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1.  Mitochondrial DNA Heteroplasmy Associations With Neurosensory and Mobility Function in Elderly Adults 
Background.
Mitochondrial DNA (mtDNA) heteroplasmy is a mixture of normal and mutated mtDNA molecules in a cell. High levels of heteroplasmy at specific mtDNA sites lead to inherited mitochondrial diseases with neurological, sensory, and movement impairments. Here we test the hypothesis that heteroplasmy levels in elderly adults are associated with impaired function resembling mild forms of mitochondrial disease.
Methods.
We examined platelet mtDNA heteroplasmy at 20 disease-causing sites for associations with neurosensory and mobility function among 137 participants from the community-based Health, Aging, and Body Composition Study.
Results.
Elevated mtDNA heteroplasmy at four mtDNA sites in complex I and tRNA genes was nominally associated with reduced cognition, vision, hearing, and mobility: m.10158T>C with Modified Mini-Mental State Examination score (p = .009); m.11778G>A with contrast sensitivity (p = .02); m.7445A>G with high-frequency hearing (p = .047); and m.5703G>A with 400 m walking speed (p = .007).
Conclusions.
These results indicate that increased mtDNA heteroplasmy at disease-causing sites is associated with neurosensory and mobility function in older persons. We propose the novel use of mtDNA heteroplasmy as a simple, noninvasive predictor of age-related neurologic, sensory, and movement impairments.
doi:10.1093/gerona/glv097
PMCID: PMC4612388  PMID: 26328603
Mitochondrial DNA; Heteroplasmy; Cognition; Vision; Hearing; Mobility.
2.  A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants 
Fritsche, Lars G. | Igl, Wilmar | Cooke Bailey, Jessica N. | Grassmann, Felix | Sengupta, Sebanti | Bragg-Gresham, Jennifer L. | Burdon, Kathryn P. | Hebbring, Scott J. | Wen, Cindy | Gorski, Mathias | Kim, Ivana K. | Cho, David | Zack, Donald | Souied, Eric | Scholl, Hendrik P. N. | Bala, Elisa | Lee, Kristine E. | Hunter, David J. | Sardell, Rebecca J. | Mitchell, Paul | Merriam, Joanna E. | Cipriani, Valentina | Hoffman, Joshua D. | Schick, Tina | Lechanteur, Yara T. E. | Guymer, Robyn H. | Johnson, Matthew P. | Jiang, Yingda | Stanton, Chloe M. | Buitendijk, Gabriëlle H. S. | Zhan, Xiaowei | Kwong, Alan M. | Boleda, Alexis | Brooks, Matthew | Gieser, Linn | Ratnapriya, Rinki | Branham, Kari E. | Foerster, Johanna R. | Heckenlively, John R. | Othman, Mohammad I. | Vote, Brendan J. | Liang, Helena Hai | Souzeau, Emmanuelle | McAllister, Ian L. | Isaacs, Timothy | Hall, Janette | Lake, Stewart | Mackey, David A. | Constable, Ian J. | Craig, Jamie E. | Kitchner, Terrie E. | Yang, Zhenglin | Su, Zhiguang | Luo, Hongrong | Chen, Daniel | Ouyang, Hong | Flagg, Ken | Lin, Danni | Mao, Guanping | Ferreyra, Henry | Stark, Klaus | von Strachwitz, Claudia N. | Wolf, Armin | Brandl, Caroline | Rudolph, Guenther | Olden, Matthias | Morrison, Margaux A. | Morgan, Denise J. | Schu, Matthew | Ahn, Jeeyun | Silvestri, Giuliana | Tsironi, Evangelia E. | Park, Kyu Hyung | Farrer, Lindsay A. | Orlin, Anton | Brucker, Alexander | Li, Mingyao | Curcio, Christine | Mohand-Saïd, Saddek | Sahel, José-Alain | Audo, Isabelle | Benchaboune, Mustapha | Cree, Angela J. | Rennie, Christina A. | Goverdhan, Srinivas V. | Grunin, Michelle | Hagbi-Levi, Shira | Campochiaro, Peter | Katsanis, Nicholas | Holz, Frank G. | Blond, Frédéric | Blanché, Hélène | Deleuze, Jean-François | Igo, Robert P. | Truitt, Barbara | Peachey, Neal S. | Meuer, Stacy M. | Myers, Chelsea E. | Moore, Emily L. | Klein, Ronald | Hauser, Michael A. | Postel, Eric A. | Courtenay, Monique D. | Schwartz, Stephen G. | Kovach, Jaclyn L. | Scott, William K. | Liew, Gerald | Tƒan, Ava G. | Gopinath, Bamini | Merriam, John C. | Smith, R. Theodore | Khan, Jane C. | Shahid, Humma | Moore, Anthony T. | McGrath, J. Allie | Laux, Reneé | Brantley, Milam