Applications of long-read sequencing to Mendelian genetics

FK Mastrorosa, DE Miller, EE Eichler - Genome medicine, 2023 - Springer
Advances in clinical genetic testing, including the introduction of exome sequencing, have
uncovered the molecular etiology for many rare and previously unsolved genetic disorders …

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 …

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants

TV Nguyen, CJ Vander Jagt, J Wang… - Genetics Selection …, 2023 - Springer
Studies have demonstrated that structural variants (SV) play a substantial role in the
evolution of species and have an impact on Mendelian traits in the genome. However, unlike …

Local read haplotagging enables accurate long-read small variant calling

A Kolesnikov, D Cook, M Nattestad, L Brambrink… - Nature …, 2024 - nature.com
Long-read sequencing technology has enabled variant detection in difficult-to-map regions
of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving …

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

JA Gustafson, SB Gibson, N Damaraju, MPG Zalusky… - medRxiv, 2024 - ncbi.nlm.nih.gov
Less than half of individuals with a suspected Mendelian condition receive a precise
molecular diagnosis after comprehensive clinical genetic testing. Improvements in data …

3-hour genome sequencing and targeted analysis to rapidly assess genetic risk

M Galey, P Reed, T Wenger, E Beckman, IJ Chang… - medRxiv, 2022 - medrxiv.org
Rapid genetic testing in the critical care setting enables targeted evaluations, directs
therapies, and helps families and care providers make informed decisions about goals of …

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

N Flack, M Drown, C Walls, J Pratte… - NAR Genomics and …, 2023 - academic.oup.com
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands
and steppes of central Asia. Population strongholds in Mongolia and China face growing …

MethPhaser: methylation-based long-read haplotype phasing of human genomes

Y Fu, S Aganezov, M Mahmoud, J Beaulaurier… - Nature …, 2024 - nature.com
The assignment of variants across haplotypes, phasing, is crucial for predicting the
consequences, interaction, and inheritance of mutations and is a key step in improving our …

HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing

JM Holt, CT Saunders, WJ Rowell, Z Kronenberg… - …, 2024 - academic.oup.com
Motivation In diploid organisms, phasing is the problem of assigning the alleles at
heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing …

JTK: targeted diploid genome assembler

B Masutani, Y Suzuki, Y Suzuki, S Morishita - Bioinformatics, 2023 - academic.oup.com
Motivation Diploid assembly, or determining sequences of homologous chromosomes
separately, is essential to elucidate genetic differences between haplotypes. One approach …