Towards population-scale long-read sequencing

W De Coster, MH Weissensteiner… - Nature Reviews …, 2021 - nature.com
Long-read sequencing technologies have now reached a level of accuracy and yield that
allows their application to variant detection at a scale of tens to thousands of samples …

A draft human pangenome reference

WW Liao, M Asri, J Ebler, D Doerr, M Haukness… - Nature, 2023 - nature.com
Abstract Here the Human Pangenome Reference Consortium presents a first draft of the
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

M Byrska-Bishop, US Evani, X Zhao, AO Basile… - Cell, 2022 - cell.com
Summary The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-
genome sequencing (WGS) data consented for public distribution without access or use …

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

P Ebert, PA Audano, Q Zhu, B Rodriguez-Martin… - Science, 2021 - science.org
INTRODUCTION The characterization of the full spectrum of genetic variation is critical to
understanding human health and disease. Recent technological advances have made it …

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

H Cheng, GT Concepcion, X Feng, H Zhang, H Li - Nature methods, 2021 - nature.com
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence
variations in a genome. However, existing algorithms either collapse heterozygous alleles …

NanoPack2: population-scale evaluation of long-read sequencing data

W De Coster, R Rademakers - Bioinformatics, 2023 - academic.oup.com
Increases in the cohort size in long-read sequencing projects necessitate more efficient
software for quality assessment and processing of sequencing data from Oxford Nanopore …

Epigenetic patterns in a complete human genome

A Gershman, MEG Sauria, X Guitart, MR Vollger… - Science, 2022 - science.org
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has
resolved complex regions of the genome, including repetitive and homologous regions …

A framework for individualized splice-switching oligonucleotide therapy

J Kim, S Woo, CM de Gusmao, B Zhao, DH Chin… - Nature, 2023 - nature.com
Splice-switching antisense oligonucleotides (ASOs) could be used to treat a subset of
individuals with genetic diseases, but the systematic identification of such individuals …

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

M Kolmogorov, KJ Billingsley, M Mastoras… - Nature …, 2023 - nature.com
Long-read sequencing technologies substantially overcome the limitations of short-reads
but have not been considered as a feasible replacement for population-scale projects, being …

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

AS Deshpande, N Ulahannan, M Pendleton… - Nature …, 2022 - nature.com
Abstract High-order three-dimensional (3D) interactions between more than two genomic
loci are common in human chromatin, but their role in gene regulation is unclear. Previous …