Genome Research publishes a special issue on long-read DNA and RNA sequencing applications in biology and medicine

 

Genome Research publishes a Special Issue on Long-read DNA and RNA Sequencing Applications in Biology and Medicine 

 

April 14, 2025 – Genome Research (https://genome.org) publishes a second special issue highlighting advances in long-read sequencing applications in biology and medicine.

In this second Special Issue, guest-edited by Dr. Ana Conesa, Dr. Alexander Hoischen, and Dr. Fritz Sedlazeck, Genome Research publishes a diverse collection of research, methods, and review articles highlighting novel applications and developments in long-read sequencing (LRS). Papers in this issue focus on original research offering novel biological and clinical insights gained using long-read DNA and RNA sequencing technologies and other long molecule approaches. This issue offers significant advances in long-read sequencing analysis, including epigenetics, transcriptome analysis, structural variation (SV) analysis, optical mapping, and rare disease diagnostics. Several of the studies are highlighted below. 

Several studies focus on human disease detection and diagnosis of rare disease (Jensen et al. 2025, neurological disorders (Rafehi et al. 2025), and cancer (Black et al. 2025; Karakulak et al. 2025; Porter et al. 2025; Zeng et al. 2025). Chen et al. (2025) present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which uses RCA and consensus calling based on genome-wide long-read nanopore sequencing to detect tumor fractions in cell-free DNA. Steyaert and colleagues, as part of the European Solve-RD consortium, applied long-read genome sequencing to ~300 individuals from previously undiagnosed rare disease families. They found (likely) disease-causing genetic variants in about 12% of previously unsolved families and additional candidate disease-causing structural variants in another 5.4% of these families. 

Several studies highlight the use of optical genome mapping, a nonsequencing approach that detects large complex structural variants, in identifying pathogenic repeat expansions (van der Sanden et al. 2025), structural variants in neural tube defects (Sahajpal et al. 2025), and resolving complex segmental duplications in microdeletion disorders (Vervoort et al. 2025).

Novel long-read sequencing data approaches are presented including tools enabling genome assembly, overcoming challenges posed by repetitive regions (Chakravarty et al. 2025; Vrček et al. 2025), SV analysis (Munro et al. 2025), and long-read RNA sequencing (Pryszcz et al. 2025; Park et al 2025). Zhang et al. present MotifScope, a novel algorithm for characterization and visualization of tandem repeats, identifying a greater number of motifs and more accurately representing the underlying repeat sequence, which can be applied across diverse fields, including population genetics, clinical settings, and forensic analyses. Dondi and colleagues present LongSom, a computational workflow to call de novo somatic single-nucleotide variants (SNVs), copy-number alterations (CNAs), and gene fusions in long-read single-cell RNA-seq data. When applied to an ovarian cancer sample, LongSom detected clinically relevant somatic SNVs that could not be detected with short-read single-cell RNA-seq and identified subclones with different predicted treatment outcomes.

Several studies highlight the use of long-read technologies beyond human biology. Horsfiel et al. (2025) developed GNASTy, a new pangenome-graph algorithm for serotype detection and surveillance of Streptococcus pneumoniae. Oggenfuss et al. (2025) identified distinct SVs across clinical isolates of Candida albicans at centromeres. Milia et al. (2024) constructed a graph pangenome to identify and characterize SVs associated with cattle phenotypes. Paniagua et al. (2025) analyze how long-read RNA sequencing platforms enhance genome annotation and incorporate long-read transcripts into an annotation pipeline applied to a nonmodel species, the Florida manatee.

In addition, this issue reviews applications of LRS in human diseases (Del Gobbo and Boycott 2025; Li et al. 2025) population-scale genomics (Rausch et al. 2025), genome annotation (Monzó et al. 2025), and methodological advances (Mahmoud et al. 2025; Montano and Timp 2025).  

This collection of reviews and research demonstrates the biological and clinical advances made possible with long-read technologies that were unattainable with previous techniques.

