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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...for further biomedical and population genetic use, but there is a need to consider each downstream analysis tool individually for its imputation quality thresholds and filtering requirements.Until recently, genotyping arrays were the only cost-effective approach for generating data for medical genomics...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered: by negative cross-regulation of DDX3X and DDX3Y in 46,XY...
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Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
- Nathan LaPierre,
- Boyang Fu,
- Steven Turnbull,
- Eleazar Eskin,
- and Sriram Sankararaman
Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
.... 2020) and may even cause false positives in MR analysis (Haworth et al. 2019; Cinelli et al. 2022). In addition, although the confounding effects of population stratification are well known, less attention has been directed toward confounding from other phenomena such as (cross-trait) assortative...
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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
...Genetic analysis of complex traits in the emerging Collaborative Cross David L. Aylor 1 , William Valdar 1 , 13 , Wendy Foulds-Mathes 1 , 13 , Ryan J. Buus 1 , 13 , Ricardo A. Verdugo 2 , 13 , Ralph S. Baric 3 , 4...
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Method: Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
...cell class-switching and help the development of high-affinity antibodies (Crotty 2014). More recently, a study described an expanded population of CD4+ helper T cells in SLE patient blood that are distinct from TFHs but still help activate B cells, further confirming heightened cross...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, -wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize...
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Research: Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection
- Caroline Durrant,
- Hanna Tayem,
- Binnaz Yalcin,
- James Cleak,
- Leo Goodstadt,
- Fernando Pardo-Manuel de Villena,
- Richard Mott,
- and Fuad A. Iraqi
Genome Res. August 2011 21: 1239-1248; Published in Advance April 14, 2011, doi:10.1101/gr.118786.110
...Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection Caroline Durrant 1 , 5 , Hanna Tayem 2 , 5 , Binnaz Yalcin 1 , James Cleak 1 , Leo Goodstadt 1 , Fernando Pardo-Manuel de...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...conspecific and interspecific variations, and their potential impact on hybrid incompatibility, remains lacking. Here, we present a pan study of populations from both species, revealing that C. nigoni consistently possesses larger s and higher gene counts than C. briggsae. This difference primarily results...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...). However, the founder strains used for the generation of the Collaborative Cross mice analyzed in this study include other subspecies, which may result in atypical recombination patterns. Moreover, mitotic recombination may occur at a much higher rate than meiotic recombination in tandemly repetitive...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...-Mulia and Gilbert 2016b; Vouzas and Gilbert 2023). One limitation is the lack of methods enabling the simultaneous measurement of RT and gene expression from the same samples. Although multiple RT profiling methods exist at the ensemble population level (Marchal et al. 2018; Hulke et al. 2020; Rivera-Mulia et al...
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