Correcting Population Structure using Mixed Models Webcast

Golden Helix yesterday hosted a excellent webcast on correcting population structure in association studies using mixed models and they highlighted our EMMA(10.1534/genetics.107.080101) and EMMAX(10.1038/ng.548) algorithms.  The webcast was given by Greta Peterson and is available at  The webcast is a great overview of mixed models applied to population structure in general as well as specifically how to use the Golden Helix software to use mixed models in association studies.

A interesting aspect of the story is that we found out about the webcast from an email advertising that they will cover the EMMAX algorithm.  It turns out that there were 863 people registered for the webcast which surpassed their previous record (for a webcast on NGS) by almost 100!  It is exciting to see how much interest there is in mixed models and in our EMMA paper which we published in 2008.

On our website, we have a bunch of resources for mixed models including the EMMA, EMMAX and ICE softwares.  We recently posted an overview of mixed models here.  Below is a list of our papers related to mixed models.


Yao, Douglas W; Balanis, Nikolas G; Eskin, Eleazar; Graeber, Thomas G

A linear mixed model approach to gene expression-tumor aneuploidy association studies Journal Article

In: Sci. Rep., 9 (1), pp. 11944, 2019, ISSN: 2045-2322.

Abstract | Links | BibTeX


Sul, Jae Hoon; Martin, Lana S; Eskin, Eleazar

Population structure in genetic studies: Confounding factors and mixed models. Journal Article

In: PLoS Genet, 14 (12), pp. e1007309, 2018, ISSN: 1553-7404.

Abstract | Links | BibTeX


Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun Y; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models. Journal Article

In: PLoS Genet, 12 (3), pp. e1005849, 2016, ISSN: 1553-7404.

Abstract | Links | BibTeX


Joo, Jong Wha J; Hormozdiari, Farhad; Han, Buhm; Eskin, Eleazar

Multiple testing correction in linear mixed models. Journal Article

In: Genome Biol, 17 (1), pp. 62, 2016, ISSN: 1474-760X.

Abstract | Links | BibTeX


Joo, Jong Wha J; Kang, Eun Yong; Org, Elin; Furlotte, Nick; Parks, Brian; Hormozdiari, Farhad; Lusis, Aldons J; Eskin, Eleazar

Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure. Journal Article

In: Genetics, 204 (4), pp. 1379-1390, 2016, ISSN: 1943-2631.

Abstract | Links | BibTeX


Schweiger, Regev; Kaufman, Shachar; Laaksonen, Reijo; Kleber, Marcus E; März, Winfried; Eskin, Eleazar; Rosset, Saharon; Halperin, Eran

Fast and Accurate Construction of Confidence Intervals for Heritability. Journal Article

In: Am J Hum Genet, 98 (6), pp. 1181-92, 2016, ISSN: 1537-6605.

Abstract | Links | BibTeX


Furlotte, Nicholas A; Eskin, Eleazar

Efficient Multiple Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed-Model. Journal Article

In: Genetics, 200 (1), pp. 59-68, 2015, ISSN: 1943-2631.

Abstract | Links | BibTeX


Kostem, Emrah; Eskin, Eleazar

Improving the accuracy and efficiency of partitioning heritability into the contributions of genomic regions. Journal Article

In: Am J Hum Genet, 92 (4), pp. 558-64, 2013, ISSN: 1537-6605.

Abstract | Links | BibTeX


Sul, Jae Hoon; Eskin, Eleazar

Mixed models can correct for population structure for genomic regions under selection. Journal Article

In: Nat Rev Genet, 2013, ISSN: 1471-0064.

Links | BibTeX


Sul, Jae Hoon; Han, Buhm ; Ye, Chun ; Choi, Ted ; Eskin, Eleazar

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches Journal Article

In: PLoS Genet, 9 (6), pp. e1003491, 2013, ISSN: 1553-7404.

Abstract | Links | BibTeX


Listgarten, Jennifer; Lippert, Christoph ; Kadie, Carl M; Davidson, Robert I; Eskin, Eleazar ; Heckerman, David

Improved linear mixed models for genome-wide association studies. Journal Article

In: Nat Methods, 9 (6), pp. 525-6, 2012, ISSN: 1548-7105.

Links | BibTeX


Kenny, Eimear E; Kim, Minseung ; Gusev, Alexander ; Lowe, Jennifer K; Salit, Jacqueline ; Smith, Gustav J; Kovvali, Sirisha ; Kang, Hyun Min ; Newton-Cheh, Christopher ; Daly, Mark J; Stoffel, Markus ; Altshuler, David M; Friedman, Jeffrey M; Eskin, Eleazar ; Breslow, Jan L; Pe'er, Itsik

Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Journal Article

In: Hum Mol Genet, 20 (4), pp. 827-39, 2010, ISSN: 1460-2083.

Abstract | Links | BibTeX


Kang, Hyun Min; Sul, Jae Hoon ; Service, Susan K; Zaitlen, Noah A; Kong, Sit-Yee Y; Freimer, Nelson B; Sabatti, Chiara ; Eskin, Eleazar

Variance component model to account for sample structure in genome-wide association studies. Journal Article

In: Nat Genet, 42 (4), pp. 348-54, 2010, ISSN: 1546-1718.

Abstract | Links | BibTeX


Kang, Hyun Min; Ye, Chun ; Eskin, Eleazar

Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Journal Article

In: Genetics, 180 (4), pp. 1909-25, 2008, ISSN: 0016-6731.

Abstract | Links | BibTeX