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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...between the Alu sites, splitting each copy between the reference and insertion sequences and producing a chimeric TD copy in the SV insertion (Supplemental Fig. 2). This SV may represent an Alu-mediated duplication with an incorrect breakpoint, or the reference may be the result of a TD deletion...
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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
...that this rearrangement was mediated by inverted copies of ANXA8 duplicons and the breakpoints occur at ANXA8 loci (Table 3; Fig. 3C; Supplemental Fig. S5; Supplemental Table S3). Breakpoint analysis of H11 and H10 haplotypes, respectively, with the deletion of the distal and proximal copy of the NPY4R duplicon, showed...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; 4Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France ↵5 These authors contributed equally to this work. Corresponding author: dgresham@nyu.eduAbstractCopy number variants (CNVs), duplications and deletions of genomic...
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Research: The 22q11 low copy repeats are characterized by unprecedented size and structural variability
- Wolfram Demaerel,
- Yulia Mostovoy,
- Feyza Yilmaz,
- Lisanne Vervoort,
- Steven Pastor,
- Matthew S. Hestand,
- Ann Swillen,
- Elfi Vergaelen,
- Elizabeth A. Geiger,
- Curtis R. Coughlin,
- Stephen K. Chow,
- Donna McDonald-McGinn,
- Bernice Morrow,
- Pui-Yan Kwok,
- Ming Xiao,
- Beverly S. Emanuel,
- Tamim H. Shaikh,
- and Joris R. Vermeesch
Genome Res. September 2019 29: 1389-1401; doi:10.1101/gr.248682.119
..., driving variability and evolution. The Chromosome 22 LCRs (LCR22s) mediate nonallelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS). However, LCR22s are among the most complex regions in the , and their structure remains unresolved. The difficulty in generating accurate...
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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
...pathogenic mechanism associated with CGG STRs is repeat expansion. When a CGG STR expands beyond its full mutation breakpoint (typically more than 200 repeat units), it initiates an epigenetic event that results in hypermethylation of the repeat and the surrounding CpG islands. This, in turn, leads...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
.... 2004; Tuzun et al. 2005; Kidd et al. 2008; Mills et al. 2011; Eichler 2019). SVs can include “balanced” rearrangements, such as inversions and translocations, or genomic imbalances (duplications and deletions), commonly referred to as copy number variants (CNVs). Inversions represent an intriguing...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome. Chromosome Res 22: 335–350. doi:10.1007/s10577-014-9424-x ↵Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, Huang SC, Sanborn AL, Machol I, Shamim M, et al. 2016. Deletion of DXZ4 on the human inactive X chromosome...
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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
...synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...one palindrome. Deletions ranged from 3 kb up to 587 kb in size, and in four cases removed one or more copies of a protein-coding gene family (Table 2). In two cases, breakpoints fell within tandem repeats, suggesting that they arose through NAHR (Supplemental Fig. S10). All other breakpoints fell...
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Method: TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
- Ken Chen,
- Lei Chen,
- Xian Fan,
- John Wallis,
- Li Ding,
- and George Weinstock
Genome Res. February 2014 24: 310-317; Published in Advance December 4, 2013, doi:10.1101/gr.162883.113
...the sequence reads aligned to the reference (Li et al. 2009). An input breakpoint can be specified with different levels of detail. At a minimum, it must have the genomic coordinates of the predicted breakpoint. In addition, it can include the type of SV (e.g., deletion or insertion) that produced...

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