 

References

Black GS, Huang X, Qiao Y, Moos P, Sampath D, Stephens DM, Woyach JA, Marth GT. 2025. Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia. Genome Res (this issue) 35: 686–697. doi:10.1101/gr.279049.124

Chakravarty S, Logsdon G, Lonardi S. 2025. RAmbler resolves complex repeats in human Chromosomes 8, 19, and X. Genome Res (this issue) 35: 863–876. doi:10.1101/gr.279308.124

Chen L-T, Jager M, Rebergen D, Brink GJ, van den Ende T, Vanderlinden W, Kolbeck P, Pagès-Gallego M, van der Pol Y, Besselink N, et al. 2025. Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling. Genome Res (this issue) 35: 886–899. doi:10.1101/gr.279144.124

Del Gobbo GF, Boycott KM. 2025. The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases. Genome Res (this issue) 35: 575–587. doi:10.1101/gr.279970.124

Dondi A, Borgsmüller N, Ferreira PF, Haas BJ, Jacob F, Heinzelmann-Schwarz V, Tumor Profiler Consortium, Beerenwinkel N. 2025. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. Genome Res (this issue) 35: 900–913. doi:10.1101/gr.279281.124

Horsfield ST, Fok BCT, Fu Y, Turner P, Lees JA, Croucher NJ. 2025. Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm. Genome Res (this issue) 35: 1025–1040. doi:10.1101/gr.279435.124

Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, et al. 2025. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. Genome Res (this issue) 35: 914–928. doi:10.1101/gr.279323.124

Karakulak T, Zajac N, Bolck HA, Bratus-Neuenschwander A, Zhang Q, Qi W, Basu D, Oltra TC, Rehrauer H, von Mering C, et al. 2025. Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids. Genome Res (this issue) 35: 698–711. doi:10.1101/gr.279345.124

Li Q, Keskus AG, Wagner J, Izydorczyk MB, Timp W, Sedlazeck FJ, Klein AP, Zook JM, Kolmogorov M, Schatz MC. 2025. Unraveling the hidden complexity of cancer through long-read sequencing. Genome Res (this issue) 35: 588–609. doi:10.1101/gr.280041.124

Mahmoud M, Agustinho DP, Sedlazeck F. 2025. A Hitchhiker’s Guide to long-read genomic analysis. Genome Res (this issue) 35: 545–558. doi:10.1101/gr.279975.124

Milia S, Leonard AS, Mapel XM, Bernal Ulloa SM, Drögemüller C, Pausch H. 2025. Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle. Genome Res (this issue) 35: 1041–1052. doi:10.1101/gr.279064.124

Montano C, Timp W. 2025. Evolution of genome-wide methylation profiling technologies. Genome Res (this issue) 35: 610–620. doi:10.1101/gr.278407.123

Monzó C, Frankish A, Conesa A. 2025. Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation. Genome Res (this issue) 35: 559–568. doi:10.1101/gr.279865.124

Munro R, Payne A, Holmes N, Moore C, Cahyani I, Loose M. 2025. Enhancing nanopore adaptive sampling for PromethION using readfish at scale. Genome Res (this issue) 35: 877–885. doi:10.1101/gr.279329.124

Oggenfuss U, Todd RT, Soisangwan N, Kemp B, Guyer A, Beach A, Selmecki A. 2025. Candida albicansisolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres. Genome Res (this issue) 35: 824–838. doi:10.1101/gr.279301.124

Paniagua A, Agustín-García C, Pardo-Palacios FJ, Brown T, De Maria M, Denslow ND, Mazzoni CJ, Conesa A. 2025. Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq. Genome Res (this issue) 35: 1053–1064. doi:10.1101/gr.279864.124

Park D, Cenik C. 2025. Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications. Genome Res (this issue) 35: 999–1011. doi:10.1101/gr.279270.124

Porter VL, Ng M, O’Neill K, MacLennan S, Corbett RD, Culibrk L, Hamadeh Z, Iden M, Schmidt R, Tsaih S-W, et al. 2025. Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation. Genome Res (this issue) 35: 653–670. doi:10.1101/gr.279041.124

Pryszcz LP, Diensthuber G, Llovera L, Medina R, Delgado-Tejedor A, Cozzuto L, Ponomarenko J, Novoa EM. 2025. Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger. Genome Res (this issue) 35: 956–966. doi:10.1101/gr.279290.124

Rafehi H, Fearnley LG, Read J, Snell P, Davies KC, Scott L, Gillies G, Thompson GC, Field TA, Eldo A, et al. 2025. A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia. Genome Res (this issue) 35: 769–785. doi:10.1101/gr.279634.124

Rausch T, Marschall T, Korbel JO. 2025. The impact of long-read sequencing on human population-scale genomics. Genome Res (this issue) 35: 569–574. doi:10.1101/gr.280120.124

Sahajpal NS, Dean J, Hilton B, Fee T, Skinner C, Hastie A, DuPont BR, Chaubey A, Friez MJ, Stevenson RE. 2025. Optical genome mapping identifies rare structural variants in neural tube defects. Genome Res (this issue) 35: 798–809. doi:10.1101/gr.279318.124

