Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis.
BACKGROUND
Retinal dystrophies (RD) are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES) as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context.


RESULTS
We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations) in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases.


CONCLUSIONS
Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.
Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain.
Marta
M
Corton
Koji M
KM
Nishiguchi
Almudena
A
Avila-Fernández
Konstantinos
K
Nikopoulos
Rosa
R
Riveiro-Alvarez
Sorina D
SD
Tatu
Carmen
C
Ayuso
Carlo
C
Rivolta
D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D054815:Cyclic Nucleotide-Gated Cation Channels / Q000235:genetics; D059472:Exome / Q000235:genetics*; D016326:Extracellular Matrix Proteins / Q000235:genetics; D005136:Eye Proteins / Q000235:genetics; D005260:Female; D020022:Genetic Predisposition to Disease / Q000235:genetics; D006801:Humans; D057130:Leber Congenital Amaurosis / Q000235:genetics; D008297:Male; D008869:Microtubule-Associated Proteins; D009612:Nicotinamide-Nucleotide Adenylyltransferase / Q000235:genetics; D010375:Pedigree; D058499:Retinal Dystrophies / Q000235:genetics*; D012174:Retinitis Pigmentosa / Q000235:genetics; D013030:Spain; D052245:Usher Syndromes / Q000235:genetics
C056475:ABCA4 protein, human; D018528:ATP-Binding Cassette Transporters; D048868:Adaptor Proteins, Signal Transducing; C081787:CHM protein, human; C415904:CNGB3 protein, human; D054815:Cyclic Nucleotide-Gated Cation Channels; D016326:Extracellular Matrix Proteins; D005136:Eye Proteins; D008869:Microtubule-Associated Proteins; C120042:RP1 protein, human; C112735:USH2A protein, human; C484007:NMNAT1 protein, human; D009612:Nicotinamide-Nucleotide Adenylyltransferase