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A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.

León-Novelo LG, McIntyre LM, Fear JM, Graze RM - BMC Genomics (2014)

Bottom Line: The proposed model always has a lower type I error rate compared to the binomial test.Consequently, as variant identification improves, the need for DNA controls will be reduced.Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, 36849 Auburn, AL, USA. rmgraze@auburn.edu.

ABSTRACT

Background: One method of identifying cis regulatory differences is to analyze allele-specific expression (ASE) and identify cases of allelic imbalance (AI). RNA-seq is the most common way to measure ASE and a binomial test is often applied to determine statistical significance of AI. This implicitly assumes that there is no bias in estimation of AI. However, bias has been found to result from multiple factors including: genome ambiguity, reference quality, the mapping algorithm, and biases in the sequencing process. Two alternative approaches have been developed to handle bias: adjusting for bias using a statistical model and filtering regions of the genome suspected of harboring bias. Existing statistical models which account for bias rely on information from DNA controls, which can be cost prohibitive for large intraspecific studies. In contrast, data filtering is inexpensive and straightforward, but necessarily involves sacrificing a portion of the data.

Results: Here we propose a flexible Bayesian model for analysis of AI, which accounts for bias and can be implemented without DNA controls. In lieu of DNA controls, this Poisson-Gamma (PG) model uses an estimate of bias from simulations. The proposed model always has a lower type I error rate compared to the binomial test. Consistent with prior studies, bias dramatically affects the type I error rate. All of the tested models are sensitive to misspecification of bias. The closer the estimate of bias is to the true underlying bias, the lower the type I error rate. Correct estimates of bias result in a level alpha test.

Conclusions: To improve the assessment of AI, some forms of systematic error (e.g., map bias) can be identified using simulation. The resulting estimates of bias can be used to correct for bias in the PG model, without data filtering. Other sources of bias (e.g., unidentified variant calls) can be easily captured by DNA controls, but are missed by common filtering approaches. Consequently, as variant identification improves, the need for DNA controls will be reduced. Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain. The PG model developed here performs well when bias is known, or slightly misspecified. The model is flexible and can accommodate differences in experimental design and bias estimation.

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Related in: MedlinePlus

Type I error rate of the PG model withq= 1/2 and the binomial test, with increasing levels of bias. The x axis is the percentage of misspecification as bias increases above 0.5. That is, B = 0.5(1 + x%) with x represented by the the horizontal axis. The horizontal line (grey) through 0.05 is shown for reference.
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Fig2: Type I error rate of the PG model withq= 1/2 and the binomial test, with increasing levels of bias. The x axis is the percentage of misspecification as bias increases above 0.5. That is, B = 0.5(1 + x%) with x represented by the the horizontal axis. The horizontal line (grey) through 0.05 is shown for reference.

Mentions: Both the PG model with a fixed effect of q = 1/2 and the binomial exact, assume that there is no bias. That is, the expectation is equal amounts of reads from the paternal and maternal alleles. However, error variance is handled differently by the two approaches. Is the PG model with q = 1/2 different from the binomial test? We compare these models using simulated data sets of allele-specific read counts under a scenario in which there is bias (B≠0.5) and no allelic imbalance (R = 1) and simulated data sets with both bias and allelic imbalance (R≠1). Comparing the type I error rates for data generated with increasing levels of bias shows that while in both cases the model assumptions are violated and type I error increases with increasing bias, the PG model always has a lower type I error rate (Figure 2).Figure 2


A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.

León-Novelo LG, McIntyre LM, Fear JM, Graze RM - BMC Genomics (2014)

Type I error rate of the PG model withq= 1/2 and the binomial test, with increasing levels of bias. The x axis is the percentage of misspecification as bias increases above 0.5. That is, B = 0.5(1 + x%) with x represented by the the horizontal axis. The horizontal line (grey) through 0.05 is shown for reference.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230747&req=5

Fig2: Type I error rate of the PG model withq= 1/2 and the binomial test, with increasing levels of bias. The x axis is the percentage of misspecification as bias increases above 0.5. That is, B = 0.5(1 + x%) with x represented by the the horizontal axis. The horizontal line (grey) through 0.05 is shown for reference.
Mentions: Both the PG model with a fixed effect of q = 1/2 and the binomial exact, assume that there is no bias. That is, the expectation is equal amounts of reads from the paternal and maternal alleles. However, error variance is handled differently by the two approaches. Is the PG model with q = 1/2 different from the binomial test? We compare these models using simulated data sets of allele-specific read counts under a scenario in which there is bias (B≠0.5) and no allelic imbalance (R = 1) and simulated data sets with both bias and allelic imbalance (R≠1). Comparing the type I error rates for data generated with increasing levels of bias shows that while in both cases the model assumptions are violated and type I error increases with increasing bias, the PG model always has a lower type I error rate (Figure 2).Figure 2

Bottom Line: The proposed model always has a lower type I error rate compared to the binomial test.Consequently, as variant identification improves, the need for DNA controls will be reduced.Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, 36849 Auburn, AL, USA. rmgraze@auburn.edu.

ABSTRACT

Background: One method of identifying cis regulatory differences is to analyze allele-specific expression (ASE) and identify cases of allelic imbalance (AI). RNA-seq is the most common way to measure ASE and a binomial test is often applied to determine statistical significance of AI. This implicitly assumes that there is no bias in estimation of AI. However, bias has been found to result from multiple factors including: genome ambiguity, reference quality, the mapping algorithm, and biases in the sequencing process. Two alternative approaches have been developed to handle bias: adjusting for bias using a statistical model and filtering regions of the genome suspected of harboring bias. Existing statistical models which account for bias rely on information from DNA controls, which can be cost prohibitive for large intraspecific studies. In contrast, data filtering is inexpensive and straightforward, but necessarily involves sacrificing a portion of the data.

Results: Here we propose a flexible Bayesian model for analysis of AI, which accounts for bias and can be implemented without DNA controls. In lieu of DNA controls, this Poisson-Gamma (PG) model uses an estimate of bias from simulations. The proposed model always has a lower type I error rate compared to the binomial test. Consistent with prior studies, bias dramatically affects the type I error rate. All of the tested models are sensitive to misspecification of bias. The closer the estimate of bias is to the true underlying bias, the lower the type I error rate. Correct estimates of bias result in a level alpha test.

Conclusions: To improve the assessment of AI, some forms of systematic error (e.g., map bias) can be identified using simulation. The resulting estimates of bias can be used to correct for bias in the PG model, without data filtering. Other sources of bias (e.g., unidentified variant calls) can be easily captured by DNA controls, but are missed by common filtering approaches. Consequently, as variant identification improves, the need for DNA controls will be reduced. Filtering does not significantly improve performance and is not recommended, as information is sacrificed without a measurable gain. The PG model developed here performs well when bias is known, or slightly misspecified. The model is flexible and can accommodate differences in experimental design and bias estimation.

Show MeSH
Related in: MedlinePlus