Steyaert W, Sagath L, Demidov G, Yépez V, Esteve-Codina A, Gagneur J, Ellwanger K, Derks R, Weiss M, den Ouden A, et al. 2025. Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing. Genome Res (this issue) 35: 755–768. doi:10.1101/gr.279414.124

van der Sanden B, Neveling K, Shukor S, Gallagher MD, Lee J, Burke SL, Pennings M, van Beek R, Oorsprong M, Kater-Baats E, et al. 2025. Optical genome mapping enables accurate testing of large repeat expansions. Genome Res (this issue) 35: 810–823. doi:10.1101/gr.279491.124

Vervoort L, Dierckxsens N, Sousa Santos M, Meynants S, Souche E, Cools R, Heung T, Devriendt K, Peeters H, McDonald-McGinn DM, et al. 2025. Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome. Genome Res (this issue) 35: 786–797. doi:10.1101/gr.279331.124

Vrček L, Bresson X, Laurent T, Schmitz M, Kawaguchi K, Šikić M. 2025. Geometric deep learning framework for de novo genome assembly. Genome Res (this issue) 35: 839–849. doi:10.1101/gr.279307.124

Zeng T, Liao H, Xia L, You S, Huang Y, Zhang J, Liu Y, Liu X, Xie D. 2025. Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis. Genome Res (this issue) 35: 671–685. doi:10.1101/gr.279617.124

Zhang Y, Hulsman M, Salazar A, Tesi N, Knoop L, van der Lee S, Wijesekera S, Krizova J, Kamsteeg E-J, Holstege H. 2025. Multisample motif discovery and visualization for tandem repeats. Genome Res (this issue) 35: 850–862. doi:10.1101/gr.279278.124

 

In addition to the articles highlighted above, the following will also appear in the issue: 

Beaulaurier J, Ly L, Duty JA, Tyer C, Stevens C, Hung C-T, Sookdeo A, Drong AX,  Kowdle S, Guzman-Solis A, et al. 2025. De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies. Genome Res (this issue) 35: 929–941. doi:10.1101/gr.279392.124

Choquet K, Chaumont L-P, Bache S, Baxter-Koenigs AR, Churchman LS. 2025. Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing. Genome Res (this issue) 35: 712–724. doi:10.1101/gr.279203.124

Genner R, Akeson S, Meredith M, Alvarez Jerez P, Malik L, Baker B, Miano-Burkhardt A, CARD-long-read Team, Paten B, Billingsley KJ, et al. 2025. Assessing DNA methylation detection for primary human tissue using Nanopore sequencing. Genome Res (this issue) 35: 632–643. doi:10.1101/gr.279159.124

Groza C, Ge B, Cheung WA, Pastinen T, Bourque G. 2025. Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA. Genome Res (this issue) 35: 644–652. doi:10.1101/gr.279240.124

Keil N, Monzó C, McIntyre L, Conesa A. 2025. Quality assessment of long read data in multisample lrRNA-seq experiments with SQANTI-reads. Genome Res (this issue) 35: 987–998. doi:10.1101/gr.280021.124

Murali M, Saquing J, Lu S, Gao Z, Watts EF, Jordan B, Wakefield ZP, Fiszbein A, Cooper DR, Castaldi PJ, et al. 2025. Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity. Genome Res (this issue) 35: 1012–1024. doi:10.1101/gr.279317.124

Paulin LF, Fan J, O’Neill K, Pleasance E, Porter VL, Jones SJM, Sedlazeck FJ. 2025. Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T. Genome Res (this issue) 35: 621–631. doi:10.1101/gr.279352.124

Peng H, Jabbari JS, Tian L, Wang C, You Y, Chua CC, Anstee NS, Amin N, Wei AH, Davidson NM, et al. 2025. Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes. Genome Res (this issue) 35: 942–955. doi:10.1101/gr.279322.124

Qin Q, Popic V, Wienand K, Yu H, White E, Khorgade A, Shin A, Georgescu C, Campbell CD, Dondi A, et al. 2025. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution. Genome Res (this issue) 35: 967–986. doi:10.1101/gr.279200.124

Stemerdink M, Riepe T, Zomer N, Salz R, Kwint M, Oostrik J, Timmermans R, Ferrari B, Ferrari S, Dueñas Rey A, et al. 2025. Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches. Genome Res (this issue) 35: 725–739. doi:10.1101/gr.280060.124

Wang M, Li Y, Wang J, Oh SH, Cao Y, Chen R. 2025. Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina. Genome Res (this issue) 35: 740–754. doi:10.1101/gr.279167.124

 

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About Genome Research: Launched in 1995, Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.

 

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