Investigating the Molecular Basis of Retinal Degeneration in a Familial Cohort of Pakistani Decent by Exome Sequencing

<div><p>Purpose</p><p>To define the molecular basis of retinal degeneration in consanguineous Pakistani pedigrees with early onset retinal degeneration.</p><p>Methods</p><p>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.</p><p>Results</p><p>We identified a total of nine causal mutations, including six novel variants in <i>RPE65</i>, <i>LCA5</i>, <i>USH2A</i>, <i>CNGB1</i>, <i>FAM161A</i>, <i>CERKL</i> and <i>GUCY2D</i> 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.</p><p>Conclusions</p><p>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.</p></div

Members of the pedigree enrolled in this study are indicated by the presence of a genotype below their icon.

<p>“+” indicates presence of the variant, “-” indicates absence of the variant indicated to the left of the pedigree. Icons representing the individual(s) selected for exome capture and sequencing are outlined in red. A question mark (?) within the icon indicates the patient was not available for clinical evaluation. (A) PKRD077. (B) PKRD078. (C) PKRD103. (D) PKRD138. (E) PKRD141. (F) PKRD142. (G) PKRD176 (H) PKRD185.</p

Members of the pedigree enrolled in this study are indicated by the presence of a genotype below their icon.

<p>“+” indicates presence of the variant, “-” indicates absence of RPE65 variant (NM_000329.2:c.1087 C>A, NP_000320.1:p.Pro363Thr). Icons representing the individual(s) selected for exome capture and sequencing are outlined in red. A question mark (?) within the icon indicates the patient was not clinically examined. (A) PKRD281. (B) PKRD282. (C) PKRD283. (D) PKRD284. (E) PKRD285.</p

Electroretinography recordings of affected individuals with inherited retinal degeneration.

<p>Scotopic 0 dB response, and photopic 0 dB 30Hz flicker response of A) OD and B) OS of individual VI:9 of family PKRD138; C) OD and D) OS of individual V:5 of family PKRD141; E) OD and F) OS of individual VI:2 of family PKRD142; G) OD and H) 374 OS of individual V:7 of family PKRD176; I) OD and J) OS of an unaffected control. The electroretinography responses of affected individuals illustrate loss of rod and cone response. OD = oculus dexter (right eye); OS = oculus sinister (left eye).</p