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West Ashley Library
9 a.m. – 7 p.m.
Phone: (843) 766-6635
Main Library
9 a.m. - 8 p.m.
Phone: (843) 805-6930
Folly Beach Library
Closed for renovations
Phone: (843) 588-2001
John L. Dart Library
9 a.m. – 7 p.m.
Phone: (843) 722-7550
St. Paul's/Hollywood Library
9 a.m. - 8 p.m.
Phone: (843) 889-3300
Mt. Pleasant Library
9 a.m. – 8 p.m.
Phone: (843) 849-6161
Dorchester Road Library
9 a.m. - 8 p.m.
Phone: (843) 552-6466
Edgar Allan Poe/Sullivan's Island Library
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John's Island Library
9 a.m. – 8 p.m.
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McClellanville Library
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Edisto Library
9 a.m. - 6 p.m.
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Wando Mount Pleasant Library
9 a.m. - 8 p.m.
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Otranto Road Library
9 a.m. - 8 p.m.
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Hurd/St. Andrews Library
9 a.m. - 8 p.m.
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Baxter-Patrick James Island
9 p.m. - 8 p.m.
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Bees Ferry West Ashley Library
9 a.m. - 8 p.m.
Phone: (843) 805-6892
Village Library
9 a.m. - 6 p.m.
Phone: (843) 884-9741
Keith Summey North Charleston Library
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Phone: (843) 805-6909
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eQTL mapping of rare variant associations using RNA-seq data: An evaluation of approaches.
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- Author(s): Lutz, Sharon Marie; Thwing, Annie; Fingerlin, Tasha
- Source:
PLoS ONE; 10/3/2019, Vol. 14 Issue 10, p1-9, 9p- Subject Terms:
- Source:
- Additional Information
- Subject Terms:
- Abstract: Expression quantitative trait loci (eQTL) provide insight on transcription regulation and illuminate the molecular basis of phenotypic outcomes. High-throughput RNA sequencing (RNA-seq) is becoming a popular technique to measure gene expression abundance. Traditional eQTL mapping methods for microarray expression data often assume the expression data follow a normal distribution. As a result, for RNA-seq data, total read count measurements can be normalized by normal quantile transformation in order to fit the data using a linear regression. Other approaches model the total read counts using a negative binomial regression. While these methods work well for common variants (minor allele frequencies > 5% or 1%), an extension of existing methodology is needed to accommodate a collection of rare variants in RNA-seq data. Here, we examine 2 approaches that are direct applications of existing methodology and apply these approaches to RNAseq studies: 1) collapsing the rare variants in the region and using either negative binomial regression or Poisson regression and 2) using the normalized read counts with the Sequence Kernel Association Test (SKAT), the burden test for SKAT (SKAT-Burden), or an optimal combination of these two tests (SKAT-O). We evaluated these approaches via simulation studies under numerous scenarios and applied these approaches to the 1,000 Genomes Project. [ABSTRACT FROM AUTHOR]
- Abstract: Copyright of PLoS ONE is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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