reconstructed according to NEMA standards (- 4 to + 12%). CONCLUSION:SNR may be dramatically higher for digital PET than for analog PET, especially when optimized for small lesions. This superiority is mostly attributable to enhanced TOF resolution and is significantly underestimated in NEMA-based analyses.

Project description:MotivationTarget-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis.ResultsIn this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment and performed using the Affymetrix platform, contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second type includes oligonucleotides that have a specific target on the genomic DNA and their signals are derived from specific and cross-hybridization components combined together in a total signal. A comparative analysis of hybridization specificity of oligo-probes, as well as their nucleotide sequences and thermodynamic features was performed on the database. The comparison has revealed that hybridization specificity was negatively affected by low stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, including GGG motifs, low sequence complexity and nucleotide composition symmetry.ConclusionFiltering out the probes with defined 'negative' characteristics significantly increases specific hybridization and dramatically decreasing genome-wide cross-hybridization. Selected oligo-probes have two times higher hybridization specificity on average, compared to the probes that were filtered from the analysis by applying suggested cutoff thresholds to the described parameters. A new approach for efficient oligo-probe design is described in our study.Contactshabalin@ncbi.nlm.nih.gov or olga.matveeva@gmail.comSupplementary informationSupplementary data are available at Bioinformatics online.

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Maximizing signal-to-noise ratio in the random mutation capture assay.

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Maximizing signal-to-noise ratio in the random mutation capture assay.

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