The application of the entropy-based statistic for genomic association study of QTL

Abstract

An entropy-based statistic has been proposed for genomic association study for disease-susceptibility locus. The statistic may be directly adopted and/or extended to quantitative-trait locus (QTL) mapping for quantitative traits. In this article, the statistic was extended and applied to quantitative trait for association analysis of QTL by means of selective genotyping. The statistical properties (the type I error rate and the power) were examined under a range of parameters and population-sampling strategies (e.g., various genetic models, various heritabilities, and various sample-selection threshold values) by simulation studies. The results indicated that the statistic is robust and powerful for genomic association study of QTL. A simulation study based on the haplotype frequencies of 10 single nucleotide polymorphisms (SNPs) of angiotensin-I converting enzyme genes was conducted to evaluate the performance of the statistic for genetic association study.
- entropy,
- quantitative-trait locus,
- association analysis,
- extreme sample

FullText(HTML)

References(13)

References

[1]	Abecasis, G.R., Cardon, L.R., Cookson, W.O.C. A general test of association for quantitative traits in nuclear families Am. J. Hum. Genet., 66 (2000),pp. 279-292
[2]	Abecasis, G.R., Cookson, W.O.C., Cardon, L.R. Pedigree tests of linkage disequilibrium Eur. J. Hum. Genet., 8 (2000),pp. 545-551
[3]	Akey, J., Jin, L., Xiong, M. Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur. J. Hum. Genet., 9 (2001),pp. 291-300
[4]	Chapman, N.H., Wijsman, E.M. Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility Am. J. Hum. Genet., 63 (1998),pp. 1872-1885
[5]	Deng, H.W., Chen, W.M., Recker, R.R. QTL fine mapping by measuring and test for Hardy-Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations Am. J. Hum. Genet., 66 (2000),pp. 1027-1045
[6]	Fan, R.Z., Spinka, C., Jin, L. et al. Pedigree linkage disequilibrium mapping of quantitative trait loci Eur. J. Hum. Genet., 13 (2005),pp. 216-231
[7]	Keavney, B., McKenzie, C.A., Connell, J.M. et al. Hum. Mol. Genet., 7 (1998),pp. 1745-1751
[8]	Lehmann, E.L.
[9]	Li, Y.M., Xiang, Y., Sun, Z.Q. An entropy-based measure for QTL mapping using extreme samples of population Hum. Hered., 65 (2007),pp. 121-128
[10]	Shannon, C.E. A mathematical theory of communication MD Comput., 14 (1997),pp. 306-317
[11]	Xiong, M., Zhao, J., Boerwinkle, E. Haplotype block linkage disequilibrium mapping Front Biosci., 8 (2003),pp. a85-a93
[12]	Xiang, Y., Li, Y.M., Liu, Z.M. et al. An entropy-based index for fine-scale mapping of QTL J. Genet. Genomic, 34 (2007),pp. 373-380
[13]	Zhao, J.Y., Boerwinkle, E., Xiong, M. An entropy-based statistic for genomewide association studies Am. J. Hum. Genet., 77 (2005),pp. 27-40

