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Research: Thousands of human mutation clusters are explained by short-range template switching
- Ari Löytynoja
Genome Res. August 2022 32: 1437-1447; Published in Advance June 27, 2022, doi:10.1101/gr.276478.121
...–903. doi:10.1016/j.cell.2011.07.042 ↵Löytynoja A, Goldman N. 2017. Short template switch events explain mutation clusters in the human . Genome Res 27: 1039–1049. doi:10.1101/gr.214973.116 ↵Marks P, Garcia S, Barrio AM, Belhocine K, Bernate J, Bharadwaj R, Bjornson K, Catalanotti C, Delaney J, Fehr A, et...
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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
...the raw HiFi read data back to the assembly to quantify the read coverage across the locus and validate this result. In a well-assembled region, the read coverage should be uniform, lacking sudden and dramatic changes in coverage in a short span. The sudden drop and rise in coverage and doubled coverage...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...-read-based manatee annotation with the NCBI annotationWe compared our LRB annotation to the available NCBI T. manatus latirostris Annotation Release 102, obtained using short reads and the NCBI Eukaryotic Genome Annotation Pipeline, to evaluate any gain or loss of information. We first determined the number...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...length of 16.4 kbp (NGI SciLifeLab).For the BH16643 family, short-read trio sequencing was performed at the Baylor College of Medicine Human Genome Sequencing Center (HGSC) with KAPA Hyper PCR-free reagents on the NovaSeq 6000 to an average of 37× coverage. Postsequencing data analysis was performed...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...poly(A) stretch was present (families 1, 2 CGR BPJ 2, Table 2). Such findings suggest that the rearrangement formed through fork stalling and template switching (FoSTes) (Lee et al. 2007), which commonly underlie chromoanasynthesis. Short microhomologies can also be consistent with nonhomologous end...
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Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...DNA into its actual composition using the relatively short “reads” that were obtained from the sequencing technology of those days. However, the recent development of DNA polymerase-independent long-read sequencing technologies, such as the Oxford Nanopore Technologies or Pacific Biosciences (PacBio) systems...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...; however, unaligned contributed more than any single rearrangement type. A more detailed examination of the relative size and frequency of syntenic, rearrangement, and unaligned events showed that syntenic regions were long and common, unaligned regions were short and common, inversions were long and very...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
....35%) and of TTAGGC in LJ2400 (98.11%) and LJ2406 (99.73%) (Fig. 1G; Supplemental Fig. S6; Supplemental Table S9). These findings supported our TRM study using short-read WGS data and revealed that the TTAGAC telomere had evolved in the family Panagrolaimidae.TTAGAC-containing units cluster near telomeric regions...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...dynamics and mutational landscape operating within intestinal neoplasia over the short lifespan of the adult fly. Our findings provide unique insight into mutational dynamics operating over a short timescale in the genetic model system, Drosophila melanogaster.The accumulation of mutations in somatic...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...genomic fragments and assign them to whole derivative chromosomes (Dudchenko et al. 2017; Ghavi-Helm et al. 2019). The long-range information can assist in connecting even repeat-rich sequences, which are impossible to assemble with standard short-read paired-end sequencing. Although Hi-C data can detect...
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