title: Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing.
abstract: While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10. Sequence reads were aligned to hg19 using BWA-MEM and variant calling was performed with Genome Analysis Toolkit. The called variants were annotated with SnpEff v4.11, PolyPhen v2.2.2, and CADD v1.3. Copy number variations were called using Genome STRiP (svtoolkit 2.00.1611) and SpeedSeq software. Variants were filtered to detect rare potentially deleterious variants segregating with disease. Candidate variants were validated by dideoxy sequencing. Clinical evaluation revealed typical adolescent-onset recessive retinitis pigmentosa (arRP) in affected members. WGS identified about 4 million variants in each individual. Two rare and potentially deleterious compound heterozygous variants p.Arg281Cys and p.Arg487* were identified in the gene ATP/GTP binding protein like 5 (AGBL5) as likely causal variants. No additional variants in IRD genes that segregated with disease were identified. Mutation analysis confirmed the segregation of these variants with the IRD in the pedigree. Homology models indicated destabilization of AGBL5 due to the p.Arg281Cys change. Our findings establish the involvement of mutations in AGBL5 in RP and validate the WGS variant filtering pipeline we designed.
authors.affiliation: Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan.
authors.forename: Kari
authors.initials: K
authors.lastname: Branham
authors.affiliation: Institute for Genomic Medicine, University of California San Diego, La Jolla, California.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Matsui
authors.affiliation: Shiley Eye Institute, University of California San Diego, La Jolla, California.
authors.forename: Pooja
authors.identifier: 0000-0002-8545-9296
authors.initials: P
authors.lastname: Biswas
authors.affiliation: Shiley Eye Institute, University of California San Diego, La Jolla, California.
authors.forename: Aditya A
authors.initials: AA
authors.lastname: Guru
authors.affiliation: Human Longevity Incorporated, San Diego, California.
authors.forename: Michael
authors.initials: M
authors.lastname: Hicks
authors.affiliation: Shiley Eye Institute, University of California San Diego, La Jolla, California.
authors.forename: John J
authors.initials: JJ
authors.lastname: Suk
authors.affiliation: Institute for Genomic Medicine, University of California San Diego, La Jolla, California.
authors.forename: He
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute for Genomic Medicine, University of California San Diego, La Jolla, California.
authors.forename: David
authors.initials: D
authors.lastname: Jakubosky
authors.affiliation: Human Longevity Incorporated, San Diego, California.
authors.forename: Tao
authors.initials: T
authors.lastname: Long
authors.affiliation: Human Longevity Incorporated, San Diego, California.
authors.forename: Amalio
authors.initials: A
authors.lastname: Telenti
authors.affiliation: Institute for Genomic Medicine, University of California San Diego, La Jolla, California.
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.affiliation: Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan.
authors.forename: John R
authors.initials: JR
authors.lastname: Heckenlively
authors.affiliation: Institute for Genomic Medicine, University of California San Diego, La Jolla, California.|Department of Pediatrics and Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, California; and.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
authors.affiliation: National Eye Institute, National Institutes of Health, Bethesda, Maryland.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Sieving
authors.affiliation: Shiley Eye Institute, University of California San Diego, La Jolla, California; rayyagari@ucsd.edu.
authors.forename: Radha
authors.initials: R
authors.lastname: Ayyagari
mesh_terms: D000293:Adolescent; D002268:Carboxypeptidases / Q000235:genetics*; D004252:DNA Mutational Analysis; D004596:Electroretinography / Q000379:methods; D005260:Female; D056726:Genetic Association Studies / Q000379:methods; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics; D010375:Pedigree; D012162:Retinal Degeneration / Q000235:genetics; D012174:Retinitis Pigmentosa / Q000235:genetics*; D000073336:Whole Genome Sequencing / Q000379:methods; D055815:Young Adult
chemical_list: C000607347:AGBL5 protein, human; D002268:Carboxypeptidases
keywords: ophthalmology; whole genome sequencing