Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

In silico methods for predicting functional synonymous variants

BC Lin, U Katneni, KI Jankowska, D Meyer… - Genome Biology, 2023 - Springer
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous
SNVs are previously considered to be “silent,” but mounting evidence has revealed that …

Performance evaluation of differential splicing analysis methods and splicing analytics platform construction

K Li, T Luo, Y Zhu, Y Huang, A Wang… - Nucleic Acids …, 2022 - academic.oup.com
A proportion of previously defined benign variants or variants of uncertain significance in
humans, which are challenging to identify, may induce an abnormal splicing process. An …

Genetic evidence for involvement of β2-adrenergic receptor in brown adipose tissue thermogenesis in humans

Y Ishida, M Matsushita, T Yoneshiro, M Saito… - International Journal of …, 2024 - nature.com
Background Sympathetic activation of brown adipose tissue (BAT) thermogenesis can
ameliorate obesity and related metabolic abnormalities. However, crucial subtypes of the β …

[HTML][HTML] Nonsynonymous synonymous variants demand for a paradigm shift in genetics

M Vihinen - Current Genomics, 2023 - ncbi.nlm.nih.gov
Synonymous (also known as silent) variations are by definition not considered to change the
coded protein. Still many variations in this category affect either protein abundance or …

Effect predictor of driver synonymous mutations based on multi-feature fusion and iterative feature representation learning

N Cheng, C Bi, Y Shi, M Liu, A Cao… - IEEE Journal of …, 2023 - ieeexplore.ieee.org
Accurate identification of driver mutations is crucial in genetic studies of human cancers.
While numerous cancer driver missense mutations have been identified, research into …

[HTML][HTML] Pathogenicity of intronic and synonymous variants of ATP7B in Wilson disease

WQ Xu, RM Wang, Y Dong, ZY Wu - The Journal of Molecular Diagnostics, 2023 - Elsevier
Wilson disease (WD) is a hereditary disorder of copper metabolism, resulting from mutations
within ATP7B. Early diagnosis is essential for affected individuals. However, there are still …

Populational pan-ethnic screening panel enabled by deep whole genome sequencing

L Yang, Z Lin, Y Gao, J Zhang, H Peng, Y Li… - NPJ Genomic …, 2023 - nature.com
Birth defect is a global threat to the public health systems. Mitigating neonatal anomalies is
hampered by elusive molecular mechanisms of pathogenic mutations and poor subsequent …

Prioritizing de novo potential non-canonical splicing variants in neurodevelopmental disorders

K Li, J Xiao, Z Ling, T Luo, J Xiong, Q Chen, L Dong… - Ebiomedicine, 2024 - thelancet.com
Background Genomic variants outside of the canonical splicing site (±2) may generate
abnormal mRNA splicing, which are defined as non-canonical splicing variants (NCSVs) …

[HTML][HTML] Deep mutational scanning in disease-related genes with saturation Mutagenesis-reinforced functional assays (SMuRF)

K Ma, S Huang, KK Ng, NJ Lake, S Joseph, J Xu, A Lek… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Interpretation of disease-causing genetic variants remains a challenge in human genetics.
Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing …