Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species DOI
Katarina C. Stuart, Hui Zhen Tan, Annabel Whibley

и другие.

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

ABSTRACT The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged the management threatened species. functional consequences SVs are more complex than for single nucleotide polymorphisms (SNPs), as typically impact a larger proportion genome due to their size thus may likely contribute load. While impacts SV‐specific genetic load less consequential large populations, interplay between weakened selection stochastic processes means that smaller such those Aotearoa hihi/New Zealand stitchbird ( Notiomystis cincta ), harbour high SV Hihi were once confined remnant population, but have been reestablished into six sanctuaries reserves, often via secondary bottlenecks, resulting low diversity, adaptive potential, inbreeding depression. In this study, we use whole resequencing 30 individuals from Tiritiri Matangi population identify nature distribution both SNPs within small avian population. We find SNP individual mutation only moderately correlated, because arise regions recombination evolutionarily conserved. Finally, leverage long‐term monitoring dataset pedigree fitness data assess loads on fitness, realised had similar negative correlations with lifetime fitness. However, masked metrics, positive significant correlation indicating masking deleterious alleles important SNPs. results study indicate examining neglects aspects intra‐specific variation studying has direct implications linking diversity genomic health inform decisions.

Язык: Английский

HiFi long-read genomes for difficult-to-detect, clinically relevant variants DOI

Wolfram Höps,

Marjan M. Weiss, Ronny Derks

и другие.

The American Journal of Human Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

1
Genome-wide association testing beyond SNPs DOI
Laura Harris, Ellen M. McDonagh, Xiaolei Zhang

и другие.

Nature Reviews Genetics, Год журнала: 2024, Номер unknown

Опубликована: Окт. 7, 2024

Язык: Английский

Процитировано

6
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation DOI Creative Commons
Joseph Lalli, Andrew N Bortvin, Rajiv C. McCoy

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 28, 2025

The T2T-CHM13 complete human reference genome contains ∼200 Mb of newly resolved sequence, improving read mapping and variant calling compared to GRCh38. However, the benefits using genomes in other contexts are unclear. Here, we present a recombination map phased haplotype panel derived from 3202 samples 1000 Genomes Project (1KGP). Using published long-read based assemblies as reference-neutral ground truth, our 1KGP previously released GRCh38 callset. We find that alignment resulted 38% fewer assembly-discordant genotypes 16% switch errors. largest gains accuracy observed on chromosome X regions flanking disease-causing CNVs. Simons Genome Diversity were more accurately imputed when panel. Our study demonstrates use T2T-native improves statistical phasing imputation for diverse populations.

Язык: Английский

Процитировано

0
Variations and Polymorphisms: The Human Pangenome Project DOI
Shweta Pandey, Sanjiv S. Gambhir, Vipin Kumar Singh

и другие.

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 282 - 294

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
Genome assembly resources of genitourinary cancers for chromosomal aberration at the single nucleotide level DOI Creative Commons
Hyun Ho Han, Hyung Ho Lee, Min Kim

и другие.

Scientific Data, Год журнала: 2025, Номер 12(1)

Опубликована: Апрель 1, 2025

Язык: Английский

Процитировано

0
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing DOI
Ayşe Gökçe Keşküş, Asher Bryant, Tanveer Ahmad

и другие.

Nature Biotechnology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 4, 2025

Язык: Английский

Процитировано

0
The impact of long-read sequencing on human population-scale genomics DOI
Tobias Rausch, Tobias Marschall, Jan O. Korbel

и другие.

Genome Research, Год журнала: 2025, Номер 35(4), С. 593 - 598

Опубликована: Апрель 1, 2025

Long-read sequencing technologies, particularly those from Pacific Biosciences and Oxford Nanopore Technologies, are revolutionizing genome research by providing high-resolution insights into complex repetitive regions of the human that were previously inaccessible. These advances have been enabling for comprehensive detection genomic structural variants (SVs), which is critical linking genotype to phenotype in population-scale rare disease studies, as well cancer. Recent developments throughput computational methods, such pangenome graphs haplotype-resolved assemblies, paving way future inclusion long-read clinical cohort studies diagnostics. DNA methylation signals directly obtained long reads enhance utility single-molecule technologies molecular phenotypes be interpreted, allowing identification parent origin de novo mutations. Despite this recent progress, challenges remain scaling large populations due cost, complexity, lack tools facilitate efficient interpretation SVs graphs. This perspective provides a succinct review on current state genomics highlighting its transformative potential key hurdles, emphasizing opportunities advancing understanding genetic diversity diseases through analysis.

Язык: Английский

Процитировано

0
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations DOI Open Access
Boris Noyvert, A. Mesut Erzurumluoglu, Dmitriy Drichel

и другие.

Опубликована: Апрель 15, 2025

Advancements in long-read sequencing technology have accelerated the study of large structural variants (SVs). We created a curated, publicly available, multi-ancestry SV imputation panel by 888 samples from 1000 Genomes Project. This high-quality was used to impute SVs approximately 500,000 UK Biobank participants. demonstrated feasibility conducting genome-wide association studies at biobank scale using 32 disease-relevant phenotypes related respiratory, cardiometabolic and liver diseases, addition 1,463 protein levels. analysis identified thousands significant associations, including hundreds conditionally independent signals, thereby enabling novel biological insights. Focusing on genetic lung function as an example, we demonstrate added value for prioritising causal genes gene-rich loci compared traditional GWAS only short variants. envision that future post-GWAS gene-prioritisation workflows will incorporate analyses this framework.

Язык: Английский

Процитировано

0
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations DOI Open Access
Boris Noyvert, A. Mesut Erzurumluoglu, Dmitriy Drichel

и другие.

Опубликована: Апрель 15, 2025

Advancements in long-read sequencing technology have accelerated the study of large structural variants (SVs). We created a curated, publicly available, multi-ancestry SV imputation panel by 888 samples from 1000 Genomes Project. This high-quality was used to impute SVs approximately 500,000 UK Biobank participants. demonstrated feasibility conducting genome-wide association studies at biobank scale using 32 disease-relevant phenotypes related respiratory, cardiometabolic and liver diseases, addition 1,463 protein levels. analysis identified thousands significant associations, including hundreds conditionally independent signals, thereby enabling novel biological insights. Focusing on genetic lung function as an example, we demonstrate added value for prioritising causal genes gene-rich loci compared traditional GWAS only short variants. envision that future post-GWAS gene-prioritisation workflows will incorporate analyses this framework.

Язык: Английский

Процитировано

0
Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR DOI Creative Commons
Wouter De Coster, Ida Höijer,

Inge Bruggeman

и другие.

Genome Research, Год журнала: 2024, Номер 34(11), С. 2074 - 2080

Опубликована: Авг. 15, 2024

The lack of population-scale databases hampers research and diagnostics for medically relevant tandem repeats repeat expansions. We attempt to fill this gap using our pathSTR web tool, which leverages long-read sequencing large cohorts determine length sequence composition in a healthy population. current version includes 1040 individuals 1000 Genomes Project cohort sequenced on the Oxford Nanopore Technologies PromethION. A comprehensive set has been genotyped STRdust LongTR composition. PathSTR provides rich visualizations data feature upload one's comparison along control cohort. demonstrate implementation application from targeted nanopore patient with myotonic dystrophy type 1. This resource will empower genetics community get more complete overview normal variation and, as such, enable better assessment rare alleles observed patients.

Язык: Английский

Процитировано

3