Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan

PLoS One. 2015 Mar 16;10(3):e0119806. doi: 10.1371/journal.pone.0119806. eCollection 2015.

Abstract

Background: Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD).

Methods: We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.

Results: Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.

Conclusions: Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Consanguinity
  • DNA Mutational Analysis
  • Female
  • Genotype
  • Homozygote
  • Humans
  • Leber Congenital Amaurosis / epidemiology
  • Leber Congenital Amaurosis / genetics
  • Male
  • Mutation*
  • Pakistan / epidemiology
  • Pedigree
  • Polymorphism, Single Nucleotide
  • Retina / metabolism
  • Retina / pathology
  • Retinal Diseases / epidemiology
  • Retinal Diseases / genetics*
  • Retinitis Pigmentosa / epidemiology
  • Retinitis Pigmentosa / genetics

Grants and funding

This work was supported by grant no. PAS/I-9/Project awarded to R.Q. and M.Az., by the Pakistan Academy of Sciences, and a core grant from the COMSATS Institute of Information Technology (CIIT) to R.Q. This work was also supported by CIIT grant No. 16-64/CRGP/CIIT/IBD/12/919 awarded to M.M., grant No. 16-83/CRGP/CIIT/IBD/13/144 awarded to M.Aj. and grant No.16-82-CRGP-CIIT-IBD-13/145 awarded to M.Az. This work was also financially supported by the Stichting Nederlands Oogheelkundig Onderzoek, the Nelly Reef Foundation, the Stichting ter Verbetering van het Lot der Blinden (to F.P.M.C., R.W.J.C., and A.I.d.H.), the Gelderse Blinden Stichting (to F.P.M.C.), the Rotterdamse Stichting Blindenbelangen, the Stichting Blindenhulp, the Stichting A.F. Deutman Researchfonds Oogheelkunde, and the Stichting voor Ooglijders (to F.P.M.C. and M.I.K.). F.P.M.C. and M.I.K. were also supported by the following foundations: the Algemene Nederlandse Vereniging ter Voorkoming van Blindheid, the Landelijke Stichting voor Blinden en Slechtzienden, the Stichting Retina Nederland Fonds, and the Novartis fund, contributed through UitZicht. The work of L.H-W. was supported by the Foundation Fighting Blindness USA C-GE-0811-0545-RAD01 (to F.P.M.C.). The funding organizations provided unrestricted grants and had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.