Genome Research 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.

Source – Cold Spring Harbor Laboratory Press