Abstract
Association mapping uses statistical analyses to test for relationships between genomic markers called single nucleotide polymorphisms (SNPs) and traits. This research focuses on the use of logistic regression to assess the additive, dominance, and epistatic effects when investigating associations between SNPs and binary traits, such as disease status. A very specific phenomenon that results in infinite maximum likelihood estimates (MLEs) of logistic regression parameters, called quasi-separation of points (QSP), is investigated. We provide a solution that relies on the use of Firth’s MLE to estimate logistic regression parameters. Simulated and real data are utilized to investigate the use of Firth’s MLE in a QSP setting.
Keywords
Single nucleotide polymorphism, quantitative trait loci (QTL), quasi-separation of points
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Recommended Citation
Lipka, Alexander E.; McCabe, George P.; and Doerge, R. W.
(2009).
"ASSOCIATING SNPS WITH BINARY TRAITS,"
Conference on Applied Statistics in Agriculture.
https://doi.org/10.4148/2475-7772.1073
ASSOCIATING SNPS WITH BINARY TRAITS
Association mapping uses statistical analyses to test for relationships between genomic markers called single nucleotide polymorphisms (SNPs) and traits. This research focuses on the use of logistic regression to assess the additive, dominance, and epistatic effects when investigating associations between SNPs and binary traits, such as disease status. A very specific phenomenon that results in infinite maximum likelihood estimates (MLEs) of logistic regression parameters, called quasi-separation of points (QSP), is investigated. We provide a solution that relies on the use of Firth’s MLE to estimate logistic regression parameters. Simulated and real data are utilized to investigate the use of Firth’s MLE in a QSP setting.
