Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease
Terry A. Braun,Robert F. Mullins,Alex H. Wagner,Jeaneen L. Andorf,Rebecca M. Johnston,Benjamin Bakall,Adam P. DeLuca,Gerald A. Fishman,Byron L. Lam,Richard G. Weleber,Artur V. Cideciyan,Samuel G. Jacobson,Val C. Sheffield,Budd A. Tucker,Edwin M. Stone +14 more
TLDR
In this paper, the authors demonstrate the utility of RNA sequence analysis of human donor tissue and patient-derived cell lines to identify mutations that would be undetectable by exome sequencing.Abstract:
Mutations in ABCA4 cause Stargardt disease and other blinding autosomal recessive retinal disorders. However, sequencing of the complete coding sequence in patients with clinical features of Stargardt disease sometimes fails to detect one or both mutations. For example, among 208 individuals with clear clinical evidence of ABCA4 disease ascertained at a single institution, 28 had only one disease-causing allele identified in the exons and splice junctions of the primary retinal transcript of the gene. Haplotype analysis of these 28 probands revealed 3 haplotypes shared among ten families, suggesting that 18 of the 28 missing alleles were rare enough to be present only once in the cohort. We hypothesized that mutations near rare alternate splice junctions in ABCA4 might cause disease by increasing the probability of mis-splicing at these sites. Next-generation sequencing of RNA extracted from human donor eyes revealed more than a dozen alternate exons that are occasionally incorporated into the ABCA4 transcript in normal human retina. We sequenced the genomic DNA containing 15 of these minor exons in the 28 one-allele subjects and observed five instances of two different variations in the splice signals of exon 36.1 that were not present in normal individuals (P < 10−6). Analysis of RNA obtained from the keratinocytes of patients with these mutations revealed the predicted alternate transcript. This study illustrates the utility of RNA sequence analysis of human donor tissue and patient-derived cell lines to identify mutations that would be undetectable by exome sequencing.read more
Citations
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Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing.
Isabella Bernardis,Laura Chiesi,Elena Tenedini,Lucia Artuso,Antonio Percesepe,Valentina Artusi,Maria Luisa Simone,Rossella Manfredini,Monica Camparini,Chiara Rinaldi,Antonio P. Ciardella,Claudio Graziano,Nicole Balducci,Antonia Tranchina,Gian Maria Cavallini,Antonello Pietrangelo,Valeria Marigo,Enrico Tagliafico +17 more
TL;DR: This study demonstrates that NGS represents a comprehensive cost-effective approach for IRDs molecular diagnosis, and the identification of the genetic alterations underlying the phenotype enabled the clinicians to achieve a more accurate diagnosis.
Journal ArticleDOI
Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease
Keren J. Carss,Gavin Arno,M Erwood,J Stephens,Alba Sanchis-Juan,Sarah Hull,K Megy,D Grozeva,E Dewhurst,Samantha Malka,Vincent Plagnol,Christopher J. Penkett,K Stirrups,R Rizzo,Genevieve A. Wright,Dragana Josifova,Maria Bitner-Glindzicz,R H Scott,E Clement,Louise E. Allen,R Armstrong,A F Brady,J Carmichael,Manali Chitre,Henderson Rhh.,J Hurst,Robert E MacLaren,E Murphy,Joan Paterson,E Rosser,D A Thompson,E Wakeling,Willem H. Ouwehand,Michel Michaelides,Anthony T. Moore,Andrew R. Webster,F L Raymond +36 more
TL;DR: Findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing, whole-exomes sequencing, or both performed, are presented, as part of the NIHR-BioResource Rare Diseases research study.
Journal ArticleDOI
Deep intronic mutations and human disease.
TL;DR: Evidence from mRNA analysis and entire genomic sequencing indicates that pathogenic mutations can occur deep within the introns of over 75 disease-associated genes, highlighting the importance of studying variation in deep intronic sequence as a cause of monogenic disorders as well as hereditary cancer syndromes.
Journal ArticleDOI
Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.
Edwin M. Stone,Edwin M. Stone,Jeaneen L. Andorf,Jeaneen L. Andorf,S. Scott Whitmore,S. Scott Whitmore,Adam P. DeLuca,Adam P. DeLuca,Joseph C. Giacalone,Joseph C. Giacalone,Luan M. Streb,Luan M. Streb,Terry A. Braun,Terry A. Braun,Robert F. Mullins,Robert F. Mullins,Todd E. Scheetz,Todd E. Scheetz,Val C. Sheffield,Budd A. Tucker,Budd A. Tucker +20 more
TL;DR: A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost and genetic testing for inherited retinal disease is now more than 75% sensitive.
Journal ArticleDOI
Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing
Mark Consugar,Daniel Navarro-Gomez,Emily Place,Kinga M. Bujakowska,Maria E. Sousa,Zoe Fonseca-Kelly,Daniel G. Taub,Maria Janessian,Dan Yi Wang,Elizabeth D. Au,Katherine B. Sims,David A. Sweetser,Anne B. Fulton,Qin Liu,Janey L. Wiggs,Xiaowu Gai,Eric A. Pierce +16 more
TL;DR: Based on quantified performance metrics, the data suggest that selective targeted enrichment is preferable to whole-exome sequencing for genetic diagnostic testing of patients with inherited eye disorders.
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