National Eye Institute Workshop to Identify Gaps, Needs, and Opportunities in Ophthalmic Genetics [NEI Strategic Planning]

National Eye Institute Workshop to Identify Gaps, Needs, and Opportunities in Ophthalmic Genetics

June 4-5, 2009

Diseases, Biological Systems, Approaches and Methodologies

White Papers

Prior to the workshop, short white papers were prepared summarizing the progress in various fields of disease research, biological systems, approaches, and methodologies. These white papers represent the opinions of their authors, but not necessarily the views of the NEI. All white papers were distributed to participants in advance of the meeting.

Contents:


Congenital Strabismus

Elizabeth Engle

Background

Strabismus and secondary amblyopia is a leading cause of visual impairment in those under 60 years of age. For the sake of genetic analysis it is helpful to divide strabismus into incomitant and comitant forms. Individuals with incomitant (complex or paralytic) strabismus have an ocular misalignment of greater magnitude in one direction. Incomitant strabismus includes the various forms of Duane syndrome, horizontal gaze palsy, and CFEOM (congenital fibrosis of the extraocular muscles), each of which is relatively rare and can be inherited as a Mendelian trait. Individuals with comitant strabismus have a similar magnitude of deviation in all gaze positions. Comitant strabismus includes various forms of eso-, exo-, hyper- and hypodeviations. Although it is much more common and does cluster in families, comitant strabismus appears to segregate as a complex trait (as was noted by Hippocrates).

Genetics of incomitant strabismus: Heritability has been established by identification of Mendelian inheritance in families. Gene identification has been through family-based linkage analysis and sequencing of positional candidate genes. This has resulted in the publication of the phenotypic features and genetic etiology of multiple syndromes, now referred to as the congenital cranial dysinnervation disorders (CCDDs). A subset is nonsyndromic. Genetics suggest that these disorders can result from errors in the development of ocular motor neurons and, in particular, in the appropriate guidance and/or targeting of axons to extraocular muscles.

Genetics of comitant strabismus: The incidence of nonsyndromic comitant strabismus is estimated to be between 1-5%, and varies for specific types of strabismus and between different races. In addition, over 270 entries in OMIM are associated with comitant strabismus, most of which is syndromic. Population, twin, and family studies support inheritance of nonsyndromic comitant strabismus as a complex trait with an odds ratio for concordant sibs of 3 and of a first-degree relative of 3 to 5. Families are usually concordant for either esotropia or exotropia; families with both may reflect the presence of two relatively common variants or a common underlying genetic susceptibility. Low birth weight, maternal smoking in pregnancy, and advanced maternal age have each been identified as contributing risk factors in some but not all studies. Several family-based linkage analyses are reviewed below. No GWAS studies reported.

Consensus on phenotyping: (a) Incomitant strabismus: Phenotyping has been based primarily on phenotype-genotype studies following gene identification. There may be ascertainment bias. (b) Comitant strabismus: In most cases it is clear if someone is affected, and the Olmsted, Baltimore, and MEPED studies were in close agreement as to phenotypic definitions. GWAS studies may benefit from consensus on diagnostic cutoffs, data collection, and patient population. If strabismus is a quantitative trait it may be indicated to enroll patients at risk.

Genetic resources for strabismus: Researcher-based cohorts, population-based cohorts, EyeGENE.

Major strabismus genetics studies

Incomitant strabismus: Multiple publications of linkage and gene identification for incomitant strabismus genes. These are family-based linkage using STRP or SNP-based methods followed by position-based candidate gene sequencing.

1. Elizabeth Engle PI. NEI support for the identification of CCDD genes includes: Molecular Basis of Congenital Strabismus, 5R01EY012498-09; Genetic and anatomic basis of the fibrosis syndromes, 5R01EY013583-08; and Genetic Etiologies of Horizontal Strabismus, 5R01EY015298-05 - Current enrollment of 997 CCDD pedigrees from ascertainment world-wide. Phenotyping typically performed prospectively by collaborating clinician and, as necessary, in a targeted fashion following gene identification. Mutations identified in 153 probands, or 15% of ascertained cohort. Phenotyping parameters: incomitant strabismus or ptosis.
2. Ascertainment of incomitant strabismus by investigators in the Middle East, Japan, Europe, Australia, and the USA.

Comitant strabismus: Four manuscripts of linkage studies published from three populations. There are two family-based STRP genome-wide screens using 400 markers and one family-based linkage to previously reported locus.