A. | Agarwal, Anita | Ersoy, Lebriz | Caramoy, Albert | Langmann, Thomas | Saksens, Nicole T. M. | de Jong, Eiko K. | Hoyng, Carel B. | Cain, Melinda S. | Richardson, Andrea J. | Martin, Tammy M. | Blangero, John | Weeks, Daniel E. | Dhillon, Bal | van Duijn, Cornelia M. | Doheny, Kimberly F. | Romm, Jane | Klaver, Caroline C. W. | Hayward, Caroline | Gorin, Michael B. | Klein, Michael L. | Baird, Paul N. | den Hollander, Anneke I. | Fauser, Sascha | Yates, John R. W. | Allikmets, Rando | Wang, Jie Jin | Schaumberg, Debra A. | Klein, Barbara E. K. | Hagstrom, Stephanie A. | Chowers, Itay | Lotery, Andrew J. | Léveillard, Thierry | Zhang, Kang | Brilliant, Murray H. | Hewitt, Alex W. | Swaroop, Anand | Chew, Emily Y. | Pericak-Vance, Margaret A. | DeAngelis, Margaret | Stambolian, Dwight | Haines, Jonathan L. | Iyengar, Sudha K. | Weber, Bernhard H. F. | Abecasis, Gonçalo R. | Heid, Iris M.
Nature genetics  2015;48(2):134-143.
Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly with limited therapeutic options. Here, we report on a study of >12 million variants including 163,714 directly genotyped, most rare, protein-altering variant. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5×10–8) distributed across 34 loci. While wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first signal specific to wet AMD, near MMP9 (difference-P = 4.1×10–10). Very rare coding variants (frequency < 0.1%) in CFH, CFI, and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.
doi:10.1038/ng.3448
PMCID: PMC4745342  PMID: 26691988
3.  De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa 
PLoS ONE  2016;11(3):e0150944.
Background
Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa.
Methods
Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing.
Results and Conclusions
A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in ARL3. Follow-up testing established that this variant occurred de novo in the index case. No additional putative causal variants in ARL3 were identified in the follow-up cohort, suggesting that if ARL3 variants can cause adRP it is an extremely rare phenomenon.
doi:10.1371/journal.pone.0150944
PMCID: PMC4786330  PMID: 26964041
4.  HLA class II genotypes are not associated with age related macular degeneration in a case-control, population-based study 
Human immunology  2015;76(0):142-145.
Multiple lines of evidence support an immunologic basis and genetic disposition for the development of age-related macular degeneration (AMD). Comprehensive Human Leukocyte Antigens (HLA) class II typing at four loci (DRB1, DQA1, DQB1, and DPB1) was assessed using next generation sequencing methods and tested for association with Age-related Macular Degeneration (AMD) in a case-control study of 456 AMD cases and 499 controls from the population-based Study of Osteoporotic Fractures (SOF) cohort. No statistically significant associations were identified for any of the class II loci and a previously identified association between DRB1*13:01 was not replicated in this dataset. These results reported here suggest that common HLA class II genetic variation does not contribute to AMD disease risk.
doi:10.1016/j.humimm.2015.01.010
PMCID: PMC4476503  PMID: 25665771
AMD; age related macular degeneration; HLA; Class II; next generation sequencing
5.  Genetic ME–a visualization application for merging and editing pedigrees for genetic studies 
BMC Research Notes  2015;8:241.
Background
In order to study the genetics of diseases more accurately and effectively, one often collects large families. Different members of a large family may provide differing information about the structure and make-up of their pedigree. Thus, software is needed to facilitate reconciliation of pedigrees collected independently from multiple informants from a single large family to create a unified pedigree that is based on the best composite information available.
