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In some manufacturing processes, the quality of a product can be characterized by the functional relationship between the response variable and the explanatory variables. Profile monitoring is a tool used to examine the stability of the functional relationship over time. Many studies have pointed out that the measurements within a profile are uncorrelated. In this research, to take advantage of the ability to provide a comprehensive description of a wide variety of data, the Tweedie exponential dispersion process model is used to account for the within-profile correlation. Then, two exponentially weighted moving average control charts are developed to detect process changes during a Phase II application. In the simulation studies, we showed that our proposed control charts outperform the existing methods for monitoring linear and nonlinear profiles. Finally, two numerical examples are given to demonstrate the usefulness of our proposed control charts. [ABSTRACT FROM AUTHOR]

Abstract Background When using Illumina high throughput short read data, sometimes the genotype inferred from the positive strand and negative strand are significantly different, with one homozygous and the other heterozygous. This phenomenon is known as strand bias. In this study, we used Illumina short-read sequencing data to evaluate the effect of strand bias on genotyping quality, and to explore the possible causes of strand bias. Result We collected 22 breast cancer samples from 22 patients and sequenced their exome using the Illumina GAIIx machine. By comparing the consistency between the genotypes inferred from this sequencing data with the genotypes inferred from SNP chip data, we found that, when using sequencing data, SNPs with extreme strand bias did not have significantly lower consistency rates compared to SNPs with low or no strand bias. However, this result may be limited by the small subset of SNPs present in both the exome sequencing and the SNP chip data. We further compared the transition and transversion ratio and the number of novel non-synonymous SNPs between the SNPs with low or no strand bias and those with extreme strand bias, and found that SNPs with low or no strand bias have better overall quality. We also discovered that the strand bias occurs randomly at genomic positions across these samples, and observed no consistent pattern of strand bias location across samples. By comparing results from two different aligners, BWA and Bowtie, we found very consistent strand bias patterns. Thus strand bias is unlikely to be caused by alignment artifacts. We successfully replicated our results using two additional independent datasets with different capturing methods and Illumina sequencers. Conclusion Extreme strand bias indicates a potential high false-positive rate for SNPs.

Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv) ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase). For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase). For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase). Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

In today's manufacturing industries, if the quality characteristic of a product or a process is assumed to be represented by a functional relationship between the response variable and one or more explanatory variables, then the data generated from such a relationship are called profile data. Generally speaking, the functional relationship of the profile data rarely occurs in linear form, and the real data usually do not follow normal distribution. Thus, in this paper, the functional relationship of profile data is described via a nonparametric regression model and a nonparametric exponentially weighted moving average (EWMA) control chart is developed for detecting the process shifts for nonlinear profile data in the Phase II monitoring. We first fit the nonlinear profile data via a support vector regression model and use the fitted values to calculate the five metrics. Then, the nonparametric EWMA control chart with the five metrics can be constructed accordingly. Moreover, a simulation study is conducted to evaluate the detecting performance of the new control chart under various process shifts using the out‐of‐control average run length. Finally, a realistic nonlinear profile example is used to demonstrate the usefulness of our proposed nonparametric EWMA control chart and its monitoring schemes. It is expected that the proposed nonparametric EWMA control chart can enhance the monitoring efficiency for nonlinear profile data in the phase II study. [ABSTRACT FROM AUTHOR]

Power/sample size (power) analysis estimates the likelihood of successfully finding the statistical significance in a data set. There has been a growing recognition of the importance of power analysis in the proper design of experiments. Power analysis is complex, yet necessary for the success of large studies. It is important to design a study that produces statistically accurate and reliable results. Power computation methods have been well established for both microarray-based gene expression studies and genotyping microarray-based genome-wide association studies. High-throughput sequencing (HTS) has greatly enhanced our ability to conduct biomedical studies at the highest possible resolution (per nucleotide). However, the complexity of power computations is much greater for sequencing data than for the simpler genotyping array data. Research on methods of power computations for HTS-based studies has been recently conducted but is not yet well known or widely used. In this article, we describe the power computation methods that are currently available for a range of HTS-based studies, including DNA sequencing, RNA-sequencing, microbiome sequencing and chromatin immunoprecipitation sequencing. Most importantly, we review the methods of power analysis for several types of sequencing data and guide the reader to the relevant methods for each data type. [ABSTRACT FROM AUTHOR]