1. Jeremy Nathans, PI (USA). Dr. Nathan’s 2003 PNAS paper reported ascertainment of 209 pedigrees with nonsyndromic strabismus from the USA (most in mid-Atlantic region), from which 7 of the first 150 families were chosen for STRP genome-wide linkage analysis by CIDR. Phenotypes were based on telephone interviews and, in some cases, retrospective chart review and did not necessarily distinguish eso- and exotropia. They reported linkage of 1 pedigree to 7p22.1 (STBMS1) as a recessive trait with incomplete penetrance and high carrier frequency. Funded by NEI and HHMI.
2. Toshihiko Matsuo, PI (Japan). Dr. Matsuo’s 2003 Acta Med. Okayama and 2009 IOVS papers report a combined ascertainment of 55 Japanese pedigrees with 2 or more affected members (average number of affected per family was 2.2 with range of 2-7) and family-based genome-wide STRP analysis of all families. Phenotyping based on exam of all probands and all available relatives, history, and medical record review. Data was analyzed in collaboration with Dr. Jurg Ott under various assumptions. The 2009 paper reports linkage to 4q28.3 under a dominant model (HLOD 3.62, NPL 2.68) and to two loci at 7q31.2 under a recessive model (HLOD 4.4 and 3.93); they did not identify linkage to STBMS1.
3. Aine Rice, PI (UK). Dr. Rice’s 2009 IOVS paper reported linkage analysis to the STMBS1 locus using STR markers in 12 British pedigrees with primary nonsyndromic comitant strabismus. Phenotyping was done by exam whenever possible. One pedigree mapped to the locus with a lod score of >3 assuming autosomal dominant inheritance with reduced penetrance.
4. Elizabeth Engle, PI (USA). Dr. Engle is currently collaborating with Dr. Hunter and the Ophthalmology Dept at Children’s Hospital Boston to ascertain and enroll families and individuals with comitant strabismus or associated risk factors. The last several years were focused on developing the infrastructure for accurate, high-throughput enrollment and phenotyping, and developing the database program for phenotype and genotype entry and sample management. This is complete and enrollment is underway.

Known Genes

Locus Inherit. Linkage Gene Mutation Protein Ref
INCOMITANT STRABISMUS
CFEOM1 AD 12q12 KIF21A missense Kinesin 1
CFEOM2 ar 11q13.3 PHOX2A LOF Transc. factor 2
CFEOM3 AD 16qter       3
CFEOM4 (3B) AD t(2:13)(q37.3;q12.11)       4
Turkel ar 21q22       5
DURS1 spor 8q13 (CPA6) cytogen   6 7
DURS2 AD 2q31-q32.1 CHN1 missense Cell signaling RacGAP 8
DRRS AD 20q13.13-q13.2 SALL4 haploinsuf Transc. factor 9
BSAS/ABDS ar 7p15.3 HOXA1 LOF Transc. factor 10
HGPPS ar 11q23-q25 ROBO3 LOF Axon guide receptor 11
COMITANT STRABISMUS
STBMS1 ar/AD 7p22.1       12 13
  ar 7q31.2       14
  AD 4q28.3       14

Next Steps

Short-term goals to advance the field:
Incomitant:
1. Continue ascertainment of new syndromes & identification of genes
2. GWAS and CNV analysis of Duane syndrome

Comitant:
1. Continue family-based linkage studies
2. Initial GWAS(s) to determine if existing cohorts can identify common variants that explain a sizable fraction of strabismus heritability.
3. Establish consortia for standardized large-scale enrollment and phenotyping of patients with all common forms of strabismus, anisometropia, hypermetropia > 3 D, and amblyopia
4. Standardized and/or centralized data entry and biospecimen banking
5. Establish ophthalmic consortia for statistical genetic analysis of GWAS data

Long-term goals to advance the field:
Incomitant:
1. Functional studies of molecular etiologies with eventual translation to treatment

Comitant:
1. Linkage, GWAS meta-analysis, replication, identification of causal variants
2. Functional studies of variants / associated genes to understand molecular etiologies
3. Improved treatment and outcome prediction through accurate genetic characterization in advance of intervention

Communal strabismus research resources that would represent a good investment for NEI:
1. Consortium of clinicians and investigators for standardized identification, characterization of phenotype, and collection of genetic material.
2. Centralized sample banking and storage

Reviews

1: Donahue SP. Clinical practice. Pediatric strabismus. N Engl J Med. 2007 Mar 8;356(10): 1040-7.
2: Engle EC. Genetic basis of congenital strabismus. Arch Ophthalmol. 2007 Feb;125(2):189-95.

