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Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data.
Nat Commun
January 2025
Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
Genomic variants causing abnormal splicing play important roles in genetic disorders and cancer development. Among them, variants that cause the formation of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs).
View Article and Find Full Text PDFMosaicism and intronic variants in RB1 gene revealed by next generation sequencing in a cohort of Spanish retinoblastoma patients.
Exp Eye Res
January 2025
Genetic Diagnosis Unit, Institute for Rare Diseases Research (IIER), Carlos III Institute of Health (ISCIII), Madrid, Spain; Center for Biomedical Research on Rare Diseases Network, Carlos III Institute of Health (ISCIII), Madrid, Spain (U758; CB06/07/1009; CIBERER-ISCIII).
Constitutional variants in the RB1 gene predispose individuals to the development of Retinoblastoma (RB) and the occurrence of second tumors in adulthood. Detection of causal RB1 gene variants is essential to establish the genetic diagnosis and to performing familial studies and counseling. In our cohort of 579 Spanish RB patients, 15% of cases suspected to have a genetic origin remained negative after traditional Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) of RB1 gene, likely due to the possibility of mosaicism or non-coding variants.
View Article and Find Full Text PDFRescue of Aberrant Splicing Caused by a Novel Complex Deep-intronic Allele.
Genes (Basel)
November 2024
Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland.
Stargardt disease (STGD1) is an autosomal recessive disorder caused by pathogenic variants in that affects the retina and is characterised by progressive central vision loss. The onset of disease manifestations varies from childhood to early adulthood. Whole exome (WES), whole gene, and whole genome sequencing (WGS) were performed for a patient with STGD1.
View Article and Find Full Text PDFGenome sequencing reveals the impact of non-canonical exon inclusions in rare genetic disease.
medRxiv
December 2024
Institute for Clinical and Translational Science, University of California, Irvine, CA, USA.
Introduction: Advancements in sequencing technologies have significantly improved clinical genetic testing, yet the diagnostic yield remains around 30-40%. Emerging sequencing technologies are now being deployed in the clinical setting to address the remaining diagnostic gap.
Methods: We tested whether short-read genome sequencing could increase diagnostic yield in individuals enrolled into the UCI-GREGoR research study, who had suspected Mendelian conditions and prior inconclusive clinical genetic testing.
Trifunctional protein deficiency (TFP) is a disorder of fatty acid beta-oxidation associated with metabolic, cardiac, and liver dysfunction in severe forms. We present two siblings diagnosed by newborn screening and confirmed by biochemical testing at birth. Their clinical course was complicated by recurrent rhabdomyolysis, retinopathy, and hypoparathyroidism.
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