Investigating the Molecular Basis of Retinal Degeneration in a Familial Cohort of Pakistani Decent by Exome Sequencing.
OBJECTIVE
To define the molecular basis of retinal degeneration in consanguineous Pakistani pedigrees with early onset retinal degeneration.


METHODS
A cohort of 277 individuals representing 26 pedigrees from the Punjab province of Pakistan was analyzed. Exomes were captured with commercial kits and sequenced on an Illumina HiSeq 2500. Candidate variants were identified using standard tools and analyzed using exomeSuite to detect all potentially pathogenic changes in genes implicated in retinal degeneration. Segregation analysis was performed by dideoxy sequencing and novel variants were additionally investigated for their presence in ethnicity-matched controls.


RESULTS
We identified a total of nine causal mutations, including six novel variants in RPE65, LCA5, USH2A, CNGB1, FAM161A, CERKL and GUCY2D as the underlying cause of inherited retinal degenerations in 13 of 26 pedigrees. In addition to the causal variants, a total of 200 variants each observed in five or more unrelated pedigrees investigated in this study that were absent from the dbSNP, HapMap, 1000 Genomes, NHLBI ESP6500, and ExAC databases were identified, suggesting that they are common in, and unique to the Pakistani population.


CONCLUSIONS
We identified causal mutations associated with retinal degeneration in nearly half of the pedigrees investigated in this study through next generation whole exome sequencing. All novel variants detected in this study through exome sequencing have been cataloged providing a reference database of variants common in, and unique to the Pakistani population.
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Bruno
B
Maranhao
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Pooja
P
Biswas
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Alexander D H
AD
Gottsch
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Mili
M
Navani
National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
Muhammad Asif
MA
Naeem
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
John
J
Suk
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Justin
J
Chu
National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
Sheen N
SN
Khan
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Rachel
R
Poleman
Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.
Javed
J
Akram
National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.
Sheikh
S
Riazuddin
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Pauline
P
Lee
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America; National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
S Amer
SA
Riazuddin
OGVF branch, National Eye Institute, NIH, Bethesda, MD, United States of America.
J Fielding
JF
Hejtmancik
Department of Ophthalmology, University of California La Jolla, La Jolla, CA, United States of America.
Radha
R
Ayyagari
D017668:Age of Onset; D003241:Consanguinity; D004596:Electroretinography; D005006:Ethnicity / Q000235:genetics*; D059472:Exome / Q000235:genetics*; D005136:Eye Proteins / Q000235:genetics; D005260:Female; D005654:Fundus Oculi; D005808:Genes, Recessive; D056726:Genetic Association Studies; D005838:Genotype; D006801:Humans; D008297:Male; D009154:Mutation; D010154:Pakistan; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics; D012162:Retinal Degeneration / Q000208:ethnology / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
D005136:Eye Proteins; D012333:RNA, Messenger