Findings
Our implementation demonstrates that Genetic ME performs merging in terms of adding, replacing and combining information from two pedigrees. Through a tracking process, all of the changes made to the data set for the individuals can be traced back to their original source material. A new pedigree structure can be easily visualized while reconciling disparate information from multiple pedigrees.
Methods
We developed the Genetic Merging & Editing (Genetic ME) program, an open source Java application built on top of CraneFoot and Ghostscript, to support comparing, editing and merging of pedigrees collected from multiple sources in a visually-oriented manner.
Conclusions
Genetic ME constitutes an ideal addition to software packages for reconciling pedigree information from multiple sources. Genetic ME provides a friendly graphical user interface, traces the changes made by users, and produces viewable merged pedigree structures able to be further used by other popular analysis programs.
Electronic supplementary material
The online version of this article (doi:10.1186/s13104-015-1131-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s13104-015-1131-y
PMCID: PMC4478623  PMID: 26076732
Algorithms; Human; Java; Pedigree; Software
6.  Peripheral Sensory Neurons Expressing Melanopsin Respond to Light 
The ability of light to cause pain is paradoxical. The retina detects light but is devoid of nociceptors while the trigeminal sensory ganglia (TG) contain nociceptors but not photoreceptors. Melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) are thought to mediate light-induced pain but recent evidence raises the possibility of an alternative light responsive pathway independent of the retina and optic nerve. Here, we show that melanopsin is expressed in both human and mouse TG neurons. In mice, they represent 3% of small TG neurons that are preferentially localized in the ophthalmic branch of the trigeminal nerve and are likely nociceptive C fibers and high-threshold mechanoreceptor Aδ fibers based on a strong size-function association. These isolated neurons respond to blue light stimuli with a delayed onset and sustained firing, similar to the melanopsin-dependent intrinsic photosensitivity observed in ipRGCs. Mice with severe bilateral optic nerve crush exhibit no light-induced responses including behavioral light aversion until treated with nitroglycerin, an inducer of migraine in people and migraine-like symptoms in mice. With nitroglycerin, these same mice with optic nerve crush exhibit significant light aversion. Furthermore, this retained light aversion remains dependent on melanopsin-expressing neurons. Our results demonstrate a novel light-responsive neural function independent of the optic nerve that may originate in the peripheral nervous system to provide the first direct mechanism for an alternative light detection pathway that influences motivated behavior.
doi:10.3389/fncir.2016.00060
PMCID: PMC4978714  PMID: 27559310
ipRGC; sensory ganglion; migraine; optic nerve injury; cornea; choroid
7.  Analysis of the ABCA4 genomic locus in Stargardt disease 
Human Molecular Genetics  2014;23(25):6797-6806.
Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of ABCA4 in STGD patients identifies compound heterozygous or homozygous disease-associated alleles in 65–70% of patients and only one mutation in 15–20% of patients. This study was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic variants per sample. Filtering of these data resulted in 141 candidates for new mutations. Two variants were detected in four samples, two in three samples, and 20 variants in two samples, the remaining 117 new variants were detected only once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in STGD patients of European-American descent. Defining disease-associated alleles in the ABCA4 locus requires exceptionally well characterized large cohorts and extensive analyses by a combination of various approaches.
doi:10.1093/hmg/ddu396
PMCID: PMC4245042  PMID: 25082829
8.  Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration 
Human Molecular Genetics  2014;23(21):5827-5837.
Neurodegenerative diseases affecting the macula constitute a major cause of incurable vision loss and exhibit considerable clinical and genetic heterogeneity, from early-onset monogenic disease to multifactorial late-onset age-related macular degeneration (AMD). As part of our continued efforts to define genetic causes of macular degeneration, we performed whole exome sequencing in four individuals of a two-generation family with autosomal dominant maculopathy and identified a rare variant p.Glu1144Lys in Fibrillin 2 (FBN2), a glycoprotein of the elastin-rich extracellular matrix (ECM). Sanger sequencing validated the segregation of this variant in the complete pedigree, including two additional affected and one unaffected individual. Sequencing of 192 maculopathy patients revealed additional rare variants, predicted to disrupt FBN2 function. We then undertook additional studies to explore the relationship of FBN2 to macular disease. We show that FBN2 localizes to Bruch′s membrane and its expression appears to be reduced in aging and AMD eyes, prompting us to examine its relationship with AMD. We detect suggestive association of a common FBN2 non-synonymous variant, rs154001 (p.Val965Ile) with AMD in 10 337 cases and 11 174 controls (OR = 1.10; P-value = 3.79 × 10−5). Thus, it appears that rare and common variants in a single gene—FBN2—can contribute to Mendelian and complex forms of macular degeneration. Our studies provide genetic evidence for a key role of elastin microfibers and Bruch′s membrane in maintaining blood–retina homeostasis and establish the importance of studying orphan diseases for understanding more common clinical phenotypes.
