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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
...1000Res 6: 664. doi:10.12688/f1000research.11168.1 Eisfeldt J, Ameur A, Lenner F, Ten Berk de Boer E, Ek M, Wincent J, Vaz R, Ottosson J, Jonson T, Ivarsson S, et al. 2024. A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities. Genome Res 34: 1774–1784. doi:10...
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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
...predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...University, Houston, Texas 77005, USA ↵4 These authors contributed equally to this work. Corresponding author: fritz.sedlazeck@bcm.eduAbstractOver the past decade, long-read sequencing has evolved into a pivotal technology for uncovering the hidden and complex regions of the . Significant cost efficiency...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...SVs, primarily due to their ability to uncover SVs and their breakpoints at single-nucleotide resolution and additionally by allowing to assemble complex variant sequences (Chaisson et al. 2019; Ebert et al. 2021; Zhao et al. 2021; Liao et al. 2023). These differences between short- and long-read...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...of these limitations, long-read sequencing (LRS) technologies were developed, enabling the -wide sequencing of native DNA fragments at multiple orders of magnitude larger than those in SR-GS, over 10 kb and up to megabases in size. In this mini-review, we review the existing evidence for LRS to increase diagnostic...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-resolved assemblies have become the norm in eukaryotic genomics with advances in long-read sequencing technologies. Complete assemblies are fundamental for addressing key questions in biology that were previously hidden in the “dark matter” of s. Key breakthroughs have revolved around centromeres and the embedded...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...QTLs, resolving these QTLs would not have been possible without characterization of pangenomic variation. Furthermore, long-read sequencing facilitated correct genotyping of SGE1 SNPs, a prerequisite for QTL resolution, in strains with SGE1 copies on multiple chromosomes.SUC gene content affects...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...alleles of a complex SV upstream of KIT and the phenotype.ResultsHead pigmentation segregates among sequenced breedsWe analyzed 24 long-read sequencing-based assemblies representing seven taurine cattle breeds to investigate the genetic underpinnings of head pigmentation. These assemblies included 14...
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Research: Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
- Maria Nattestad,
- Sara Goodwin,
- Karen Ng,
- Timour Baslan,
- Fritz J. Sedlazeck,
- Philipp Rescheneder,
- Tyler Garvin,
- Han Fang,
- James Gurtowski,
- Elizabeth Hutton,
- Elizabeth Tseng,
- Chen-Shan Chin,
- Timothy Beck,
- Yogi Sundaravadanam,
- Melissa Kramer,
- Eric Antoniou,
- John D. McPherson,
- James Hicks,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. August 2018 28: 1126-1135; Published in Advance June 28, 2018, doi:10.1101/gr.231100.117
...rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer available...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...option is probe-based target sequencing, with either long reads and de novo assembly, as utilized in the IGenotyper approach (Rodriguez et al. 2020, 2022; Gibson et al. 2023; Engelbrecht et al. 2024), or short reads (Lin et al. 2022). Studies using these approaches have successfully found that germline...
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