Searching journal content for articles similar to Harvey et al. 33 (12): 2029.

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  1. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...55421, USA Corresponding author: jshaw@ds.dfci.harvard.eduAbstractReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized...
  2. Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
    • Can Luo,
    • Zimeng Jamie Zhou,
    • Yichen Henry Liu,
    • and Xin Maizie Zhou
    Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
    ...significant potential for advancing precision medicine. Despite notable progress in single-molecule long-read sequencing technologies, accurately identifying SV breakpoints and resolving their sequence remains a major challenge. Current alignment-based tools often struggle with precise breakpoint detection...
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  3. Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    • Nathan Hammond,
    • Linda Liao,
    • Pun Wai Tong,
    • Zena Ng,
    • Thuy-Mi P. Nguyen,
    • Chandler Ho,
    • Yao Yang,
    • and Stuart A. Scott
    Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
    ..., comparisons of sequencing platforms and variant calling strategies have recently been reported by the PrecisionFDA Truth Challenge V2, which found long-read HiFi sequencing to outperform both short-read and long-read nanopore sequencing with -wide variant calling accuracy (Olson et al. 2022).Although long-read...
  4. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...fails at multiple levels: read initiation (very few reads start within satellite regions), read elongation (satellite-containing reads are shorter on average), and basecalling (quality scores drop as sequencing enters a satellite sequence). These findings challenge the assumption that long-read...
  5. 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
    ...and preparation protocols for different organisms. The optimal choice of technology is contingent upon the specific application, with factors such as the complexity of variant calling or the desired level of assembly influencing the decision.View larger version: In this window In a new window Figure 1. Long-read...
  6. 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
    ...(CML) (Kovaka et al. 2024). (C–F, adapted from Thibodeau et al. 2020, Sakamoto et al. 2021a, Xu et al. 2023, and Kovaka et al. 2024).Related studies such as the PrecisionFDA Challenge (Olson et al. 2022) helped show how long reads improved variant call accuracy in regions difficult to map with short...
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  7. 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 first aligning these to a reference . Variant calling from LRS assemblies against the reference can improve the precision and recall of SVs and indels compared to standard reference-based variant detection (Ebert et al. 2021; Harvey et al. 2023). Alternatively, these assemblies can be further leveraged...
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  8. Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    ....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
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  9. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ....63 and 0.51 for long-read and short-read sequencing, respectively) (Supplemental Fig. 2C,D). Taken together, these measures of quality control underscore the high precision in allelic assignment.We then employed a supervised machine learning approach (Liu et al. 2019; Hendra et al. 2022) to quantify m6A...
  10. Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
    • Jesper Eisfeldt,
    • Adam Ameur,
    • Felix Lenner,
    • Esmee Ten Berk de Boer,
    • Marlene Ek,
    • Josephine Wincent,
    • Raquel Vaz,
    • Jesper Ottosson,
    • Tord Jonson,
    • Sofie Ivarsson,
    • Sofia Thunström,
    • Alexandra Topa,
    • Simon Stenberg,
    • Anna Rohlin,
    • Anna Sandestig,
    • Margareta Nordling,
    • Pia Palmebäck,
    • Magnus Burstedt,
    • Frida Nordin,
    • Eva-Lena Stattin,
    • Maria Sobol,
    • Panagiotis Baliakas,
    • Marie-Louise Bondeson,
    • Ida Höijer,
    • Kristine Bilgrav Saether,
    • Lovisa Lovmar,
    • Hans Ehrencrona,
    • Malin Melin,
    • Lars Feuk,
    • and Anna Lindstrand
    Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
    ...- long-read sequencing downsampling and its effect on variant-calling precision and recall. Genome Res 33: 2029–2040. doi:10.1101/gr.278070.123 ↵Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009. Mechanisms of change in gene copy number. Nat Rev Genet 10: 551–564. doi:10.1038/nrg2593 ↵Heller D, Vingron M...
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