References

  1. Yamada, K. et al. Heterozygous mutations of the kinesin KIF21A in congenital fibrosis of the extraocular muscles type 1 (CFEOM1). Nat Genet 35, 318-321 (2003).
  2. Nakano, M. et al. Homozygous mutations in ARIX(PHOX2A) result in congenital fibrosis of the extraocular muscles type 2. Nat Genet 29, 315-320. (2001).
  3. Doherty, E.J. et al. CFEOM3: a new extraocular congenital fibrosis syndrome that maps to 16q24.2-q24.3. Invest Ophthalmol Vis Sci 40, 1687-94 (1999).
  4. Aubourg, P. et al. Assignment of a new congenital fibrosis of extraocular muscles type 3 (CFEOM3) locus, FEOM4, based on a balanced translocation t(2;13) (q37.3;q12.11) and identification of candidate genes. J Med Genet 42, 253-9 (2005).
  5. Tukel, T. et al. A new syndrome, congenital extraocular muscle fibrosis with ulnar hand anomalies, maps to chromosome 21qter. J Med Genet 42, 408-15 (2005).
  6. Calabrese, G. et al. Narrowing the Duane syndrome critical region at chromosome 8q13 down to 40 kb. Eur J Hum Genet 8, 319-24 (2000).
  7. Pizzuti, A. et al. A peptidase gene in chromosome 8q is disrupted by a balanced translocation in a duane syndrome patient. Invest Ophthalmol Vis Sci 43, 3609-12 (2002).
  8. Miyake, N. et al. Human CHN1 mutations hyperactivate alpha2-chimaerin and cause Duane’s retraction syndrome. Science 321, 839-43 (2008).
  9. Al-Baradie, R. et al. Duane Radial Ray Syndrome (Okihiro Syndrome) Maps to 20q13 and Results from Mutations in SALL4, a New Member of the SAL Family. Am J Hum Genet 71, 1195-9 (2002).
  10. Tischfield, M.A. et al. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. Nat Genet 37, 1035-7 (2005).
  11. Jen, J.C. et al. Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis. Science 304, 1509-13 (2004).
  12. Parikh, V. et al. A strabismus susceptibility locus on chromosome 7p. Proc Natl Acad Sci U S A 100, 12283-8 (2003).
  13. Rice, A. et al. Replication of the recessive STBMS1 locus but with dominant inheritance. Investigative Ophthalmology and Visual Science (2009).
  14. Shaaban, S. et al. Chromosomes 4q28.3 and 7q31.2 as new susceptibility loci for comitant strabismus. Investigative Ophthalmology and Visual Science 50, 654-61 (2009).

Retinal Degenerations

Michael Gorin

Background

Historically, the major advances in the molecular genetics of retinal degenerations have been based on a combination of family-based linkage studies and candidate gene screening. These approaches have been used in combination and independently of each other. The greatest success has been for autosomal dominant and X-linked conditions, though recessive conditions have been successfully studied using homozygosity mapping and inbred populations with strong founder effects. In a number of instances (e.g. Bardet Biedl Syndrome), multiple disease-causing genes have been found by using initial mapping and gene screening in conjunction with subsequent candidate gene analyses based on genes that were suspected based on biological pathway analyses. A summary of the current status of the molecular genetics of retinal degenerations can be found at RetNet.

Large-scale mutation screening efforts for specific genes such as ABCA4 have been undertaken by several groups but never in a coordinated manner. For most forms of retinal degenerations, there remains a significant number of patients for whom mutations in the known disease-causing genes have not been found and this is the result of a combination of genetic heterogeneity as well as the limitation of current mutation screening methods. There currently remains a place for family-based linkage analysis and candidate gene testing for retinal degenerations, but funding for such studies has virtually disappeared from NIH or private foundations. In part this is due to a shift in priorities of these groups towards translational research and new therapies, as well as greater emphasis on genome-wide association studies and sequencing to find disease-causing genes. The advantages and disadvantages of these alternative approaches are beyond the scope of this summary.

There are several groups that provide either research or CLIA- approved molecular diagnostic testing for a number of retinal degenerations (LCA, Bardet Biedl, autosomal dominant RP, X-linked RP, cone dystrophies (autosomal recessive and X-linked), achromatopsias, CSNB, albinism, Stargardt disease (including AD Stargardt-like dystrophy, Bietti crystalline dystrophy).(see GeneTests.org) The mutation detection rate of these screening programs is not known, nor are there standards for phenotyping prior to the submission of samples. All of these testing groups rely on the referring clinician to have a suspected diagnosis. In cases of RP, it is unclear if most referring physicians take an adequate family history or examine family members to clearly establish an inheritance pattern.

