The application of long-read sequencing in clinical settings

Human Genomics, Год журнала: 2023, Номер 17(1)

Опубликована: Авг. 8, 2023

Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large complex regions of the genome makes them ideal for clinical applications molecular diagnosis therapy selection, thereby providing a valuable tool precision medicine. In third-generation duopoly, Oxford Nanopore Technologies Pacific Biosciences work towards increasing accuracy, throughput, portability long-read methods while trying keep costs low. These trades made an attractive use research settings. This article provides overview current limitations explores its potential point-of-care testing health care remote

Язык: Английский

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Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 4, 2024

Abstract Solve-RD is a pan-European rare disease (RD) research program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilised 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural (SVs), single nucleotide (SNVs), insertion-deletions (InDels), and short tandem repeat (STR) expansions extensively studied families without clear molecular diagnoses. Our cohort includes 293 individuals from 114 genetically selected by European Rare Disease Network (ERN) experts. Of these, 21 were affected so-called ‘unsolvable’ syndromes which causes remain unknown, 93 with at least one individual neurological, neuromuscular, or epilepsy disorder diagnosis despite extensive prior testing. Clinical interpretation orthogonal validation of known genes yielded thirteen novel diagnoses due de novo inherited SNVs, InDels, SVs, STR expansions. In an additional four families, we identified candidate SV affecting several including MCF2 / FGF13 fusion PSMA3 deletion. However, no common cause was any the syndromes. Taken together, found (likely) 13.0% unsolved SVs another 4.3% these conclusion, our results demonstrate added value genome diseases.

Язык: Английский

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Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders

Neural Regeneration Research, Год журнала: 2023, Номер 19(6), С. 1256 - 1261

Опубликована: Сен. 22, 2023

Abstract The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding disease-modifying mechanisms. Methylation N6 adenosine (m 6 A) and C5 cytosine 5 C) bases occur on mRNAs, tRNA, mt-tRNA, rRNA species well non-coding RNAs. With emerging knowledge binding proteins that act writer, reader, eraser effector proteins, comes a new physiological processes controlled by these systems. Such when spatiotemporally disrupted within cellular nanodomains highly specialized tissues such the brain, give rise to different forms disease. In this review, we discuss accumulating evidence changes m A C methylation systems contribute neurocognitive disorders. Early studies first identified mutations FMR1 cause intellectual disability Fragile X syndromes several years before was an reader protein. Subsequently, familial writer gene METTL5 , genes NSUN2 NSUN3 NSUN5 NSUN6 THOC2 THOC6 form protein complex with ALYREF, were recognized development Similarly, differences expression NSUN7 ALYREF brain tissue are indicated individuals Alzheimer’s disease, high neuropathological load or have suffered traumatic injury. Likewise, abundance anti-reader reported change across regions Lewy bodies diseases, cognitive reserve. A-modified RNAs also significantly more abundant dementia but reduced Parkinson’s disease tissue, whilst misplaced diseased cells, particularly where synapses located. parahippocampal modification is enriched transcripts associated psychiatric disorders including conditions clear deficits. These findings indicate diverse set molecular mechanisms influenced can neuronal synaptic dysfunction underlying Targeting brings prospects for neural regenerative therapies.

Язык: Английский

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Closing the gap: Solving complex medically relevant genes at scale

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 18, 2024

Comprehending the mechanism behind human diseases with an established heritable component represents forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or so-called 'dark regions' genome. The advent PacBio as a long-read platform has provided new insights, yet HiFi whole-genome (WGS) cost remains frequently prohibitive. We introduce targeted framework, Twist Alliance Dark Genes Panel (TADGP), designed offer phased variants across 389 complex autosomal genes. highlight TADGP accuracy eleven control samples compare it WGS. This demonstrates that achieves variant calling comparable HiFi-WGS data, but at fraction cost. Thus, enabling scalability broad applicability for studying rare complementing previously sequenced gain insights into these revealed several candidate all cases insight

Язык: Английский

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Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 26, 2024

Rare structural variants (SVs) – insertions, deletions, and complex rearrangements can cause Mendelian disease, yet they remain difficult to accurately detect interpret. We sequenced analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations short-read sequencing. Using our optimized SV detection pipelines 571 control genomes, we detected 716 rare (MAF < 0.01) alleles per genome on average, achieving a 2.4x increase short-reads. To characterize functional effects SVs, assessed their relationship gene expression blood or fibroblasts same individuals, found that SVs overlapping enhancers were enriched (LOR = 0.46) near outliers. also evaluated tandem repeat expansions (TREs) 14 TREs genome; notably these overexpression prioritize candidate developed Watershed-SV, probabilistic model integrates data SV-specific genomic annotations, which significantly outperforms baseline models do not incorporate data. Watershed-SV median eight high-confidence UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, likely causal for neurodevelopmental disorder. Our observations demonstrate promise integrating sequencing towards improving prioritization disease patients.

