Long read sequencing on its way to the routine diagnostics of genetic diseases

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Март 6, 2024

The clinical application of technological progress in the identification DNA alterations has always led to improvements diagnostic yields genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects genomic microarrays detecting cryptic copy variants, at molecular level, Sanger method studying nucleotide sequence single genes high-throughput next-generation sequencing (NGS) technologies, resolution sensitivity progressively increased expanding considerably range detectable anomalies alongside Mendelian disorders with known causes. However, particular regions (i.e., repetitive GC-rich sequences) are inefficiently analyzed by standard tests, still relying on laborious, time-consuming low-sensitive approaches southern-blot for repeat expansion or long-PCR highly homologous pseudogenes), accounting least part patients undiagnosed disorders. Third generation sequencing, generating long reads improved mappability, is more suitable detection hardly accessible regions. Although recently implemented not yet clinically available, read (LRS) technologies have already shown their potential medicine research that might greatly impact yield reporting times, through translation settings. main investigated LRS concerns variants expansions, probably because evolved as rapidly those dedicated (SNV) identification: gold analyses karyotyping balanced unbalanced rearrangements, respectively, southern blot repeat-primed PCR amplification sizing expanded alleles, impaired limited been significantly advent NGS. Nevertheless, recently, accuracy provided latest product releases, tested also SNV detection, especially pseudogenes haplotype reconstruction assess parental origin alleles de novo pathogenic variants. We provide a review relevant recent scientific papers exploring diagnosis diseases its future applications routine testing.

Язык: Английский

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Targeting RNA splicing modulation: new perspectives for anticancer strategy?

Journal of Experimental & Clinical Cancer Research, Год журнала: 2025, Номер 44(1)

Опубликована: Янв. 30, 2025

Язык: Английский

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Advances in single-cell long-read sequencing technologies

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(2)

Опубликована: Апрель 4, 2024

Abstract With an increase in accuracy and throughput of long-read sequencing technologies, they are rapidly being assimilated into the single-cell pipelines. For transcriptome sequencing, these techniques provide RNA isoform-level information addition to gene expression profiles. Long-read technologies not only help uncovering complex patterns cell-type specific splicing, but also offer unprecedented insights origin cellular complexity thus potentially new avenues for drug development. Additionally, DNA enables high-quality assemblies, structural variant detection, haplotype phasing, resolving high-complexity regions, characterization epigenetic modifications. Given that significant progress has primarily occurred isoform (scRiso-seq), this review will delve advancements depth highlight practical considerations operational challenges, particularly pertaining downstream analysis. We aim a concise introduction complementary genome, epigenome epitranscriptome. conclude by identifying certain key areas innovation may drive further foster more widespread application biomedical science.

Язык: Английский

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Single-cell Rapid Capture Hybridization sequencing to reliably detect isoform usage and coding mutations in targeted genes

Genome Research, Год журнала: 2025, Номер unknown, С. gr.279322.124 - gr.279322.124

Опубликована: Янв. 10, 2025

Single-cell long-read sequencing has transformed our understanding of isoform usage and the mutation heterogeneity between cells. Despite unbiased in-depth analysis, low throughput often results in insufficient read coverage thereby limiting ability to perform calling for specific genes. Here, we developed a single-cell Rapid Capture Hybridization (scRaCH-seq) method that demonstrated high specificity efficiency capturing targeted transcripts using sequencing, allowing an analysis status transcript genes interest. The includes creating probe panel capture, barcoded primers pooling efficient via Oxford Nanopore Technologies platforms. scRaCH-seq is applicable stored indexed cDNA which allows be combined with existing short-read RNA-seq datasets. In investigation BTK SF3B1 samples from patients chronic lymphocytic leukaemia (CLL), detected isoforms mutations sensitivity. Integration scRNA-seq data revealed significant gene expression differences -mutated CLL cells, though it did not impact sensitivity anti-cancer drug venetoclax. scRaCH-seq's capability study multiple makes powerful tool genomics.