There is no central clearing house for the collection of mutations that have been found by research or clinical testing. If such a central system were established, it would probably be necessary to also identify samples for which no mutation is found and to be able to distinguish when an individual has been tested multiple times or at different laboratories. A standard forensic DNA genotyping of each tested person (or comparable set of genetic markers) would solve this issue, but would raise significant legal and ethical issues (and raise testing costs). However having a unique genetic tag for each individual would be a means of ensuring anonymity of the person while still allowing the system to know if the person has undergone multiple testing.

There is also no clear consensus as to what is sufficient to define a disease-causing mutation. Some laboratories such as the Carver Laboratory, have a methodology for describing if a variant is definitely disease-causing, probably disease-causing, possibly disease-causing, or not disease-causing. A central database of variants could greatly facilitate these efforts. This issue becomes even more critical as the newer sequencing technologies makes it feasible to sequence not only the entire coding regions of genes and splice sites but also introns and promoters that may harbor functionally active variants. The explosion of genetic variants that can be readily identified makes their interpretation all the more important and challenging, especially when compared to some of the current technologies that test only for known disease-causing variants and avoid this issue but also miss out on discovering new disease-causing mutations.

Known Genes

Last updated April 26, 2009

A. Number of Genes and Loci by Disease Category (One Disease per Gene/Locus)
Disease Category Total # of Genes and Loci No. of Identified Genes
Bardet-Biedl syndrome, autosomal recessive 12 12
Chorioretinal atrophy or degeneration, autosomal dominant 1 1
Cone or cone-rod dystrophy, autosomal dominant 7 5
Cone or cone-rod dystrophy, autosomal recessive 5 3
Cone or cone-rod dystrophy, X-linked 2 0
Congenital stationary night blindness, autosomal dominant 1 1
Congenital stationary night blindness, autosomal recessive 5 5
Congenital stationary night blindness, X-linked 2 2
Leber congenital amaurosis, autosomal recessive 9 8
Macular degeneration, autosomal dominant 12 6
Macular degeneration, autosomal recessive 2 2
Ocular-retinal developmental disease, autosomal dominant 1 1
Optic atrophy, autosomal dominant 3 1
Optic atrophy, autosomal recessive 2 1
Optic atrophy, X-linked 1 0
Retinitis pigmentosa, autosomal dominant 16 15
Retinitis pigmentosa, autosomal recessive 20 16
Retinitis pigmentosa, X-linked 6 2
Syndromic/systemic diseases with retinopathy, autosomal dominant 8 6
Syndromic/systemic diseases with retinopathy, autosomal recessive 29 22
Syndromic/systemic diseases with retinopathy, X-linked 2 1
Usher syndrome, autosomal recessive 11 9
Other retinopathy, autosomal dominant 9 4
Other retinopathy, autosomal recessive 14 12
Other retinopathy, mitochondrial 7 7
Other retinopathy, X-linked 9 7
TOTALS 196 149
Prevalence of Retinitis Pigmentosa and Estimated Percentages of Retinitis Pigmentosa Types
Category Type % of Total*
Nonsyndromic RP Autosomal dominant RP 20
Autosomal recessive RP 13
X-linked RP 8
Isolated or unknown RP 20
Leber congenital amaurosis 4
Subtotal 65
Syndromic and systemic RP Usher syndrome 10
Bardet-Biedl syndrome 5
Other 10
Subtotal 25
Other or unknown types of RP 10
  Total 100

Abbreviation: RP, retinitis pigmentosa.
*The total prevalence is 1 case per 3100 persons (range, 1 case per 3000 persons to 1 case per 7000 persons), or 32.2 cases per 100 000 persons.Arch Ophthalmol. 2007 February; 125(2): 151-158.

Nonsyndromic, nonsystemic RP encompasses 65% of all cases, or about 65 000 people in the United States. Of the total number of nonsyndromic, nonsystemic cases, roughly 30% are adRP, 20% are autosomal recessive RP, 15% are X-linked RP, and 5% are early-onset forms of RP that are typically diagnosed as recessive LCA. The remaining cases, at least 30%, are isolated or simplex cases. The simplex cases are likely to include many individuals with recessive mutations, but dominant-acting de novo mutations are also found in these individuals.