Язык: Английский

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When less is more: sketching with minimizers in genomics

Genome biology, Год журнала: 2024, Номер 25(1)

Опубликована: Окт. 14, 2024

The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows reducing the quantity of handled while maintaining some its key properties. We provide a basic introduction cover recent methodological developments, review diverse applications minimizers analyze genomic data, including de novo genome assembly, metagenomics, read alignment, correction, pangenomes. also touch on alternative sketching techniques universal hitting sets, syncmers, or strobemers. Minimizers their alternatives have rapidly become indispensable tools handling vast amounts data.

Язык: Английский

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When should the nephrologist think about genetics in patients with glomerular diseases?

Clinical Kidney Journal, Год журнала: 2025, Номер 18(3)

Опубликована: Фев. 13, 2025

ABSTRACT This review discusses the significance of genetics in diagnosing glomerular diseases. Advances genetic testing, particularly next-generation sequencing, have improved accessibility and accuracy monogenic diseases, allowing for targeted gene panels whole-exome/genome sequencing to identify variants associated with Key indicators considering a cause include age onset, extrarenal features, family history, inconclusive kidney biopsy results. Early-onset instance, higher likelihood being genetically caused, while manifestations can also suggest an underlying condition. A thorough history reveal patterns inheritance that point causes, although complexities like incomplete penetrance, skewed X inactivation mosaicism complicate assessment. Also, autosomal recessive conditions imply asymptomatic parents, making suspicion less likely, de novo mutations occur without any further obscuring Focal segmental glomerulosclerosis (FSGS) is characterized by podocyte injury depletion, presenting various forms, including primary, genetic, secondary FSGS. Accurate classification FSGS patients based on clinical histological features essential guiding treatment decisions, optimizing therapeutic plans, avoiding unnecessary immunosuppression, predicting relapse risk after transplantation. Overall, clinicopathological approach, enriched offers precise framework diagnosis management Future directions research practice potential advancements testing personalized medicine, which could improve diagnostic precision individualized strategies.

Язык: Английский

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How structural variants shape avian phenotypes: Lessons from model systems

Molecular Ecology, Год журнала: 2024, Номер 33(11)

Опубликована: Апрель 23, 2024

Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although advances long-read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review role SVs shaping phenotypes avian model systems, identify some general patterns type, length their associated traits. found that most so far identified are short indels chickens, which frequently with changes body weight plumage colouration. Overall, we relatively more detected, likely due to a combination prevalence compared large SVs, detection bias, stemming primarily from widespread use short-read sequencing analytical methods. commonly involve non-coding regions, especially introns, when inheritance were reported, dominant discrete summarise several examples convergence across different species, mediated by same or genes types gene can lead various phenotypes. Complex rearrangements supergenes, simultaneously affect link genes, tend pleiotropic effects. Additionally, co-occur single-nucleotide polymorphisms, highlighting need consider all genetic understand basis end summarising expectations for technologies become implemented non-model birds, leading an increase discovery characterisation. The growing interest this subject suggests our understanding effects upcoming years.

Язык: Английский

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Local read haplotagging enables accurate long-read small variant calling

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июль 13, 2024

Abstract Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and rapid genetic diagnosis clinical settings. Rapidly evolving third-generation platforms like Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT) are introducing newer data types. It been demonstrated that calling methods based on deep neural networks can use local haplotyping information with long-reads to improve genotyping accuracy. However, using haplotype creates an overhead as needs be performed multiple times which ultimately makes it difficult extend new types they get introduced. In this work, we have developed a approximate method enables state-of-the-art performance including PacBio Revio system, ONT R10.4 simplex duplex data. This addition approximation simplifies long-read DeepVariant.

Язык: Английский

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SUMMER: an integrated nanopore sequencing pipeline for variants detection and clinical annotation on the human genome

Functional & Integrative Genomics, Год журнала: 2025, Номер 25(1)

Опубликована: Янв. 21, 2025

Long-read sequencing has emerged as a transformative technology in recent years, offering significant potential for the molecular diagnosis of unresolved genetic disorders. Despite its promise, comprehensive detection and clinical annotation genomic variants remain intricate technically demanding. We present SUMMER, an integrated structured workflow specifically designed to process raw Nanopore reads. SUMMER facilitates in-depth analysis multiple variant types, including SNV, SV, short tandem repeat mobile element insertion. For applications, employs SvAnna prioritize SV candidates based on phenotype relevance utilizes Straglr provide reference distributions non-pathogenic unit counts 55 known pathogenic repeats. By addressing critical challenges annotation, seeks advance utility long-read diagnostic genomics. is available web at https://github.com/carolhuaxia/summer .

Язык: Английский

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