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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
...-scale structural mutations and aneuploidies (Vanneste et al. 2009; Currie et al. 2022). Exposure to stressors unique to the in vitro environment may exacerbate genomic instability at this critical time point in early development. In particular, ART-derived embryos are often cultured at oxygen levels that do...
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Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
...-of-function properties (activating mutations); they occur exclusively in the male germline; and older men have a higher probability of having an affected child than do younger males, known as the paternal age effect (PAE) and described decades ago (Risch et al. 1987; Crow 2000, 2012). In the literature, these mutations...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
..., and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring...
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Research: The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
- Jeramiah J. Smith and
- Melissa C. Keinath
Genome Res. August 2015 25: 1081-1090; Published in Advance June 5, 2015, doi:10.1101/gr.184135.114
...to derived chromosomes as consistent with a scenario wherein all ancestral chromosomes were affected by at least one WGD.Genomic distribution of orthologs and paralogsTo further evaluate the patterns of duplication that are revealed by lamprey comparative maps, we examined the distribution of orthologies...
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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
...of de novo structural variation in mammals (e.g., Kloosterman et al. 2015; Belyeu et al. 2021; Steensma et al. 2023), but these studies have employed short-read technology, which limits the SMs detected primarily to copy-number variants and hinders the discovery of mutations within repetitive sequences...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
...cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
..., 30) used in subsequent analyses to compare across phases. TrioTrain enables structuring the bovine inputs to match inheritance expectations; variation is transmitted from parents to offspring. Pedigree data are not explicitly given to DV; instead, parental genotypes are used to inform predictions...
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Research: Rare allelic forms of PRDM9 associated with childhood leukemogenesis
- Julie Hussin,
- Daniel Sinnett,
- Ferran Casals,
- Youssef Idaghdour,
- Vanessa Bruat,
- Virginie Saillour,
- Jasmine Healy,
- Jean-Christophe Grenier,
- Thibault de Malliard,
- Stephan Busche,
- Jean-François Spinella,
- Mathieu Larivière,
- Greg Gibson,
- Anna Andersson,
- Linda Holmfeldt,
- Jing Ma,
- Lei Wei,
- Jinghui Zhang,
- Gregor Andelfinger,
- James R. Downing,
- Charles G. Mullighan,
- and Philip Awadalla
Genome Res. March 2013 23: 419-430; Published in Advance December 5, 2012, doi:10.1101/gr.144188.112
...suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B...
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Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
...by only ∼2 million years, and share much genomic structure and similarity, both with each other and with the human (Hayasaka et al. 1996; Osada et al. 2008). As such, both are widely used in preclinical studies and are useful models for accessing tissues otherwise limited in human research (Bourne 1975...
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