Leber congenital amaurosis (LCA) is a group of severe autosomal recessive retinal dystrophies defined by the onset of blindness at birth and absent electroretinographic signals. LCA is the most common cause of infant blindness in schools for the blind with approximately 200,000 humans affected worldwide. In total, 14 genes are associated with LCA and mutations in these retinal genes account for approximately 60% of patients. Koenekoop R, et al. Genetics, phenotypes, mechanisms and treatments for Leber congenital amaurosis: a paradigm shift. Expert Review of Ophthalmology; Aug2008, Vol. 3 Issue 4, p397-415

Next Steps

Areas for future investigation:

Modifier genes for retinal degenerations and their complicationsGenetics of macular edema, central serous chorioretinopathy, macular telangectasia, others.Mechanisms of photoreceptor death including cone cell death in rod dystrophies.

Potential Communal Resources to be developed:

  • Enhanced molecular diagnostics that includes mutation and causative gene discovery
    • Exomic sequencing, family-based studies
  • More inclusive mechanisms to allow for individual investigator initiative and collaboration - assist in team building (but not force people to join huge groups)
  • Central repository for results from DNA testing from multiple laboratories.
  • Coordinated efforts to identify new disease-causing genes and mutations by combined analyses (for example exomic screening of cases for which no mutations in known genes are identified)
  • National registry (patient driven, not solely physician driven) - include the ability to identify new disorders.
  • Empower more effective and consistent use of diagnostic tools to characterize disorders (you have to pay for some things)

Reviews

Mutations in Known Genes Account for 58% of Autosomal Dominant RetinitisPigmentosa (adRP)
Stephen P. Daiger, Lori S. Sullivan, Anisa I. Gire, David G. Birch, John R.Heckenlively, and Sara J. Bowne
R.E. Anderson et al. (eds.), Recent Advances in Retinal DegenerationSpringer 2008 pp203-9

Genetic Analysis of Indian Families with Autosomal Recessive Retinitis Pigmentosa by Homozygosity Screening
Hardeep Pal Singh1, Subhadra Jalali2, Raja Narayanan2, Chitra Kannabiran1*
IOVS Papers in Press. Published on April 1, 2009 as Manuscript iovs.09-3479

Perspective on Genes and Mutations Causing Retinitis Pigmentosa
Stephen P. Daiger, Ph.D., Sara J. Bowne, Ph.D., and Lori S. Sullivan, Ph.D.
Arch Ophthalmol. 2007 February; 125(2): 151-158

GeneReviewsNCBI Bookshelf
Choroideremia
Bardet-Biedl Syndrome
Cohen Syndrome
Leber Congenital Amaurosis
Retinitis Pigmentosa
Usher Syndrome

RetNet

GeneTests

Age-related Macular Degeneration (AMD)

Anand Swaroop

Background

AMD is a common multifactorial neurodegenerative disease that is a major cause of visual impairment in the elderly, accounting for approximately half of all blindness in the US. Clinical phenotypes of AMD are rather broad, ranging from the presence of drusen in early stages to focal loss of photoreceptors and RPE and neovascularization in the advanced disease. While several phenotype classifications have been proposed, the disease grading system proposed by AREDS is now used in many genetic studies.

Aging is the strongest risk factor for AMD. Environmental factors, such as smoking, diet, and probably others, can modify the risk. Genetic contribution to AMD susceptibility was first documented in early 1990s by multiple studies reporting familial aggregation, higher risk in first degree relatives of affected individuals and concordance in twins. Initial genetic studies used linkage analysis using large families and subsequently sibs or relative pairs. Despite complications associated with phenotypic variations, late age of diagnosis, and phenocopy effects, Klein and colleagues were the first to map, in 1998, an AMD locus to human chromosome 1q25-31 in a large apparently autosomal dominant family with dry form of disease. Within few years, several groups (headed by Gorin, Klein, Pericak-Vance, Seddon, Swaroop, Weber) used small families (affected sib- or relative- pairs) to map potential susceptibility loci in independent cohorts. These studies, together with a meta-analysis, identified two major loci at 1q31 and 10q26 and evidence for additional loci at several other chromosomes. Linkage studies, however, suggested only broad chromosomal regions but formed the basis for future identification of associated gene variants.

Based on a priori knowledge of AMD pathobiology and/or phenotypic similarity with early-onset macular diseases, multiple candidate genes were selected for association studies. However, the findings from these investigations have not been definitive, probably because of small sample sizes, narrow definition of the gene, and/or limited number of SNPs used.