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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...into DNA elements and retroelements. Colors represent the TE-subfamily age proxy calculated as mean divergence between genomic insertions and their consensus TE sequence. (Post-WGD) <7 Kimura distance, (WGD) 7–10 Kimura distance, (pre-WGD) >10 Kimura distance. (C) Number of TE-CREs from TEs...
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Method: Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
- Hua Zhang,
- Vamsi Krishna Polavarapu,
- Pengwei Xing,
- Miao Zhao,
- Lucy Mathot,
- Linxuan Zhao,
- Gabriela Rosen,
- Fredrik J. Swartling,
- Tobias Sjöblom,
- and Xingqi Chen
Genome Res. January 2022 32: 150-161; Published in Advance July 14, 2021, doi:10.1101/gr.275269.121
...) (Supplemental Fig. S1D,E), suggesting that DNA breaks indeed occur at accessible chromatin sites with long DNA lengths and that this further hampers PCR amplification of those regions (Fig. 1A). We then sequenced the libraries obtained through standard ATAC-seq on isolated FFPE nuclei (Supplemental Fig. S2A...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., USA; 2NVIDIA Corporation, Santa Clara, California 95051, USA Corresponding author: wwang7@mdanderson.orgAbstractAccurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
.... The analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303. doi:10.1101/gr.107524.110 ↵Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, et al. 2013. Comparative analysis of tandem repeats from hundreds...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...the same parent. Siblings should on average share 50% of their DNA. In Supplemental Figure S24, we look at the fraction of maternal and paternal genetic material shared IBD by the sibling pairs in our data set. We see that the distribution of IBD matches the expected distribution. Maternal IBD is expected...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...). These nonrandom error profiles impact precision and recall, especially for indel variant calls. When comparing the difference between all indel calls annotated with and without homopolymers, ONT call sets display a large difference between homopolymer and non-homopolymer DNA sequence precision and recall...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...and methylome analyses in oocytes revealed that DNA methylation is primarily restricted to transcribed regions (Kobayashi et al. 2012). These transcription events reshape the histone methylation landscape, guiding the DNMT complex to specific genomic regions. Specifically, the transcription-coupled loss of H3K4...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...DNA loss and A B C D E Figure 5. Cell cycle regulation of DNA replication and gene expression. (A) Exemplary genomic locus from Chromosome 4 showing enrichment of gene expression at the early replicating regions. Collapsed E/L ratios from PARTAGE Repli-seq data, PARTAGE multifraction signals...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
..._0) (Cheng et al. 2021), and SVs were called using SVIM-asm (v1.0.3) (Supplemental Code; Heller and Vingron 2021). Optical Genome Mapping Optical GenomeMapping (OGM) was performed as described previously (Bilgrav Saether et al. 2024). In brief, ultra-high-molecularweight genomic DNA from cases RD_P550 and RD...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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