The impact of genotyping error on haplotype reconstruction and frequency estimation

Abstract. Nuclear power plants located in the French Atlantic coast are designed to be protected against extreme environmental conditions. The French authorities remain cautious by adopting a strict policy of nuclear-plants flood prevention. Although coastal nuclear facilities in France are designed to very low probabilities of failure (e.g., 1000-year surge), exceptional surges (outliers induced by exceptional climatic events) have shown that the extreme sea levels estimated with the current statistical approaches could be underestimated. The estimation of extreme surges then requires the use of a statistical analysis approach having a more solid theoretical motivation. This paper deals with extreme-surge frequency estimation using historical information (HI) about events occurred before the systematic record period. It also contributes to addressing the problem of the presence of outliers in data sets. The frequency models presented in the present paper have been quite successful in the field of hydrometeorology and river flooding but they have not been applied to sea level data sets to prevent marine flooding. In this work, we suggest two methods of incorporating the HI: the peaks-over-threshold method with HI (POTH) and the block maxima method with HI (BMH). Two kinds of historical data can be used in the POTH method: classical historical maxima (HMax) data, and over-a-threshold supplementary (OTS) data. In both cases, the data are structured in historical periods and can be used only as complement to the main systematic data. On the other hand, in the BMH method, the basic hypothesis in statistical modeling of HI is that at least one threshold of perception exists for the whole period (historical and systematic) and that during a giving historical period preceding the period of tide gauging, only information about surges above this threshold have been recorded or archived. The two frequency models were applied to a case study from France, at the La Rochelle site where the storm Xynthia induced an outlier, to illustrate their potentials, to compare their performances and especially to analyze the impact of the use of HI on the extreme-surge frequency estimation.

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Impact of Individual Mutations on Increased Fitness in Adaptively Evolved Strains of Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.01976-07 ◽

2008 ◽

Vol 190 (14) ◽

pp. 5087-5094 ◽

Cited By ~ 39

Author(s):

M. Kenyon Applebee ◽

Markus J. Herrgård ◽

Bernhard Ø. Palsson

Keyword(s):

Escherichia Coli ◽

Wild Type Strain ◽

Frequency Estimation ◽

Relative Fitness ◽

Single Nucleotide ◽

Epistatic Interactions ◽

Adaptive Mutations ◽

Highly Sensitive ◽

Multiple Strains ◽

The Impact

ABSTRACT We measured the relative fitness among a set of experimentally evolved Escherichia coli strains differing by a small number of adaptive mutations by directly measuring allelic frequencies in head-to-head competitions using a mass spectrometry-based method. We compared the relative effects of mutations to the same or similar genes acquired in multiple strains when expressed in allele replacement strains. We found that the strongest determinant of fitness among the evolved strains was the impact of beneficial mutations to the RNA polymerase β and β′ subunit genes. We also identified several examples of epistatic interactions between rpoB/C and glpK mutations and identified two other mutations that are beneficial only in the presence of previously acquired mutations but that have little or no adaptive benefit to the wild-type strain. Allele frequency estimation is shown to be a highly sensitive method for measuring selection rates during competitions between strains differing by as little as a single-nucleotide polymorphism and may be of great use for investigating epistatic interactions.

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The Impact of Collisions on the Ability to Detect Rare Mutant Alleles Using Barcode-Type Next-Generation Sequencing Techniques

Cancer Informatics ◽

10.1177/1176935117719236 ◽

2017 ◽

Vol 16 ◽

pp. 117693511771923

Author(s):

Jenna VanLiere Canzoniero ◽

Karen Cravero ◽

Ben Ho Park

Keyword(s):

Next Generation Sequencing ◽

Allele Frequency ◽

Mutant Allele ◽

Negative Impact ◽

Frequency Estimation ◽

Low Frequency ◽

Next Generation ◽

Unique Identifier ◽

The Impact ◽

Generation Sequencing

Barcoding techniques are used to reduce error from next-generation sequencing, with applications ranging from understanding tumor subclone populations to detecting circulating tumor DNA. Collisions occur when more than one sample molecule is tagged by the same unique identifier (UID) and can result in failure to detect very-low-frequency mutations and error in estimating mutation frequency. Here, we created computer models of barcoding technique, with and without amplification bias introduced by the UID, and analyzed the effect of collisions for a range of mutant allele frequencies (1e−6 to 0.2), number of sample molecules (10 000 to 1e7), and number of UIDs (410-414). Inability to detect rare mutant alleles occurred in 0% to 100% of simulations, depending on collisions and number of mutant molecules. Collisions also introduced error in estimating mutant allele frequency resulting in underestimation of minor allele frequency. Incorporating an understanding of the effect of collisions into experimental design can allow for optimization of the number of sample molecules and number of UIDs to minimize the negative impact on rare mutant detection and mutant frequency estimation.

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The Impact of Time–Frequency Estimation Methods on the Performance of Wave Energy Converters Under Passive and Reactive Control

IEEE Transactions on Sustainable Energy ◽

10.1109/tste.2018.2870966 ◽

2019 ◽

Vol 10 (4) ◽

pp. 1784-1792 ◽

Cited By ~ 2

Author(s):

Paula B. Garcia-Rosa ◽

John V. Ringwood ◽

Olav B. Fosso ◽

Marta Molinas

Keyword(s):

Wave Energy ◽

Frequency Estimation ◽

Estimation Methods ◽

Reactive Control ◽

Time Frequency ◽

Wave Energy Converters ◽

The Impact ◽

Energy Converters

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The Impact of Children's and Adult's Gender Stereotypes on Recall and Frequency Estimation of Gender-Related Stimuli

PsycEXTRA Dataset ◽

10.1037/e413812005-632 ◽

2002 ◽

Author(s):

Scott J. Rogers ◽

Kimberly S. Wharton ◽

Bridget M. Bencke ◽

Joshua E. Susskind

Keyword(s):

Gender Stereotypes ◽

Frequency Estimation ◽

The Impact

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Voltage Harmonic Suppression by Means of Grid-Connected Converters Using only Local Measurements

Energies ◽

10.3390/en11102515 ◽

2018 ◽

Vol 11 (10) ◽

pp. 2515 ◽

Cited By ~ 1

Author(s):

Ya Zhang ◽

Maurice Roes ◽

Marcel Hendrix ◽

Jorge Duarte

Keyword(s):

Control Method ◽

Frequency Estimation ◽

Estimation Error ◽

Harmonic Distortion ◽

Current Control ◽

Harmonic Suppression ◽

Voltage Quality ◽

Local Measurements ◽

Grid Connected Converters ◽

The Impact

A single-phase grid-connected converter is considered in this paper in the presence of harmonic problems introduced non-linear loads. In order to compensate the harmonics caused by the loads, a local voltage support scheme is proposed. This is an added feature because its implementation is in parallel with a conventional current control method. Distinctively, the measurements of the grid or load current are not needed since the scheme is based on only local measurements. On top of a fundamental part for desired power injection, the converter output current comprises a harmonic part for compensation. Thus, the grid current harmonic distortion is minimized and the enhancement of the local voltage quality is achieved. A comprehensive model analysis indicates that the proposed strategy can help to attenuate harmonics of the local voltage without compromising on the quality of the fundamental current injection. Experimental results validate the effectiveness of the proposed control scheme. Moreover, the impact of grid frequency estimation error on the control strategy’s performance is quantified theoretically and experimentally.

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