@article {655,
	title = {A recurrent COL6A1 pseudoexon insertion causes muscular dystrophy and is effectively targeted by splice-correction therapies.},
	journal = {JCI Insight},
	volume = {4},
	year = {2019},
	month = {2019 Mar 21},
	abstract = {<p>The clinical application of advanced next-generation sequencing technologies is increasingly uncovering novel classes of mutations that may serve as potential targets for precision medicine therapeutics. Here, we show that a deep intronic splice defect in the COL6A1 gene, originally discovered by applying muscle RNA sequencing in patients with clinical findings of collagen VI-related dystrophy (COL6-RD), inserts an in-frame pseudoexon into COL6A1 mRNA, encodes a mutant collagen α1(VI) protein that exerts a dominant-negative effect on collagen VI matrix assembly, and provides a unique opportunity for splice-correction approaches aimed at restoring normal gene expression. Using splice-modulating antisense oligomers, we efficiently skipped the pseudoexon in patient-derived fibroblast cultures and restored a wild-type matrix. Similarly, we used CRISPR/Cas9 to precisely delete an intronic sequence containing the pseudoexon and efficiently abolish its inclusion while preserving wild-type splicing. Considering that this splice defect is emerging as one of the single most frequent mutations in COL6-RD, the design of specific and effective splice-correction therapies offers a promising path for clinical translation.</p>},
	issn = {2379-3708},
	doi = {10.1172/jci.insight.124403},
	author = {Bolduc, Veronique and Foley, A Reghan and Solomon-Degefa, Herimela and Sarathy, Apurva and Donkervoort, Sandra and Hu, Ying and Chen, Grace S and Sizov, Katherine and Nalls, Matthew and Zhou, Haiyan and Aguti, Sara and Cummings, Beryl B and Lek, Monkol and Tukiainen, Taru and Marshall, Jamie L and Regev, Oded and Marek-Yagel, Dina and Sarkozy, Anna and Butterfield, Russell J and Jou, Cristina and Jimenez-Mallebrera, Cecilia and Li, Yan and Gartioux, Corine and Mamchaoui, Kamel and Allamand, Val{\'e}rie and Gualandi, Francesca and Ferlini, Alessandra and Hanssen, Eric and Wilton, Steve D and Lamand{\'e}, Shireen R and MacArthur, Daniel G and Wagener, Raimund and Muntoni, Francesco and B{\"o}nnemann, Carsten G}
}
@article {364,
	title = {Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.},
	journal = {Sci Transl Med},
	volume = {9},
	year = {2017},
	month = {2017 04 19},
	abstract = {<p>Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50\%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35\%. We also report the discovery of a highly recurrent de novo intronic mutation in  that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25\% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.</p>},
	keywords = {Collagen Type VI, High-Throughput Nucleotide Sequencing, Humans, Muscular Diseases, Mutation, Transcriptome},
	issn = {1946-6242},
	doi = {10.1126/scitranslmed.aal5209},
	author = {Cummings, Beryl B and Marshall, Jamie L and Tukiainen, Taru and Lek, Monkol and Donkervoort, Sandra and Foley, A Reghan and Bolduc, Veronique and Waddell, Leigh B and Sandaradura, Sarah A and O{\textquoteright}Grady, Gina L and Estrella, Elicia and Reddy, Hemakumar M and Zhao, Fengmei and Weisburd, Ben and Karczewski, Konrad J and O{\textquoteright}Donnell-Luria, Anne H and Birnbaum, Daniel and Sarkozy, Anna and Hu, Ying and Gonorazky, Hernan and Claeys, Kristl and Joshi, Himanshu and Bournazos, Adam and Oates, Emily C and Ghaoui, Roula and Davis, Mark R and Laing, Nigel G and Topf, Ana and Kang, Peter B and Beggs, Alan H and North, Kathryn N and Straub, Volker and Dowling, James J and Muntoni, Francesco and Clarke, Nigel F and Cooper, Sandra T and B{\"o}nnemann, Carsten G and MacArthur, Daniel G}
}
