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Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
- Xinxin Wang,
- Ryan Christ,
- Erica Young,
- Chul Joo Kang,
- Indraniel Das,
- Edward A. Belter, Jr.,
- Markku Laakso,
- Louis J.M. Aslett,
- David Steinsaltz,
- Nathan O. Stitziel,
- and Ira M. Hall
Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
...the single marker test (SMT) association signal at five loci by combining independent signals from distinct alleles. LOCATER successfully recovers known quantitative trait loci not found by SMT, including LIPG, recovers known allelic heterogeneity at the APOE/C1/C4/C2 gene cluster, and suggests one novel...
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Erratum: Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 660; doi:10.1101/gr.281963.126
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pan graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...downsampled HPRC data, (5) evaluating parameter sensitivity to confirm robustness, (6) developing a novel allele call confidence metric based on ILP solution stability, and (7) providing detailed case studies of read assignments. Finally, we demonstrate its application in a disease association context using...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...this enhancer. These results demonstrate the power of caQTLs to characterize regulatory mechanisms at GWAS loci.Chromatin accessibility quantitative trait loci (caQTLs) have successfully identified functional variants and regulatory elements at a subset of gene expression QTLs (eQTLs) and -wide association...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...A novel quantitative trait locus implicates Msh3 in the propensity for -wide short tandem repeat expansions in mice Mikhail O. Maksimov1,2,12, Cynthia Wu3,12, David G. Ashbrook4, Flavia Villani4, Vincenza Colonna4,5, Nima Mousavi6, Nichole Ma1, Lu Lu4, Jonathan K. Pritchard7,8, Alon Goren1...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
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Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...techniques. These variants, however, may have substantial effects on quantitative traits (Gymrek and Goren 2021; Mukamel et al. 2021). Our findings in mice suggest that indel rates in other mammals may also exceed current estimates (Venn et al. 2014; Harland et al. 2018; Deng et al. 2019; Ohno 2019). However...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...-site resistance,” involving structural changes (mutations) in the gene encoding the insecticide target protein that make it less sensitive to the toxic effect of the insecticide, and (2) “metabolic resistance,” involving the increased production or activity of metabolic enzymes that break down or sequester...
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