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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Un marco práctico para predecir variantes de un solo nucleótido de empalme en la secuenciación del exoma

Yasuhiro Utsuno1, Kohei Hamanaka1, Masamune Sakamoto1,2

  • 1Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.

NAR genomics and bioinformatics
|December 22, 2025
PubMed
Resumen

Creamos un nuevo marco para evaluar fácilmente las variantes de un solo nucleótido de empalme patógenas (SNV) para trastornos mendelianos. Esta herramienta mejora la detección de estas variantes en los datos de secuenciación del exoma.

Palabras clave:
variantes de empalmetrastornos mendelianossecuenciación del exomadiagnóstico genéticobioinformática

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Área de la Ciencia:

  • Genética; Bioinformática; Biología Computacional

Sus antecedentes:

  • Las variantes de empalme son contribuyentes clave a los trastornos mendelianos.; Predecir la patogenicidad de las variantes de empalme sigue siendo un desafío importante en el diagnóstico genético.

Objetivo del estudio:

  • Desarrollar un marco simplificado para la evaluación de variantes de un solo nucleótido de empalme patógenas (SNV).; Alinear con las directrices ACMG/AMP 2023 y las recomendaciones de ClinGen para la clasificación de variantes.

Principales métodos:

  • Desarrolló un sistema de puntuación que asigna puntuaciones de prioridad (-10 a 14) a las SNV en regiones de marco de lectura abierto.; Validó el marco utilizando SNV de empalme patógenas de la Base de Datos de Mutaciones Genéticas Humanas y SNV comunes de gnomAD.; Comparó el poder discriminatorio del marco con SpliceAI.

Principales resultados:

  • El marco demostró una discriminación superior en comparación con SpliceAI solo (AUC 0.991 frente a 0.983, P = 2.11 × 10⁻²³).; Identificó variantes de empalme patógenas en genes conocidos (COL2A1, PDHA1, MECP2, JAKMIP1) en 1257 pacientes con diagnósticos no resueltos.; Sugirió genes candidatos potenciales causantes de enfermedades (UBN1, NFE2L1).

Conclusiones:

  • El marco desarrollado simplifica la evaluación de la patogenicidad de las SNV de empalme.; Este método mejora la detección de variantes de empalme a través de la secuenciación del exoma, lo que ayuda a diagnosticar trastornos genéticos.