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

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

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 22, 2023

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

5
Quantifying the regulatory potential of genetic variants via a hybrid sequence-oriented model with SVEN DOI Creative Commons
Yu Wang, Nan Liang, Ge Gao

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 30, 2024

Deciphering how noncoding DNA determines gene expression is critical for decoding the functional genome. Understanding transcription effects of genetic variants are still major unsolved problems, which downstream applications in human genetics and precision medicine. Here, we integrate regulatory-specific neural networks tissue-specific gradient-boosting trees to build SVEN: a hybrid sequence-oriented architecture that can accurately predict level quantify transcriptomic impacts structural across more than 350 tissues cell lines. We further systematically screen large-scale dataset derived from 3622 individuals clinical ClinVar, provide an overview population. As model, SVEN also able regulatory small variants. expect will enable effective silico analysis interpretation genome-wide disease-related

Язык: Английский

Процитировано

1
Methods to investigate somatic structural variants in synucleinopathies DOI
Caoimhe Morley, Christos Proukakis

Elsevier eBooks, Год журнала: 2024, Номер unknown, С. 75 - 100

Опубликована: Окт. 1, 2024

Язык: Английский

Процитировано

0
Loss ofCFHR5function reduces the risk for age-related macular degeneration DOI Creative Commons
Mary Pat Reeve,

Stephanie Loomis,

Eija Nissilä

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 11, 2024

Age-related macular degeneration (AMD) is a prevalent cause of vision loss in the elderly with limited therapeutic options. A single chromosomal region around complement factor H gene (

Язык: Английский

Процитировано

0
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

Процитировано

0