The complete sequence of a human genome

Science, Journal Year: 2022, Volume and Issue: 376(6588), P. 44 - 53

Published: March 31, 2022

Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be protein coding. The completed include centromeric satellite arrays, recent segmental duplications, short arms five acrocentric chromosomes, unlocking these complex variational functional studies.

Language: Английский

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Nanopore sequencing technology, bioinformatics and applications

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(11), P. 1348 - 1365

Published: Nov. 1, 2021

Language: Английский

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A complete reference genome improves analysis of human genetic variation

Science, Journal Year: 2022, Volume and Issue: 376(6588)

Published: March 31, 2022

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands structural errors, and unlocks most complex regions human for clinical functional study. We show how this reference universally improves read mapping variant calling 3202 17 globally diverse samples sequenced with short long reads, respectively. identify hundreds variants per sample in previously unresolved regions, showcasing promise T2T-CHM13 evolutionary biomedical discovery. Simultaneously, eliminates tens spurious sample, including reduction false positives 269 medically relevant genes by up a factor 12. Because these improvements discovery coupled population genomic resources, is positioned replace GRCh38 as prevailing genetics.

Language: Английский

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Towards population-scale long-read sequencing

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(9), P. 572 - 587

Published: May 28, 2021

Language: Английский

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The complete sequence of a human Y chromosome

Nature, Journal Year: 2023, Volume and Issue: 621(7978), P. 344 - 354

Published: Aug. 23, 2023

Language: Английский

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A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

Genome Medicine, Journal Year: 2022, Volume and Issue: 14(1)

Published: Feb. 28, 2022

Abstract Rare diseases affect 30 million people in the USA and more than 300–400 worldwide, often causing chronic illness, disability, premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with medical literature. A large number of patients remain undiagnosed for years many even die without an accurate diagnosis. In recent years, gene panels, microarrays, exome sequencing have helped to identify molecular cause such diseases. These technologies allowed diagnoses a sizable proportion (25–35%) patients, actionable findings. However, these undiagnosed. this review, we focus that can be adopted if is unrevealing. We discuss benefits whole genome additional benefit may offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, methyl profiling. highlight computational methods help regionally distant similar phenotypes or genetic mutations. Finally, describe approaches automate accelerate genomic analysis. The strategies discussed here are intended serve as guide clinicians researchers next steps when encountering non-diagnostic exomes.

Language: Английский

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Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Nature Computational Science, Journal Year: 2022, Volume and Issue: 2(12), P. 797 - 803

Published: Dec. 19, 2022

Language: Английский

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Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting

New England Journal of Medicine, Journal Year: 2022, Volume and Issue: 386(7), P. 700 - 702

Published: Jan. 12, 2022

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Highly contiguous assemblies of 101 drosophilid genomes

eLife, Journal Year: 2021, Volume and Issue: 10

Published: July 19, 2021

Over 100 years of studies in Drosophila melanogaster and related species the genus have facilitated key discoveries genetics, genomics, evolution. While high-quality genome assemblies exist for several this group, they only encompass a small fraction genus. Recent advances long-read sequencing allow tens or even hundreds to be efficiently generated. Here, we utilize Oxford Nanopore build an open community resource 101 lines 93 drosophilid encompassing 14 groups 35 sub-groups. The genomes are highly contiguous complete, with average contig N50 10.5 Mb greater than 97% BUSCO completeness 97/101 assemblies. We show that Nanopore-based accurate coding regions, particularly respect insertions deletions. These assemblies, along detailed laboratory protocol assembly pipelines, released as public will serve starting point addressing broad questions ecology, evolution at scale species.

Language: Английский

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Curated variation benchmarks for challenging medically relevant autosomal genes

Nature Biotechnology, Journal Year: 2022, Volume and Issue: 40(5), P. 672 - 680

Published: Feb. 7, 2022

Language: Английский

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