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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling—“stutter” artifacts—with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...of centromeric regions that limits 319 DNA accessibility and favors conserved repair mechanisms, reducing the occurrence 320 of large-scale SVs (Kashi and King 2006). Sequence annotation revealed that over 60% 321 of INS inserted in satellite/center, satellite, and simple repeat regions harbored 322 inserted...
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Method: Large-scale identification of chemically induced mutations in Drosophila melanogaster
- Nele A. Haelterman,
- Lichun Jiang,
- Yumei Li,
- Vafa Bayat,
- Hector Sandoval,
- Berrak Ugur,
- Kai Li Tan,
- Ke Zhang,
- Danqing Bei,
- Bo Xiong,
- Wu-Lin Charng,
- Theodore Busby,
- Adeel Jawaid,
- Gabriela David,
- Manish Jaiswal,
- Koen J.T. Venken,
- Shinya Yamamoto,
- Rui Chen,
- and Hugo J. Bellen
Genome Res. October 2014 24: 1707-1718; Published in Advance September 25, 2014, doi:10.1101/gr.174615.114
...Large-scale identification of chemically induced mutations in Drosophila melanogaster Nele A. Haelterman 1 , Lichun Jiang 2 , 3 , Yumei Li 2 , 3 , Vafa Bayat 1 , 4 , Hector Sandoval 2 , Berrak Ugur 1...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...insights into the molecular mechanisms underlying phenotypic variation, we next investigated the potential involvement of fm-mSTRs in human traits. Using SNV genotypes from the regions flanking fm-mSTRs (±250 kb), we computed the local LD structure of each locus to identify tag SNVs that strongly...
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RESOURCE: Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
- Anuj Kumar,
- Michael Seringhaus,
- Matthew C. Biery,
- Robert J. Sarnovsky,
- Lara Umansky,
- Stacy Piccirillo,
- Matthew Heidtman,
- Kei-Hoi Cheung,
- Craig J. Dobry,
- Mark B. Gerstein,
- Nancy L. Craig,
- and Michael Snyder
Genome Res. October 2004 14: 1975-1986; doi:10.1101/gr.2875304
...; Parks et al. 2004 ; Thibault et al. 2004 ). In the budding yeast Saccharomyces cerevisiae , we have previously employed large-scale shuttle mutagenesis to generate several -wide insertional libraries ( Ross-Macdonald et al. 1999 ). Each insertional library was constructed from a plasmid-based library...
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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
...), and other large-scale efforts, several thousands of tumors have been sequenced using short-read Illumina sequencing across dozens of major cancer types. These studies have had a tremendous impact in cancer genomics, leading to the discovery, for example, of different signatures and mutation rates across...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer and identification of drug resistance mutations Jonathan S. Brammeld,1 Mia Petljak,1 Inigo Martincorena,1 Steven P. Williams,1 Luz Garcia Alonso,2 Alba Dalmases,3 Beatriz Bellosillo,3 Carla Daniela Robles-Espinoza,4...
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RESOURCE: Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
- Gwenn M. Hansen,
- Diane C. Markesich,
- Michael B. Burnett,
- Qichao Zhu,
- Karen M. Dionne,
- Lizabeth J. Richter,
- Richard H. Finnell,
- Arthur T. Sands,
- Brian P. Zambrowicz,
- and Alejandro Abuin
Genome Res. October 2008 18: 1670-1679; Published in Advance September 17, 2008, doi:10.1101/gr.078352.108
...of trapped genes (six of 18 lines). This is probably because all available transcript data present in public databases are reviewed to select insertions located downstream from alternate promoters/TSSs. Discussion OmniBankII represents the first large-scale use of a C57BL/6 ES cell line in the production...
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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA; 8Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Mobile element insertions (MEIs) represent ∼25% of all structural variants in human s. Moreover...
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Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
...donor plasmid. In the present study, we observed that >95% cells in the BmEGCKLib harbored only a single sgRNA insertion as revealed by single-cell sequencing (Supplemental Fig. S8). Furthermore, the piggyBac transposon has the largest reported cargo capacity, up to 207 kb (Li et al. 2013...

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