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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...of megabase-scale somatic copy number variation using single-cell sequencing. Genome Res 26: 376–384. doi:10.1101/gr.198937.115 ↵Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, et al. 2019. Clonal decomposition and DNA replication states defined by scaled single-cell...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...of the long-read sequencing workflow including downstream analysis options. (B) Somatic SNV and a structural variation in the COLO829 cell line resulting in haplotype-specific copy number change and loss of heterozygosity (data from Keskus et al. 2024). Reads are grouped and colored with the alleles using...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254...
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Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
- Mikkel Dahl-Jessen,
- Thorkild Terkelsen,
- Rasmus O. Bak,
- and Uffe Birk Jensen
Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
...between deletions and inversions (Fig. 3E).Effect of DSB proximity on ligation of SV junctionsWe hypothesized that utilization of fast c-NHEJ for SV formation would require proximity between DSBs. To assess this, we employed high-throughput amplicon sequencing on five chimeric deletion junctions for each...
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Research: Complex mosaic structural variations in human fetal brains
- Shobana Sekar,
- Livia Tomasini,
- Christos Proukakis,
- Taejeong Bae,
- Logan Manlove,
- Yeongjun Jang,
- Soraya Scuderi,
- Bo Zhou,
- Maria Kalyva,
- Anahita Amiri,
- Jessica Mariani,
- Fritz J. Sedlazeck,
- Alexander E. Urban,
- Flora M. Vaccarino,
- and Alexej Abyzov
Genome Res. December 2020 30: 1695-1704; Published in Advance October 29, 2020, doi:10.1101/gr.262667.120
...-016-1103-0 ↵Knouse KA, Wu J, Whittaker CA, Amon A. 2014. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc Natl Acad Sci 111: 13409–13414. doi:10.1073/pnas.1415287111 ↵Knouse KA, Wu J, Amon A. 2016. Assessment of megabase-scale somatic copy number variation using single-cell...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...as a function of the 1D genomic distance (Fig. 3C). It can be seen that the tumor samples display large decay rates in the megabase scale, and the comparison between normal and cancerous CTG distance matrices suggests the loss of specific long-range interactions in colon cancer, as revealed by Figure 3C...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...et al. 2013a). Thesemethodologies allow for epitope-based detection of proteins and interacting partners for which high quality or specific antibodies are not available, as well as tracking of cellular proteins in real time on a single-cell basis. In addition, conditional alleles are useful...
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