doi:10.1093/hmg/ddu276
PMCID: PMC4189898  PMID: 24899048
9.  Whole exome sequencing detects homozygosity for ABCA4 p.Arg602Trp missense mutation in a pediatric patient with rapidly progressive retinal dystrophy 
BMC Medical Genetics  2014;15:11.
Background
A pediatric patient presented with rapidly progressive vision loss, nyctalopia and retinal dystrophy. This is the first report of homozygosity for the p.Arg602Trp mutation in the ABCA4 gene. The child became legally blind within a period of 2 years.
Case presentation
An eight year-old Hispanic female presented with bilateral decreased vision following a febrile gastrointestinal illness with nausea and vomiting. Extensive workup involved pediatric infectious disease and rheumatology consultations.
Initial visual acuity was 20/60 at distance and 20/30 at near in both eyes. Rapidly progressive vision loss occurred during a 2-year period resulting in visual acuities of 20/200 at distance in both eyes. Fundus exam disclosed attenuated vessels and multiple subretinal blister-like elevations. Optical coherence tomography showed far more lesions than were clinically evident with different levels of elevation. Autofluorescence imagery showed dramatic and widespread geographic areas of atrophy. The deposits that appeared drusen-like on clinical exam were hyperfluorescent, consistent with lipofuscin deposits containing A2e (N-retinylidene-N-retinylethanolamine) indicative of RPE cell dysfunction. Electroretinography was consistent with cone dystrophy, with relative preservation of rod function. Blood analysis and rheumatology evaluation found no evidence of a diffuse post-infectious/inflammatory process. The unique and rapid progression of her subretinal blister-like lesions was documented by fluorescein angiography, optical coherence tomography, autofluorescence imagery, and fundus photography. Family pedigree history disclosed consanguinity, her parents being first cousins. DNA analysis by whole exomic sequencing revealed homozygosity of p.Arg602Trp in the ABCA4 gene.
Conclusion
The pediatric patient presented with a striking clinical appearance and dramatic rate of progression that was clinically more characteristic of an infectious or inflammatory process. This case expands the diverse range of phenotypes attributed to ABCA4 mutations and further supports the role of whole exome sequencing as a powerful new tool available to aid clinicians in establishing diagnosis for challenging cases.
doi:10.1186/1471-2350-15-11
PMCID: PMC3905103  PMID: 24444108
ABCA4 retinopathy; Pediatric; Homozygosity; Consanguinity
10.  dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets 
BMC Bioinformatics  2015;16(1):91.
Background
When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources.
Results
We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format.
Conclusions
dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register. Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0505-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-015-0505-4
PMCID: PMC4407391  PMID: 25887129
Association studies; Database; Genotypes; Genome-wide association studies; Linkage; Mega2; MySQL; Phenotypes; PLINK; Python
11.  Genetic insights into age-related macular degeneration: Controversies addressing Risk, Causality, and Therapeutics 
Molecular Aspects of Medicine  2012;33(4):467-486.
