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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...-chromosomal rearrangements in cattle by searching for abnormal linkage disequilibrium patterns between markers located on different chromosomes in large paternal half-sib families genotyped as part of routine genomic evaluations. We screened 5571 families of artificial insemination sires from 15 breeds and revealed 13...
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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
...metric, the MIE rate, to assess performance across species, inferring that a lower rate indicates improvement. Although DV was not directly given pedigree information, our training approach is designed to reduce the number of Mendelian discordant genotypes during variant calling. For these analyses, we...
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Resource: A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
- Michael A. Eberle,
- Epameinondas Fritzilas,
- Peter Krusche,
- Morten Källberg,
- Benjamin L. Moore,
- Mitchell A. Bekritsky,
- Zamin Iqbal,
- Han-Yu Chuang,
- Sean J. Humphray,
- Aaron L. Halpern,
- Semyon Kruglyak,
- Elliott H. Margulies,
- Gil McVean,
- and David R. Bentley
Genome Res. January 2017 27: 157-164; Published in Advance November 30, 2016, doi:10.1101/gr.210500.116
...possible as methods for detection improve. However, compared to the small variants, the haplotypes in a single pedigree contain relatively few large structural events. A population-based approach, using aggregated whole- data, is a more appropriate strategy to identify comprehensive -wide sets of CNVs...
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Method: Parente2: a fast and accurate method for detecting identity by descent
- Jesse M. Rodriguez,
- Sivan Bercovici,
- Lin Huang,
- Roy Frostig,
- and Serafim Batzoglou
Genome Res. February 2015 25: 280-289; Published in Advance October 1, 2014, doi:10.1101/gr.173641.114
...novo mutations. Such shared segments are called identical-by-descent (IBD). Computational detection of IBD segments from genotyping or sequencing data serves as the foundation for many downstream applications (Browning and Browning 2012). IBD detection is the prevalent method for finding familial...
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Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
...callers in order to facilitate the phasing of more complete haploblocks. The resulting variant file is phased using both alignment and pedigree information (Fig. 1C). A parental graph reference is then constructed using only the parental genotypes from the joint-called VCF file (Fig. 1D). A haplotype...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...simultaneous testing for 270 diseases. Identification of component ancestry for mixed breed dogs is also big business. The widespread use of these tests is helping researchers to characterize the broad population-based allele frequencies associated with many diseases and to also help map new disease risk...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
...selection pressures than single-nucleotide polymorphisms (SNPs) (Hsieh et al. 2019; Ho et al. 2020). Yet, the role of SV introgression in highly reticulated evolutionary history of the Bos genus (Wu et al. 2018) has not been systematically investigated by using population-based detection methods...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...>90% (Fig. 3A). Genotype accuracy of the pipeline was evaluated using a family trio, for which 1747 common deletions (94.33%) were validated by pedigree information. A more global evaluation of genotype accuracy was performed using individual deletion calls as alleles of genetic markers to analyze...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...local recombination rate differences between populations, as well as improve genotype imputation accuracy from lower- to higher-density SNP arrays. Here we report creation of fine-scale recombination maps and predicted hotspot locations for the domestic horse as well as 12 individual breeds. We assess...
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LETTER: Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
- Xin Lu,
- Tianhua Niu,
- and Jun S. Liu
Genome Res. September 2003 13: 2112-2117; doi:10.1101/gr.586803
...) mappings ( Fallin and Schork 2000 ; Fallin et al. 2001 ), much effort has been made in phasing individuals' two haplotypes, either experimentally or computationally. When the family-based genetic information is available, it is relatively easy to infer the individuals' phases from their genotype data...

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