Язык: Английский

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Single-Cell Sequencing: Genomic and Transcriptomic Approaches in Cancer Cell Biology

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(5), С. 2074 - 2074

Опубликована: Фев. 27, 2025

This article reviews the impact of single-cell sequencing (SCS) on cancer biology research. SCS has revolutionized our understanding and tumor heterogeneity, clonal evolution, complex interplay between cells microenvironment. provides high-resolution profiling individual in genomic, transcriptomic, epigenomic landscapes, facilitating detection rare mutations, characterization cellular diversity, integration molecular data with phenotypic traits. The multi-omics provided a multidimensional view states regulatory mechanisms cancer, uncovering novel therapeutic targets. Advances computational tools, artificial intelligence (AI), machine learning have been crucial interpreting vast amounts generated, leading to identification new biomarkers development predictive models for patient stratification. Furthermore, there emerging technologies such as spatial transcriptomics situ sequencing, which promise further enhance microenvironment organization interactions. As its related continue advance, they are expected drive significant advances personalized diagnostics, prognosis, therapy, ultimately improving outcomes era precision oncology.

Язык: Английский

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Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing

Molecular Aspects of Medicine, Год журнала: 2024, Номер 96, С. 101255 - 101255

Опубликована: Фев. 17, 2024

Язык: Английский

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Advances in long-read single-cell transcriptomics

Human Genetics, Год журнала: 2024, Номер 143(9-10), С. 1005 - 1020

Опубликована: Май 24, 2024

Abstract Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The protocols developed for long-read sequencing platforms overcome these limitations by enabling characterization of full-length techniques initially suffered from comparatively poor accuracy compared short read scRNA-Seq. However, with improvements accuracy, accessibility, cost efficiency, long-reads gaining popularity field This review details advances scRNA-Seq, an emphasis on library preparation downstream bioinformatics analysis tools.

Язык: Английский

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Applications of single-cell technologies in drug discovery for tumor treatment

iScience, Год журнала: 2024, Номер 27(8), С. 110486 - 110486

Опубликована: Июль 11, 2024

Язык: Английский

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Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications

Bioengineering, Год журнала: 2025, Номер 12(1), С. 56 - 56

Опубликована: Янв. 12, 2025

RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability measure gene expression in highly sensitive and accurate manner. With the increasing availability of RNA-seq data from clinical studies patient samples, development effective visualization tools become increasingly important help clinicians biomedical researchers better understand complex patterns associated with health disease. This review aims outline current state-of-the-art techniques commonly used frame inferences point out their benefits, applications, limitations. A systematic English articles using PubMed, Scopus, Web Science, IEEE Xplore databases was performed. Search terms included “RNA-seq”, “visualization”, “plots”, “clinical”. Only full-text reported between 2017 2024 were analysis. Following PRISMA guidelines, total 126 identified, which 33 met inclusion criteria. We found that 18% have circular data, 56% single-cell 23% bulk 3% long non-coding data. Overall, this provides comprehensive overview common potential is useful interested various purposes (e.g., diagnosis or prognosis).

Язык: Английский

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Data Sensemaking Framework by Applying Conceptual Modeling and Data Analysis: A Case Study From the Norwegian Public Transportation Domain

Systems Engineering, Год журнала: 2025, Номер unknown

Опубликована: Янв. 31, 2025

ABSTRACT The industry aims to adopt data‐driven methods improve system availability and reliability. A critical challenge in this process is achieving data sensemaking for practitioners, including maintenance personnel decision‐makers, product developers, consultants. This article replicates a framework that combines conceptual modeling analysis achieve sensemaking. main author previously developed exemplified the through case study of an automated parking small‐and‐medium‐sized enterprise. implemented more complex context: Norwegian Metro public transportation department within large enterprise, using Oslo Metro. Applying assisted closing internal feedback loop. In context, we collected analyzed exploratively failure external weather spanning 6 years. parallel, several models co‐created with various stakeholders. These facilitated shared understanding processes guided exploratory analysis, turn, supporting modeling. evaluated on‐site participant observations, interviews, subject matter experts’ feedback, co‐creation sessions. Findings from observations emphasize complementary nature sensemaking, leading deeper behavior. aids improving their effectiveness, enhancing Despite implementation context‐dependent, findings indicate its motivating practitioners implement it other contexts.

Язык: Английский

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