Searching journal content for articles similar to Luo et al. 35 (10): 2252.

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  1. 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
    ..., Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly. Am J Hum Genet 111: 2693–2706. doi:10.1016/j.ajhg.2024.10.006 Nazaryan-Petersen L, Eisfeldt J, PetterssonM, Lundin J, Nilsson D, Wincent J, Lieden A, Lovmar L, Ottosson J, Gacic J, et al...
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  2. 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
    ...and accurate s. Additionally, the underrepresented Y-linked exons provide a valuable benchmark for refining those sequencing technologies while improving the assembly of the highly heterochromatic and often neglected Drosophila Y Chromosome.Long-read sequencing (LRS) technologies Pacific Biosciences (Pac...
  3. 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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  4. 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
    ...et al. 2017; Feng et al. 2021; Knyazev et al. 2021; Cai and Sun 2022; Cai et al. 2022; Shaw and Yu 2022; Zhou et al. 2024).We are interested in reference-based haplotyping for (1) long-read sequencing, (2) small sequences of approximately the read length, and (3) an unknown, possibly large, number...
  5. 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
    ...variants in the transcriptome (Glinos et al. 2022). Furthermore, long-read sequencing enables comprehensive analysis of splicing (Tilgner et al. 2015, 2018; Joglekar et al. 2021) which has fundamental importance for determining mRNA modifications due to their dependence on splicing patterns and transcript...
  6. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...that integrates into host genomic DNA and forms virus–virus and virus–host genomic structural rearrangements, which are unstable and lead to further intratumoral heterogeneity and clonal evolution; through long-read sequencing, unique breakpoints shared across structural variants were also observed in HPV...
  7. 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
    ...to profile DNA modifications and chromatin.Another feature of long-read sequencing is its ability to enable the phasing of variants. Phasing refers to determining whether or not two or more variants co-occur on the same DNA molecule (i.e., haplotype). Long-read-based phasing can detect rare or de novo...
  8. 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
    ...benefit of variant phasing (Ardui et al. 2018; Ameur et al. 2019). The two primary long-read sequencing chemistries currently available are single molecule real-time (SMRT; HiFi) and nanopore sequencing, which recently have been employed by the Telomere-to-Telomere (T2T) Consortium to more comprehensively...
  9. Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
    ...subclone to identify subclone-specific gene expression. (B) Genotype matrix plots visualize the genotypes of all cells at each variant of interest, showing green for reference allele, red for alternate allele, and white for no coverage.Long-read scRNA-seq enables confirmation or refinement of subclone...
  10. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    ...integration breakpoints.Benefiting from the advantages of LRS, long reads can simultaneously contain HBV DNA sequences and their adjacent human sequences. We utilized these spanning reads to further deduce the structural consequences of HBV DNA integration on the human . Based on the alignment direction...
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