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Trends in Genetics : TIG Sep 2023Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations,... (Review)
Review
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
Topics: Humans; High-Throughput Nucleotide Sequencing; Genomics; Sequence Analysis, DNA; Computational Biology; Gene Expression Profiling
PubMed: 37230864
DOI: 10.1016/j.tig.2023.04.006 -
Nature Chemical Biology Aug 2023
Topics: DNA Methylation; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37322154
DOI: 10.1038/s41589-023-01356-9 -
Journal of Immunology (Baltimore, Md. :... Dec 2023
Topics: Software; Algorithms; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37983523
DOI: 10.4049/jimmunol.2390020 -
Journal of Immunology (Baltimore, Md. :... Oct 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37782854
DOI: 10.4049/jimmunol.2390017 -
Clinical Laboratory Aug 2023Next-generation sequencing (NGS) methods have become more commonly performed in clinical and research laboratories. (Review)
Review
BACKGROUND
Next-generation sequencing (NGS) methods have become more commonly performed in clinical and research laboratories.
METHODS
This review summarizes the current laboratory NGS-based diagnostic approaches in pharmacogenomics including targeted multi-gene panel sequencing, whole-exome sequencing (WES), and whole-genome sequencing (WGS).
RESULTS
Clinical laboratories perform multiple non-uniform types of pharmacogenetic panels, which can reduce the overall number of single-gene tests to be more cost-efficient. Compared to the targeted multi-gene panels, which are not typically designed to detect novel variants, WES and WGS have a greater potential to identify secondary pharmacogenomic findings, which might be predictive for the pharmacotherapy outcome of different patient settings. WGS overcomes the limitations of WES enabling a more accurate exome-sequencing at appropriate coverage and the sequencing of non-coding regions. Different NGS-based study designs with different test strategies and study populations, varying sample sizes, and distinct analytical and interpretation procedures lead to different identification results of pharmacogenomic variants.
CONCLUSIONS
The rapid progress in gene sequencing technologies will overcome the clinical and laboratory challenges of WES and WGS. Further high throughput NGS-based pharmacogenomics studies in different populations and patient settings are necessary to expand knowledge about rare functional variants and to enhance translation in clinical practice.
Topics: Humans; Pharmacogenetics; High-Throughput Nucleotide Sequencing
PubMed: 37560847
DOI: 10.7754/Clin.Lab.2023.230103 -
Journal of Immunology (Baltimore, Md. :... Apr 2024
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 38560812
DOI: 10.4049/jimmunol.2490001 -
Journal of Immunology (Baltimore, Md. :... May 2024
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 38621194
DOI: 10.4049/jimmunol.2490002 -
Journal of Immunology (Baltimore, Md. :... Jan 2024
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 38166253
DOI: 10.4049/jimmunol.2390023 -
Nature Biotechnology May 2024
Topics: Nanopore Sequencing; Humans; Nanopores; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA
PubMed: 38760549
DOI: 10.1038/s41587-024-02231-1 -
The Journal of Applied Laboratory... Jan 2024Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and... (Review)
Review
BACKGROUND
Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and structure. Similar to the evolution of single nucleotide variant detection from Sanger sequencing to next-generation sequencing, the identification of chromosome alterations has progressed from banding to fluorescence in situ hybridization (FISH) to chromosomal microarrays. More recently, emerging technologies such as optical genome mapping and genome sequencing have made noteworthy contributions to clinical laboratory testing in the field of cytogenetics.
CONTENT
In this review, we journey through some of the most pivotal discoveries that have shaped the development of clinical cytogenetics testing. We also explore the current test offerings, their uses and limitations, and future directions in technology advancements.
SUMMARY
Cytogenetics methods, including banding and targeted assessments like FISH, continue to hold crucial roles in cytogenetic testing. These methods offer a rapid turnaround time, especially for conditions with a known etiology involving recognized cytogenetic aberrations. Additionally, laboratories have the flexibility to now employ higher-throughput methodologies to enhance resolution for cases with greater complexity.
Topics: Humans; In Situ Hybridization, Fluorescence; Chromosome Aberrations; Cytogenetics; Chromosome Mapping; High-Throughput Nucleotide Sequencing
PubMed: 38167757
DOI: 10.1093/jalm/jfad086