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Method: A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits
- Boyang Fu,
- Prateek Anand,
- Aakarsh Anand,
- Joel Mefford,
- and Sriram Sankararaman
Genome Res. September 2024 34: 1294-1303; Published in Advance August 29, 2024, doi:10.1101/gr.279140.124
...regression. We included the self-interaction of each variant when testing the quadratic effect (unless mentioned otherwise).With this strategy, we identified 32 trait-gene pairs to be statistically significant across 17 quantitative traits after accounting for the total genes and traits tested (Table 1). All...
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Method: MultiBLUP: improved SNP-based prediction for complex traits
- Doug Speed and
- David J. Balding
Genome Res. September 2014 24: 1550-1557; Published in Advance June 24, 2014, doi:10.1101/gr.169375.113
...histocompatibility complex (MHC), because for these two traits, MHC SNPs tend to have larger effects. Compared to BLUP, genetic risk scores (Wray et al. 2007), stepwise regression (Purcell et al. 2007), and Bayesian sparse linear mixed models (BSLMM) (Zhou et al. 2013), we find AdaptiveMultiBLUP to be the overall...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
..., Cleveland, Ohio 44106, USA; 2 Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA Corresponding authors: david.buchner@case.edu , jnadeau@pnri.org Abstract Quantitative trait loci (QTLs) are being used to study genetic networks, protein...
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Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...be found in Supplemental Methods. LD estimation used in baselines was the same as that adopted in PRS-Net.We adopted two metrics, AUROC and AUPRC, to measure the performance for disease classification and explained variance and R2 for quantitative trait regression. Performance of all methods was estimated...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping...
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Research: NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
- Piotr Dittwald,
- Tomasz Gambin,
- Przemyslaw Szafranski,
- Jian Li,
- Stephen Amato,
- Michael Y. Divon,
- Lisa Ximena Rodríguez Rojas,
- Lindsay E. Elton,
- Daryl A. Scott,
- Christian P. Schaaf,
- Wilfredo Torres-Martinez,
- Abby K. Stevens,
- Jill A. Rosenfeld,
- Satish Agadi,
- David Francis,
- Sung-Hae L. Kang,
- Amy Breman,
- Seema R. Lalani,
- Carlos A. Bacino,
- Weimin Bi,
- Aleksandar Milosavljevic,
- Arthur L. Beaudet,
- Ankita Patel,
- Chad A. Shaw,
- James R. Lupski,
- Anna Gambin,
- Sau Wai Cheung,
- and Pawel Stankiewicz
Genome Res. September 2013 23: 1395-1409; Published in Advance May 8, 2013, doi:10.1101/gr.152454.112
...NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits Piotr Dittwald 1 , 2 , 3 , 17 , Tomasz Gambin 1 , 4 , 17 , Przemyslaw Szafranski 1 , Jian Li 1 , Stephen...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...impacts and evolutionary patterns over time remain elusive in humans owing to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, we reveal a gradual rise in disease gene proportion as gene age increases. Logistic regression...
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REVIEW: Molecular dissection of quantitative traits: progress and prospects.
- A H Paterson
Genome Res. November 1995 5: 321-333; doi:10.1101/gr.5.4.321
...wood specific gravity in an outbred pedigree of loblolly pine. Genetics 138: 1293 – 1300. Haley, C.S. , Knott. S.A. Haley, C.S. and Knott. S.A. 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315 – 324. Haley, C.S., , Knott, S...
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Methods: Automated Detection of Informative Combined Effects in Genetic Association Studies of Complex Traits
- Nadia Tahri-Daizadeh,
- David-Alexandre Tregouet,
- Viviane Nicaud,
- Nicolas Manuel,
- François Cambien,
- and Laurence Tiret
Genome Res. August 2003 13: 1952-1960; doi:10.1101/gr.1254203
...(quantitative trait), or Cox (censored response) regression model. The algorithm explores by a forward procedure a set of competing models for which an IC is derived. Based on certain modalities developed below, this exploration leads to the selection of a best approximating model (or models). The model space...
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LETTER: Single QTL Effects, Epistasis, and Pleiotropy Account for Two-thirds of the Phenotypic F₂ Variance of Growth and Obesity in DU6i x DBA/2 Mice
- Gudrun A. Brockmann,
- Jürgen Kratzsch,
- Chris S. Haley,
- Ulla Renne,
- Manfred Schwerin,
- and Steffanie Karle
Genome Res. December 1, 2000 10: 1941-1957; Published in Advance November 21, 2000, doi:10.1101/gr.149900
...interaction between different quantitative trait loci (QTL) positions was observed ( P &lt; 0.01). Evidence was found that loci having small direct effect on growth or obesity contribute to the obese phenotype by gene–gene interaction. The effects of QTLs, epistasis, and pleiotropy account for 64% and 63...

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