Splicing in the Diagnosis of Rare Disease: Advances and Challenges

Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis

(2021) Paola Nix et al.   Familial Cancer

Comprehensive characterisation of intronic mis-splicing mutations in human cancers

(2021) Hyunchul Jung et al.   ONCOGENE

Benchmarking deep learning splice prediction tools using functional splice assays

(2021) Tabea V. Riepe et al.   HUMAN MUTATION

The Experimentally Obtained Functional Impact Assessments of 5' Splice Site GT>GC Variants Differ Markedly from Those Predicted

(2020) Jian-Min Chen et al.   CURRENT GENOMICS

Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance

(2020) Htoo A. Wai et al.   GENETICS IN MEDICINE

Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage

(2020) Yury A. Barbitoff et al.   Scientific Reports

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases

(2020) Garrett Jenkinson et al.   BIOINFORMATICS

Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq

(2020) Joseph K. Aicher et al.   GENETICS IN MEDICINE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay

(2020) Eugénie Dionnet et al.   HUMAN MUTATION

Evidence for 28 genetic disorders discovered by combining healthcare and research data

(2020) Joanna Kaplanis et al.   NATURE

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing

(2020) David R. Murdock et al.   JOURNAL OF CLINICAL INVESTIGATION

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease

(2019) Hernan D. Gonorazky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice

(2019) Jun Cheng et al.   HUMAN MUTATION

First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild‐type transcripts

(2019) Jin‐Huan Lin et al.   HUMAN MUTATION

Assessing predictions of the impact of variants on splicing in CAGI5

(2019) Stephen M. Mount et al.   HUMAN MUTATION

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts

(2019) Laure Frésard et al.   NATURE MEDICINE

High-throughput analysis revealed mutations’ diverging effects on SMN1 exon 7 splicing

(2019) Přemysl Souček et al.   RNA Biology

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing

(2019) Charlie F Rowlands et al.   Cells

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Human urine-derived renal epithelial cells provide insights into kidney-specific alternate splicing variants

(2018) Elisa Molinari et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders

(2018) Caroline F Wright et al.   GENETICS IN MEDICINE

Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides

(2018) Sidi Zhang et al.   GENOME RESEARCH

Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing

(2018) John S Mattick et al.   MEDICAL JOURNAL OF AUSTRALIA

Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis

(2018) Simon Braun et al.   Nature Communications

Pathogenicity and selective constraint on variation near splice sites

(2018) Jenny Lord et al.   GENOME RESEARCH

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

(2018) Rocky Cheung et al.   MOLECULAR CELL

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

(2018) Daniel Mapleson et al.   GigaScience

Saturation mutagenesis reveals manifold determinants of exon definition

(2017) Shengdong Ke et al.   GENOME RESEARCH

Estimating the prevalence of functional exonic splice regulatory information

(2017) Rosina Savisaar et al.   HUMAN GENETICS

Pathogenic variants that alter protein code often disrupt splicing

(2017) Rachel Soemedi et al.   NATURE GENETICS

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Nusinersen versus Sham Control in Infantile-Onset Spinal Muscular Atrophy

(2017) Richard S. Finkel et al.   NEW ENGLAND JOURNAL OF MEDICINE

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

(2017) Beryl B. Cummings et al.   Science Translational Medicine

Genetic diagnosis of Mendelian disorders via RNA sequencing

(2017) Laura S. Kremer et al.   Nature Communications

A study of splicing mutations in disorders of sex development

(2017) Flavia Leme de Calais et al.   Scientific Reports

Longitudinal effect of eteplirsen versus historical control on ambulation in Duchenne muscular dystrophy

(2016) Jerry R. Mendell et al.   ANNALS OF NEUROLOGY

Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms

(2016) Miguel de la Hoya et al.   HUMAN MOLECULAR GENETICS

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

The complete local genotype–phenotype landscape for the alternative splicing of a human exon

(2016) Philippe Julien et al.   Nature Communications

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

The Silent Sway of Splicing by Synonymous Substitutions

(2015) William F. Mueller et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

New insights into the performance of human whole-exome capture platforms

(2015) J. Meienberg et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Experimental Assessment of Splicing Variants Using Expression Minigenes and Comparison with In Silico Predictions

(2014) Neeraj Sharma et al.   HUMAN MUTATION

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eteplirsen for the treatment of Duchenne muscular dystrophy

(2013) Jerry R. Mendell et al.   ANNALS OF NEUROLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Genotype–phenotype correlations in sepiapterin reductase deficiency. A splicing defect accounts for a new phenotypic variant

(2011) Luisa Arrabal et al.   NEUROGENETICS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS