Alternative splicing and related RNA binding proteins in human health and disease

Y Tao, Q Zhang, H Wang, X Yang, H Mu - Signal Transduction and …, 2024 - nature.com
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation,
engendering transcript diversity, and modifications in protein structure and functionality …

From computational models of the splicing code to regulatory mechanisms and therapeutic implications

C Capitanchik, OG Wilkins, N Wagner… - Nature Reviews …, 2024 - nature.com
Since the discovery of RNA splicing and its role in gene expression, researchers have
sought a set of rules, an algorithm or a computational model that could predict the splice …

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

AS Leonard, XM Mapel, H Pausch - Genome Research, 2024 - genome.cshlp.org
Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic
variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts …

[HTML][HTML] Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index

IF Scheller, K Lutz, C Mertes, VA Yépez… - The American Journal of …, 2023 - cell.com
Detection of aberrantly spliced genes is an important step in RNA-seq-based rare-disease
diagnostics. We recently developed FRASER, a denoising autoencoder-based method that …

Benchmarking splice variant prediction algorithms using massively parallel splicing assays

C Smith, JO Kitzman - Genome Biology, 2023 - Springer
Background Variants that disrupt mRNA splicing account for a sizable fraction of the
pathogenic burden in many genetic disorders, but identifying splice-disruptive variants …

[HTML][HTML] X-linked hypophosphatemia caused by a deep intronic variant in PHEX identified by PCR-based RNA analysis of urine-derived cells

C Grimbly, K Ludwig, Z Wu, O Caluseriu, E Rosolowsky… - Bone, 2023 - Elsevier
X-linked hypophosphatemia (XLH) is caused by dominant inactivating mutations in the
phosphate regulating endopeptidase homology, X-linked (PHEX), resulting in elevated …

Integration of variant annotations using deep set networks boosts rare variant association testing

B Clarke, E Holtkamp, H Öztürk, M Mück, M Wahlberg… - Nature Genetics, 2024 - nature.com
Rare genetic variants can have strong effects on phenotypes, yet accounting for rare
variants in genetic analyses is statistically challenging due to the limited number of allele …

Computational prediction of human deep intronic variation

P Barbosa, R Savisaar, M Carmo-Fonseca… - …, 2023 - academic.oup.com
Background The adoption of whole-genome sequencing in genetic screens has facilitated
the detection of genetic variation in the intronic regions of genes, far from annotated splice …

A deep intronic PKHD1 variant identified by SpliceAI in a deceased neonate with autosomal recessive polycystic kidney disease

F Richter, KD Rutherford, AJ Cooke, M Meshkati… - American Journal of …, 2024 - Elsevier
The etiologies of newborn deaths in neonatal intensive care units usually remain unknown,
even after genetic testing. Whole-genome sequencing, combined with artificial intelligence …

Next-generation sequencing and bioinformatics in rare movement disorders

M Zech, J Winkelmann - Nature Reviews Neurology, 2024 - nature.com
The ability to sequence entire exomes and genomes has revolutionized molecular testing in
rare movement disorders, and genomic sequencing is becoming an integral part of routine …