A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies

Scientific Reports
Maitane Ezquerra-InchaustiJavier Ruiz-Ederra

Abstract

Inherited retinal diseases (IRD) are a heterogeneous group of diseases that mainly affect the retina; more than 250 genes have been linked to the disease and more than 20 different clinical phenotypes have been described. This heterogeneity both at the clinical and genetic levels complicates the identification of causative mutations. Therefore, a detailed genetic characterization is important for genetic counselling and decisions regarding treatment. In this study, we developed a method consisting on pooled targeted next generation sequencing (NGS) that we applied to 316 eye disease related genes, followed by High Resolution Melting and copy number variation analysis. DNA from 115 unrelated test samples was pooled and samples with known mutations were used as positive controls to assess the sensitivity of our approach. Causal mutations for IRDs were found in 36 patients achieving a detection rate of 31.3%. Overall, 49 likely causative mutations were identified in characterized patients, 14 of which were first described in this study (28.6%). Our study shows that this new approach is a cost-effective tool for detection of causative mutations in patients with inherited retinopathies.

References

Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Apr 25, 2003·The New England Journal of Medicine·Tamar Ben-YosefThomas B Friedman
Dec 19, 2003·American Journal of Human Genetics·Miquel TusonRoser Gonzàlez-Duarte
Feb 19, 2004·European Journal of Human Genetics : EJHG·Elena AllerMagdalena Beneyto
Jun 5, 2004·Community Genetics·C EspinósC Nájera
Aug 16, 2006·American Journal of Human Genetics·Anneke I den HollanderFrans P M Cremers
Sep 28, 2006·Investigative Ophthalmology & Visual Science·Lori S SullivanStephen P Daiger
Feb 14, 2007·Archives of Ophthalmology·Stephen P DaigerLori S Sullivan
Mar 16, 2007·Journal of Medical Genetics·T JaijoJ M Millan
Mar 3, 2009·Nature Methods·Todd E DruleyRobi D Mitra
Oct 21, 2009·Human Mutation·Astrid A OutFrederik J Hes
Aug 3, 2010·Nature Methods·Jana Marie SchwarzDominik Seelow
Nov 12, 2010·Human Mutation·Isabel BarragánGuillermo Antiñolo
Mar 26, 2011·Investigative Ophthalmology & Visual Science·Anne-Françoise RouxMireille Claustres
Apr 27, 2011·Investigative Ophthalmology & Visual Science·Juan I PierasGuillermo Antiñolo
Oct 19, 2011·Orphanet Journal of Rare Diseases·Gema Garcia-GarciaElena Aller
Feb 4, 2012·Investigative Ophthalmology & Visual Science·Masaki IwanamiSeishi Kato
Oct 10, 2012·The Journal of Cell Biology·Iman SahlyChristine Petit
Oct 12, 2012·PloS One·Yongwook ChoiAgnes P Chan
Feb 6, 2013·Orphanet Journal of Rare Diseases·Marta CortonCarmen Ayuso
Aug 29, 2013·Investigative Ophthalmology & Visual Science·Kaoru FujinamiMichel Michaelides
Jan 15, 2014·Experimental Eye Research·Ander AnasagastiJavier Ruiz-Ederra

❮ Previous
Next ❯

Citations

Apr 5, 2020·Nucleic Acids Research·Thanutra ZhangRoy Wollman
Feb 2, 2020·Scientific Reports·Rita Sousa SilvaJuliana Maria Ferraz Sallum
Jul 31, 2021·Frontiers in Cell and Developmental Biology·Belén García BohórquezJosé M Millán
Jul 8, 2021·Ophthalmic Genetics·Elena MermeklievaRadka Kaneva

❮ Previous
Next ❯

Methods Mentioned

BETA
Exome Sequencing
genotyping
pooled sequencing
PCR
Chips
electrophoresis

Software Mentioned

Ion Reporter
HRM
BioEdit
GeneMapper
Ion Proton System
Ion Torrent Torrent Suite
Ensembl

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.