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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
...block length of ∼540 kbp), we discovered only two SNPs and two 1-bp indels associated with homopolymer tracts of length 8 and 13.The default assembly for A4 constructed the histone cluster into 119 copies. The read depth plot shows a drop in coverage (about half) for around ∼40–50 kb towards the end...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...Institute, Kansas City, Missouri 64108, USA; 4Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, Québec H3A 0G1, Canada Corresponding authors: david.lougheed@mail.mcgill.ca, guil.bourque@mcgill.caAbstractVariation in short tandem repeats (STRs) is implicated in Mendelian...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...of variant classes beyond single-nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) (Harris et al. 2024). Pan graphs represent sequence alignment of high-quality fully phased assemblies of individuals from diverse populations (Baaijens et al. 2022). A pan graph can be represented...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
.... S49B). This evaluates the frequency of indels surrounding each of the sgRNA breakpoints, which was quantified using the TIDE method (Brinkman et al. 2014) and found to be relatively low (0.8–7.6%) (Supplemental Table S19). This may partially explain the subtle effect on MYC expression and low Cas9...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
..., and 13.7% in GRCh38. In general, low-frequency variants skewed more toward indels and mixed variation (i.e., indels and SNVs at the same site) than common variants in T2T-CHM13 (Fig. 4D). Indels were generally skewed toward deletions in all assemblies. Overall, more bases were deleted than inserted...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...blocks and classify them as concordant, insertion, or deletion. Adjacent blocks with the same classification and contiguity are combined. Each insertion or deletion block is assigned an ISCN based on unique block-type signatures, in which indel size allowance determined via simulation (Supplemental Table...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...variant had a unique set of substitutions and insertions (Fig. 4B). In contrast, in the CHROMOSOME_V array, the most frequent 10 variants match the reference by ≤92%, and they lacked unique substitutions or deletions that would allow individual variants to be unambiguously distinguished (Supplemental Fig...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...versus the A. calliptera backbone across 5000 random bubbles, shown as columns. A positive value (green) represents an insertion, and a negative value (brown) represents a deletion, with darker colors indicating larger SVs/indels. (B) Number of SV alleles by type. (C) Length deviations of nonreference...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...Table S2; Supplemental Fig. S27).Clustered dnSVs and dnPMs reveal the common occurrence of complex postfertilization eventsIt has been shown in human studies that dnSVs are accompanied by nearby dnPMs (including small indels) more often than expected by chance, generating so-called clustered DNMs...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
.... However, as a consequence of limited read length and variant calling algorithms, single-nucleotide polymorphisms (SNPs) and small indels are disproportionately overrepresented within characterized sequence variation (Audano et al. 2019). Nevertheless, a growing number of research projects indicate...

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