Age-related Macular Degeneration (AMD) Targeted Sequencing Study

Age-related Macular Degeneration (AMD) is a leading cause of incurable blindness in people over the age of 65. AMD is a late-onset multi-factorial neurodegenerative disease and its pathogenesis involves interaction of genetic and environmental factors. Several chromosomal regions have been associated with AMD susceptibility through linkage analysis (Swaroop et al., 2009). More recent studies provide strong evidence that variants within the CFH gene cluster on chromosome 1 and at/near LOC387715/ARMS2 on chromosome 10 are strongly associated with disease. Variants at other genes including C2/BF, C3, CFI and APOE4, also contribute to AMD susceptibility.

Our primary goals are to identify genetic variants and haplotypes that are associated with AMD. The underlying hypothesis is that DNA variation(s) in multiple genetic susceptibility loci will predispose individuals to AMD pathogenesis, and comparison of DNA of cases and controls should identify these susceptibility variants. Our studies are focused on the genetic analysis of advanced AMD and should provide novel insights into disease diagnosis, progression and pathology.

We have assembled a collaborative group of researchers from the University of Michigan, Mayo Clinic, University of Pennsylvania, and the AREDS group including National Eye Institute intramural investigators, who collected clinical data and DNA from a large number of patients affected with AMD and from unaffected controls.

To identify rare coding variants associated with a large increase in risk of AMD, 10 candidate loci spanning 56 genes were sequenced in over 2,330 cases and over 780 controls. Probes were designed to capture 96.5% of the coding sequence and 35% of total locus sequence, generating an average 123Mb of on-target sequence per individual at 127x average depth.

DNA was isolated from individuals in cohorts established by the University of Michigan, the University of Pennsylvania and the National Eye Institute's Age-Related Eye Disease Study (AREDS).

• Study Design:
  • Case-Control
• Study Type:
  • Case-Control
• Total number of consented subjects: 3337
• Subject Sample Telemetry Report (SSTR)

• BioProject
• Sequence Read Archive
• MeSH
• Gene

Inclusion criteria:
1. Affected with geographic atrophy, neovascularization, or large drusen in at least one eye. If any of the above are only found in one eye, then the evidence of drusen, pigment changes must be found in the fellow eye.
2. Control patients have been examined and found to have no more than 5 hard drusen and are over the age of 50 (Mayo clinic cohort) or small drusen and pigment changes in one eye only and are over the age of 60 (UMich and UPenn clinic cohorts).

Exclusion criteria:
1. Evidence or history of severe macular disease or vision loss before the age of 40, or diagnosis with symptoms consistent with a juvenile macular or retinal degeneration, or macular damage resulting from ocular trauma, retinal detachment, high myopia, chorioretinal infection, or inflammatory disease, or choroidal dystrophy or other retinal insult in which the fundus was not gradable.

The University of Michigan genetic study of AMD was started in 1998 by Dr. Anand Swaroop with the goal of identifying susceptibility loci for AMD. Affected patients were enrolled primarily from the retina clinic of the Kellogg Eye Center with the help of clinicians and staff. The control participants were enrolled primarily from the general ophthalmology clinics of the Kellogg Eye Center. After the enrollment of affected probands, we sought to enroll affected and unaffected family members. To date, more than 2300 affected and unaffected subjects have been enrolled in the study.

The University of Michigan genetic studies of AMD have resulted in several peer-reviewed manuscripts, notably a whole-genome linkage scan for age-related macular degeneration (Abecasis et al., 2004) and a joint-analysis of several linkage scans (Fisher et al., 2005), a dissection of the roles of complement factor H (Zareparsi et al., 2005a) and TLR4 (Zareparsi et al., 2005b), and recent detailed analyses of the complement factor H locus (Li et al., 2006) and LOC387715/ARMS2 locus (Kanda et al., 2007) among others.

For the University of Pennsylvania cohort, subjects were ascertained through the ophthalmology practices of the University of Pennsylvania (Dr. Dwight Stambolian and colleagues) as well as subjects who participated in the clinical trial of the CAPT study.

The Mayo subjects were enrolled from the practices of Dr. Albert Edwards and selected colleagues from Dallas, TX and Rochester, MN starting in 1998. The subjects have been used in a number of studies and contributed to one of the initial reports of association between macular degeneration and the CFH locus (Edwards et al., 2005, 2008, 2009; Park et al., 2009).

• Primary Phenotype: Macular Degeneration

• ABCA1
• APOE
• CFB
• C2
• C3
• C4A
• C4B
• CASP6
• CETP
• ATF6B
• more ...

• Principal Investigators
  • Elaine Mardis, PhD. Washington University School of Medicine, St. Louis, MO, USA.
  • Anand Swaroop, PhD. National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
  • Gonçalo Abecasis, PhD. University of Michigan, Ann Arbor, MI, USA.
  • Richard K. Wilson, PhD. Washington University School of Medicine, St. Louis, MO, USA.
  • Dwight Stambolian, MD, PhD. University of Pennsylvania, Philadelphia, PA, USA.
• Co-Investigator
  • Emily Chew, MD. National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
• Coordinator
  • Kari Branham, MS. University of Michigan, Ann Arbor, MI, USA.
• Sequencing Center
  • The Genome Institute. Washington University School of Medicine, St. Louis, MO, USA.
• Funding Source for Sequencing
  • U54 HG003079. National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.