Comprehensive Structural Variant Detection: From Mosaic to Population-Level

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: April 5, 2022

Abstract Long-read Structural Variation (SV) calling remains a challenging but highly accurate way to identify complex genomic alterations. Here, we present Sniffles2, which is faster and more than state-of-the-art SV caller across different coverages, sequencing technologies, types. Furthermore, Sniffles2 solves the problem of family- population-level produce fully genotyped VCF files by introducing gVCF file concept. Across 11 probands, accurately identified causative SVs around MECP2 , including alleles with three overlapping SVs. also enables detection mosaic in bulk long-read data. As result, successfully multiple system atrophy patient brain. The showed remarkable diversity within cingulate cortex, impacting both genes involved neuron function repetitive elements. In summary, demonstrate utility versatility from population levels.

Language: Английский

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The application of long-read sequencing in clinical settings

Human Genomics, Journal Year: 2023, Volume and Issue: 17(1)

Published: Aug. 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

Language: Английский

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Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 7, 2024

Less than half of individuals with a suspected Mendelian condition receive precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest using long-read sequencing (LRS) to streamline genomic testing, but the absence control datasets for variant filtering prioritization has made tertiary analysis LRS challenging. To address this, 1000 Genomes Project ONT Sequencing Consortium aims generate from at least 800 samples. Our goal is use identify broader spectrum variation so we may improve our understanding normal patterns human variation. Here, present first 100 samples, representing all 5 superpopulations 19 subpopulations. These sequenced an average depth coverage 37x sequence read N50 54 kbp, high concordance previous studies identifying single nucleotide indel variants outside homopolymer regions. Using multiple structural (SV) callers, 24,543 high-confidence SVs per genome, including shared private likely disrupt gene function as well pathogenic expansions within disease-associated repeats that were not detected short reads. Evaluation methylation signatures revealed expected known imprinted loci, samples skewed X-inactivation patterns, novel differentially methylated All raw data, processed summary statistics are publicly available, providing valuable resource genetics community discover SVs.

Language: Английский

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Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002697 - e3002697

Published: July 18, 2024

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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Accelerated nanopore basecalling with SLOW5 data format

Bioinformatics, Journal Year: 2023, Volume and Issue: 39(6)

Published: May 30, 2023

Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known 'basecalling', major friction any nanopore workflow. Here, we exploit advantages recently developed format 'SLOW5' streamline and accelerate basecalling on high-performance computing (HPC) cloud environments.SLOW5 permits highly efficient sequential access, eliminating potential analysis bottleneck. To take advantage this, introduce Buttery-eel, an open-source wrapper for Oxford Nanopore's Guppy basecaller that enables SLOW5 resulting performance improvements are essential scalable, affordable basecalling.Buttery-eel available at https://github.com/Psy-Fer/buttery-eel.

Language: Английский

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Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 2, 2023

Abstract Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed cost-effective hybrid Oxford Nanopore (ONT) long-read Illumina short-read approach used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing number assemblies this taxonomic group. The next challenge address culture bias taxon sampling by that cannot easily be reared lab. Here, we build upon our previous methods perform amplification-free ONT single wild flies obtained either directly field or ethanol-preserved specimens museum collections, improving representation lesser studied taxa whole-genome data. Using Novaseq X Plus P2 sequencers with R10.4.1 chemistry, set new benchmark inexpensive at US $150 per while assembling as little 35 ng genomic DNA fly. present 183 179 resource systematics, phylogenetics, comparative genomics. Of these genomes, 62 are pooled lab strains 121 adult flies. Despite sample limitations working small insects, most single-fly diploid comparable contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), accuracy (>QV40 genome-wide R10.4.1) inbred lines. well-resolved multi-locus phylogeny 360 4 outgroup encompassing publicly available (as August 2023) Finally, Progressive Cactus whole-genome, reference-free alignment built subset 298 suitably high-quality genomes. alignment, along updated protocols computational pipelines, released an open tool studying evolution scale entire insect family.

Language: Английский

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

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 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.

Language: Английский

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Detection of Biological Molecules Using Nanopore Sensing Techniques

Biomedicines, Journal Year: 2023, Volume and Issue: 11(6), P. 1625 - 1625

Published: June 2, 2023

Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed can be tailored highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount treating serious diseases. Usually, the early stages disease, number biomarkers very low sometimes difficult detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest medicine, advantages such as easy operation, speed, portability, with additional benefits costs repeated reliable results. Single-molecule sensors nanopores biomolecules at concentrations potential become clinically relevant. As such, several applications been introduced this field blood markers, nucleic acids, or proteins. The use has yet reach maturity standardization techniques, however, they promise enormous potential, progress made into stabilizing nanopore structures, enhancing chemistries, improving data collection bioinformatic analysis. This review offers perspective on current biomolecule based various types nanopores, challenges, approaches toward implementation clinical settings.

Language: Английский

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A comprehensive tandem repeat catalog of the human genome

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 20, 2024

With the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping repeat loci on a population scale becomes more feasible. Such efforts not only expand our knowledge landscape in but also enhance ability to differentiate pathogenic mutations from benign polymorphisms. To this end, we analyzed 272 genomes assembled using datasets three public initiatives that employed different technologies. Here, report catalog over 18 million loci, many which were previously unannotated. Some these are highly polymorphic, them reside within coding sequences.

Language: Английский

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Phased nanopore assembly with Shasta and modular graph phasing with GFAse

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 22, 2023

Abstract As a step towards simplifying and reducing the cost of haplotype resolved de novo assembly, we describe new methods for accurately phasing nanopore data with Shasta genome assembler modular tool extending to chromosome scale called GFAse. We test using variants Oxford Nanopore Technologies’ (ONT) PromethION sequencing, including those proximity ligation show that newer, higher accuracy ONT reads substantially improve assembly quality.

Language: Английский

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