title: Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan.
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.
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
authors.forename: Maleeha
authors.initials: M
authors.lastname: Maria
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ajmal
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
authors.forename: Maleeha
authors.initials: M
authors.lastname: Azam
authors.affiliation: Tufts University Medical School, Boston, Massachusetts, United States of America.
authors.forename: Nadia Khalida
authors.initials: NK
authors.lastname: Waheed
authors.affiliation: Al-Shifa Eye Trust Hospital, Rawalpindi, Pakistan.
authors.forename: Sorath Noorani
authors.initials: SN
authors.lastname: Siddiqui
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Bilal
authors.initials: B
authors.lastname: Mustafa
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Humaira
authors.initials: H
authors.lastname: Ayub
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Liaqat
authors.initials: L
authors.lastname: Ali
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Shakeel
authors.initials: S
authors.lastname: Ahmad
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.
authors.forename: Shazia
authors.initials: S
authors.lastname: Micheal
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Alamdar
authors.initials: A
authors.lastname: Hussain
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan.
authors.forename: Syed Tahir Abbas
authors.initials: ST
authors.lastname: Shah
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan.
authors.forename: Syeda Hafiza Benish
authors.initials: SH
authors.lastname: Ali
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; University of Haripur, Haripur, Pakistan.
authors.forename: Waqas
authors.initials: W
authors.lastname: Ahmed
authors.affiliation: Department of Chemistry, University of Science and Technology, Bannu, Pakistan.
authors.forename: Yar Muhammad
authors.initials: YM
authors.lastname: Khan
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
authors.forename: Anneke I
authors.initials: AI
authors.lastname: den Hollander
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
authors.forename: Lonneke
authors.initials: L
authors.lastname: Haer-Wigman
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
authors.forename: Rob W J
authors.initials: RW
authors.lastname: Collin
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
authors.forename: Muhammad Imran
authors.initials: MI
authors.lastname: Khan
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan.
authors.forename: Raheel
authors.initials: R
authors.lastname: Qamar
authors.affiliation: Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
authors.forename: Frans P M
authors.initials: FP
authors.lastname: Cremers
mesh_terms: D003241:Consanguinity; D004252:DNA Mutational Analysis; D005260:Female; D005838:Genotype; D006720:Homozygote; D006801:Humans; D057130:Leber Congenital Amaurosis / Q000453:epidemiology / Q000235:genetics; D008297:Male; D009154:Mutation; D010154:Pakistan / Q000453:epidemiology; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D012160:Retina / Q000378:metabolism / Q000473:pathology; D012164:Retinal Diseases / Q000453:epidemiology / Q000235:genetics*; D012174:Retinitis Pigmentosa / Q000453:epidemiology / Q000235:genetics