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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...of the last to be fully assembled. It carries copy number–variable genes associated with intellectual disability, bipolar disorder, and obesity. In this study, we characterized the structural diversity at this locus by analyzing 64 haploid assemblies produced by the Human Pan Reference Consortium. We...
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Research: Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism
- Dale J. Annear,
- Geert Vandeweyer,
- Alba Sanchis-Juan,
- F. Lucy Raymond,
- and R. Frank Kooy
Genome Res. November/December 2022 32: 1967-1980; Published in Advance November 9, 2022, doi:10.1101/gr.277011.122
...-affected proband, we determined an unprecedented rate of CGG repeat length deviation across a single generation. Although the concept of repeat length being linked to deviation rate was solidified, we show how shorter STRs display greater degrees of size variation. We observed that CGG STRs did not segregate...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li1,15, Mian Gong1,15, Xinmiao Zhang1,15, Fei Wang1,15, Zhenyu Liu1,15, Lei Zhang1,15, Qimeng Yang1, Yuan Xu1, Mengsi Xu2, Huanhuan Zhang1, Yunfeng Zhang2, Xuelei Dai1, Yuanpeng Gao1, Zhuangbiao Zhang...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li,1,15 Mian Gong,1,15 Xinmiao Zhang,1,15 Fei Wang,1,15 Zhenyu Liu,1,15 Lei Zhang,1,15 Qimeng Yang,1 Yuan Xu,1 Mengsi Xu,2 Huanhuan Zhang,1 Yunfeng Zhang,2 Xuelei Dai,1 Yuanpeng Gao,1 Zhuangbiao Zhang...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...or complex structural variants with repeat units that are larger than the size of the individual reads. Three of the T. gondii reference s in ToxoDB (Gajria et al. 2008) were constructed by combining high-quality first-generation Sanger (Sanger et al. 1977) and second-generation 454 (Roche Applied Science...
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Resource: Structural variants in 3000 rice genomes
- Roven Rommel Fuentes,
- Dmytro Chebotarov,
- Jorge Duitama,
- Sean Smith,
- Juan Fernando De la Hoz,
- Marghoob Mohiyuddin,
- Rod A. Wing,
- Kenneth L. McNally,
- Tatiana Tatarinova,
- Andrey Grigoriev,
- Ramil Mauleon,
- and Nickolai Alexandrov
Genome Res. May 2019 29: 870-880; Published in Advance April 16, 2019, doi:10.1101/gr.241240.118
...contributing to phenotypic differences, and structural variants also play an important role (Saxena et al. 2014; Francia et al. 2015).Detection and characterization of structural variants (SVs) has revolutionized the understanding of the landscape of genomic variation in different species. A structural variant...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...(SNVs) and large copy number variants (CNVs, especially those 100 kb or larger), however, several studies have found it has poor accuracy for structural variant (SV) detection (Sedlazeck et al. 2018b; Chaisson et al. 2019; Zook et al. 2020). SVs are larger mutations, 50 bp or larger, where sequence...
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Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
- Matthew B. Rogers,
- James D. Hilley,
- Nicholas J. Dickens,
- Jon Wilkes,
- Paul A. Bates,
- Daniel P. Depledge,
- David Harris,
- Yerim Her,
- Pawel Herzyk,
- Hideo Imamura,
- Thomas D. Otto,
- Mandy Sanders,
- Kathy Seeger,
- Jean-Claude Dujardin,
- Matthew Berriman,
- Deborah F. Smith,
- Christiane Hertz-Fowler,
- and Jeremy C. Mottram
Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
...Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania Matthew B. Rogers 1 , 2 , 9 , James D. Hilley 3 , 9 , Nicholas J. Dickens 3 , 9 , Jon Wilkes 3 , Paul A. Bates 4...
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Resource: Simultaneous structural variation discovery among multiple paired-end sequenced genomes
- Fereydoun Hormozdiari,
- Iman Hajirasouliha,
- Andrew McPherson,
- Evan E. Eichler,
- and S. Cenk Sahinalp
Genome Res. December 2011 21: 2203-2212; Published in Advance November 2, 2011, doi:10.1101/gr.120501.111
...Simultaneous structural variation discovery among multiple paired-end sequenced genomes Fereydoun Hormozdiari 1 , 3 , Iman Hajirasouliha 1 , 3 , Andrew McPherson 1 , Evan E. Eichler 2 and S. Cenk Sahinalp 1 , 4 1School...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...deletions were removed from our genotype set; these comprised to a large extent regions difficult to assess with short read data owing to their high repeat content. Amongst the duplications, 505 (55%)were inferred to have a copy-number genotype of at least 4 (homozygous duplication) in at least one sample...

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