Applications of long-read sequencing to Mendelian genetics

Mastrorosa, Francesco K.; Miller, Danny E.; Eichler, Evan E.

doi:10.1186/s13073-023-01194-3

Cited by 31 publications

(22 citation statements)

References 151 publications

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“…Additionally, long-read sequencing technologies are emerging approaches for detecting all types of genetic variation with a single test, including complex variants as well as variants in genomic regions that are difficult to resolve with short reads (e.g., repetitive regions). 22 Future studies could aim to evaluate the validity and utility of long-read sequencing, including at reduced depth of coverage, in the prenatal setting.…”

Section: Discussionmentioning

confidence: 99%

Validation of low‐pass genome sequencing for prenatal diagnosis

Mighton,

Noor,

Watkins

et al. 2024

Prenatal Diagnosis

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ObjectiveChromosomal microarray (CMA), while considered the gold standard for detecting copy number variants (CNVs) in prenatal diagnostics, has its limitations, including the necessity to replace aging microarray equipment, low throughput, a static design, and an inefficient multi‐day workflow. This study evaluates the feasibility of low‐pass genome sequencing (LP‐GS) as a potential replacement for CMA in prenatal diagnostics.MethodsWe comprehensively compared LP‐GS at 10x and 5x average depths with CMA in a prenatal laboratory. We examined parameters, including concordance, sensitivity, specificity, workflow efficiency, and cost‐effectiveness.ResultsWe found a high degree of agreement between LP‐GS and CMA for detecting CNVs and absence of heterozygosity. Furthermore, compared to CMA, LP‐GS increased workflow efficiency and proved to be cost‐neutral at 10x and cost‐effective at 5x.ConclusionOur study suggests that LP‐GS is a promising alternative to CMA in prenatal diagnostics, offering advantages, including a more efficient workflow and scalability for larger testing volumes. Importantly, for clinical laboratories that have adopted next‐generation sequencing in a separate capacity, LP‐GS facilitates a unified NGS‐centric approach, enabling workflow consolidation. By offering a single, streamlined platform for detecting a broad range of genetic variants, LP‐GS may represent a critical step toward enhancing the diagnostic capabilities of prenatal laboratories.

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Section: Discussionmentioning

confidence: 99%

Validation of low‐pass genome sequencing for prenatal diagnosis

Mighton,

Noor,

Watkins

et al. 2024

Prenatal Diagnosis

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“…These findings highlight the comparatively limited sensitivity of traditional sequencing techniques for resolving complex variants such as variable nucleotide tandem repeats. Future studies leveraging targeted sequencing methods such as Cas9, PCR, and hybridization capture focusing on these loci in a larger set of individuals would enable comprehensive population-level variant analysis [111].…”

Section: Discussionmentioning

confidence: 99%

Nanopore-based DNA long-read sequencing analysis of the aged human brain

Ramirez,

Sun,

Kazempour Dehkordi

et al. 2024

Preprint

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Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed “dark loci,” are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements (“jumping genes”) as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer’s disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer’s disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer’s disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer’s disease neuropathology.

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“…It is especially difficult to reconstruct individual genomes in mixed microbial communities when multiple genomes are present [ 67 ]. Additionally, short-read sequencing may encounter repetitive regions and structural variations, making genome assembly less accurate and complete [ 68 ]. For the target sequencing, one key challenge is the risk of amplification bias during enrichment, which causes the data to reflect a skew of certain microbial taxa or genomic regions, which can affect microbial diversity quantification and prevent detection of rare or novel organisms [ 69 ].…”

Section: Understanding the Role Of Iso Standards In Workflow Standard...mentioning

confidence: 99%

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

Kan,

Tsang,

Pei

et al. 2024

IJMS

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Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives.

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Applications of long-read sequencing to Mendelian genetics

Cited by 31 publications

References 151 publications

Validation of low‐pass genome sequencing for prenatal diagnosis

Validation of low‐pass genome sequencing for prenatal diagnosis

Nanopore-based DNA long-read sequencing analysis of the aged human brain

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

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