Relative Articles

[1]	Yifeng Huang, Kaixuan Cui, Zhen Zhang, Rongyao Chai, Hongguang Xie, Jianyao Shou, Junru Fu, Guolin Li, Jiyun Liu, Shuangqing Wu, Guochang Sun, Jianfu Zhang, Yiwen Deng, Zuhua He. Identification and fine-mapping of quantitative trait loci (QTL) conferring rice false smut resistance in rice[J]. Journal of Genetics and Genomics, 2023, 50(4): 276-279. doi: 10.1016/j.jgg.2022.11.010
[2]	Chen Wei, Xiaodian Cai, Shuqi Diao, Jinyan Teng, Zhiting Xu, Wenjing Zhang, Haonan Zeng, Zhanming Zhong, Xibo Wu, Yahui Gao, Jiaqi Li, Zhe Zhang. Integrating genome-wide association study with a multi-tissue transcriptome analysis provides insights into the genetic architecture of teat traits in pigs[J]. Journal of Genetics and Genomics. doi: 10.1016/j.jgg.2023.07.003
[3]	Wei Qian, Manfei Zhang, Kaiwen Wan, Yunxia Xie, Siyuan Du, Jiarui Li, Xiongzheng Mu, Jiange Qiu, Xiangyang Xue, Xiahai Zhuang, Yingzhi Wu, Fan Liu, Sijia Wang. Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness[J]. Journal of Genetics and Genomics, 2022, 49(10): 934-942. doi: 10.1016/j.jgg.2022.02.020
[4]	Wen Yao, Guangwei Li, Yanru Cui, Yiming Yu, Qifa Zhang, Shizhong Xu. Mapping quantitative trait loci using binned genotypes[J]. Journal of Genetics and Genomics, 2019, 46(7): 343-352. doi: 10.1016/j.jgg.2019.06.005
[5]	Zhong Wang, Nating Wang, Rongling Wu, Zuoheng Wang. fGWAS: An R package for genome-wide association analysis with longitudinal phenotypes[J]. Journal of Genetics and Genomics, 2018, 45(7): 411-413. doi: 10.1016/j.jgg.2018.06.006
[6]	Lan Cao, Yun Liu, Qin Shen, Xinzhi Zhao, Ting Wang, Lin He. Association Analysis of Four Single Nucleotide Polymorphisms with Leukocyte Telomere Length in Two Chinese Populations[J]. Journal of Genetics and Genomics, 2013, 40(9): 489-491. doi: 10.1016/j.jgg.2013.08.001
[7]	Lei Tian, Lubin Tan, Fengxia Liu, Hongwei Cai, Chuanqing Sun. Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon[J]. Journal of Genetics and Genomics, 2011, 38(12): 593-601. doi: 10.1016/j.jgg.2011.11.005
[8]	Li Zhang, Jin Wang, Ronghua Zhou, Jizeng Jia. Discovery of quantitative trait loci for crossability from a synthetic wheat genotype[J]. Journal of Genetics and Genomics, 2011, 38(8): 373-378. doi: 10.1016/j.jgg.2011.07.002
[9]	Gui Mei, Cengceng Yin, Xiangdong Ding, Qin Zhang. Fine mapping quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population[J]. Journal of Genetics and Genomics, 2009, 36(11): 653-660. doi: 10.1016/S1673-8527(08)60157-5
[10]	Fang Yang, Zihui Tang, Hongwen Deng. Bivariate association analysis for quantitative traits using generalized estimation equation[J]. Journal of Genetics and Genomics, 2009, 36(12): 733-743. doi: 10.1016/S1673-8527(08)60166-6
[11]	Dongling Qi, Guizhen Guo, Myung-chul Lee, Junguo Zhang, Guilan Cao, Sanyuan Zhang, Seok-cheol Suh, Qingyang Zhou, Longzhi Han. Identification of quantitative trait loci for the dead leaf rate and the seedling dead rate under alkaline stress in rice[J]. Journal of Genetics and Genomics, 2008, 35(5): 299-305. doi: 10.1016/S1673-8527(08)60043-0
[12]	Bing Yue, Weiya Xue, Lijun Luo, Yongzhong Xing. Identification of quantitative trait loci for four morphologic traits under water stress in rice (Oryza sativa L.)[J]. Journal of Genetics and Genomics, 2008, 35(9): 569-575. doi: 10.1016/S1673-8527(08)60077-6
[13]	Fengyu Zhang, Diane Wagener. An approach to incorporate linkage disequilibrium structure into genomic association analysis[J]. Journal of Genetics and Genomics, 2008, 35(6): 381-385. doi: 10.1016/S1673-8527(08)60055-7
[14]	Yongxian Wen, Weiren Wu. Interval Mapping of Quantitative Trait Loci Underlying Triploid Endosperm Traits Using F3 Seeds[J]. Journal of Genetics and Genomics, 2007, 34(5): 429-436. doi: 10.1016/S1673-8527(07)60047-2
[15]	Jinghu Zhang, Yuanzhu Xiong, Bo Zuo, Minggang Lei, Siwen Jiang, Feng'e Li, Rong Zheng, Jialian Li, Dequan Xu. Detection of Quantitative Trait Loci Associated with Several Internal Organ Traits and Teat Number Trait in a Pig Population[J]. Journal of Genetics and Genomics, 2007, 34(4): 307-314. doi: 10.1016/S1673-8527(07)60032-0
[16]	Longzhi Han, Yongli Qiao, Sanyuan Zhang, Yuanyuan Zhang, Guilan Cao, Jonghwan Kim, Kyuseong Lee, Heejong Koh. Identification of Quantitative Trait Loci for Cold Response of Seedling Vigor Traits in Rice[J]. Journal of Genetics and Genomics, 2007, 34(3): 239-246. doi: 10.1016/S1673-8527(07)60025-3
[17]	Chuanxiao Xie, Shihuang Zhang, Minshun Li, Xinhai Li, Zhuanfang Hao, Li Bai, Degui Zhang, Yehong Liang. Inferring Genome Ancestry and Estimating Molecular Relatedness Among 187 Chinese Maize Inbred Lines[J]. Journal of Genetics and Genomics, 2007, 34(8): 738-748. doi: 10.1016/S1673-8527(07)60083-6
[18]	Hengde Li, Shangzhong Xu, Xue Gao, Hongyan Ren. Structure of the Bovine ACAD8 Gene and the Association of Its Polymorphism with the Production Traits[J]. Journal of Genetics and Genomics, 2007, 34(4): 315-320. doi: 10.1016/S1673-8527(07)60033-2
[19]	Yumei Li, Yang Xiang, Hongwen Deng, Zhenqiu Sun. An Entropy-based Index for Fine-scale Mapping of Disease Genes[J]. Journal of Genetics and Genomics, 2007, 34(7): 661-668. doi: 10.1016/S1673-8527(07)60075-7
[20]	Yang Xiang, Yumei Li, Zaiming Liu, Zhenqiu Sun. An Entropy-based Index for Fine-scale Mapping of QTL[J]. Journal of Genetics and Genomics, 2007, 34(4): 373-380. doi: 10.1016/S1673-8527(07)60040-X