Age-related macular degeneration (AMD) is a common condition among the elderly population that leads to the progressive central vision loss and serious compromise of quality of life for its sufferers. It is also one of the few disorders for whom the investigation of its genetics has yielded rich insights into its diversity and causality and holds the promise of enabling clinicians to provide better risk assessments for individuals as well as to develop and selectively deploy new therapeutics to either prevent or slow the development of disease and lessen the threat of vision loss. The genetics of AMD began initially with the appreciation of familial aggregation and increase risk and expanded with the initial association of APOE variants with the disease. The first major breakthroughs came with family-based linkage studies of affected (and discordant) sibs, which identified a number of genetic loci and led to the targeted search of the 1q31 and 10q26 loci for associated variants. Three of the initial four reports for the CFH variant, Y402H, were based on regional candidate searches, as were the two initial reports of the ARMS2/HTRA1 locus variants. Case-control association studies initially also played a role in discovering the major genetic variants for AMD, and the success of those early studies have been used to fuel enthusiasm for the methodology for a number of diseases. Until 2010, all of the subsequent genetic variants associated with AMD came from candidate gene testing based on the complement factor pathway. In 2010, several large-scale genome-wide association studies (GWAS) identified genes that had not been previously identified. Much of this historical information is available in a number of recent reviews.(Chen et al., 2010b; Deangelis et al., 2011; Fafowora and Gorin, 2012b; Francis and Klein, 2011; Kokotas et al., 2011) Large meta analysis of AMD GWAS has added new loci and variants to this collection.(Chen et al., 2010a; Kopplin et al., 2010; Yu et al., 2011) This paper will focus on the ongoing controversies that are confronting AMD genetics at this time, rather than attempting to summarize this field, which has exploded in the past 5 years.
doi:10.1016/j.mam.2012.04.004
PMCID: PMC3392516  PMID: 22561651
molecular genetics; Age-related macular degeneration; Association studies; Family-based linkage; Risk factors; Genetics-based therapeutics
12.  Endophenotypes for Age-Related Macular Degeneration: Extending Our Reach into the Preclinical Stages of Disease 
Journal of clinical medicine  2014;3(4):1335-1356.
The key to reducing the individual and societal burden of age-related macular degeneration (AMD)-related vision loss, is to be able to initiate therapies that slow or halt the progression at a point that will yield the maximum benefit while minimizing personal risk and cost. There is a critical need to find clinical markers that, when combined with the specificity of genetic testing, will identify individuals at the earliest stages of AMD who would benefit from preventive therapies. These clinical markers are endophenotypes for AMD, present in those who are likely to develop AMD, as well as in those who have clinical evidence of AMD. Clinical characteristics associated with AMD may also be possible endophenotypes if they can be detected before or at the earliest stages of the condition, but we and others have shown that this may not always be valid. Several studies have suggested that dynamic changes in rhodopsin regeneration (dark adaptation kinetics and/or critical flicker fusion frequencies) may be more subtle indicators of AMD-associated early retinal dysfunction. One can test for the relevance of these measures using genetic risk profiles based on known genetic risk variants. These functional measures may improve the sensitivity and specificity of predictive models for AMD and may also serve to delineate clinical subtypes of AMD that may differ with respect to prognosis and treatment.
doi:10.3390/jcm3041335
PMCID: PMC4284143  PMID: 25568804
age-related macular degeneration; endophenotype; genetic risk; preclinical diagnostics; retinal function; predictive modeling
13.  Comparative Regional Pupillography as a Noninvasive Biosensor Screening Method for Diabetic Retinopathy 
Purpose.
We describe infrared regional pupillometry as an objective comparative assessment of midperipheral to central retinal sensitivity and to correlate with midperipheral retinal ischemia in diabetic subjects.
Methods.
We tested 12 normal and 17 diabetic subjects using bilateral infrared pupillometry. The diabetic cohort included seven subjects without, five with mild, three with moderate, and two with severe non-proliferative diabetic retinopathy (NPDR). Central and annular stimuli of varying intensity were presented to one eye, and pupillary amplitude and constriction velocity were measured from both eyes. Light stimulus of increasing intensity was presented as 20 consecutive trials (stimulus duration of 300 ms with 3000 ms intervals). The ratio of central to peripheral responses (Q values) was calculated for each stimulus configuration. Average responses with respect to the stimulus strength were regressed with Gompertz sigmoid function.
Results.
Control and moderate/severe NPDR cases comparison showed statistically significant differences in amplitude (QA) and constriction velocity (QCV) (Wilcoxon rank sum test P = 0.002, respectively). Age difference for these groups was not statistically significant (Wilcoxon rank sum test P = 0.15). The comparison of control and diabetic subjects without NPDR/mild NPDR was statistically significant for QA and QCV (Wilcoxon rank sum test P = 0.0002 and P = 0.001, respectively). QA and QCV differences were statistically significant between moderate/severe NPDR cases and subjects without or mild NPDR cases (Wilcoxon rank sum test P = 0.013).
Conclusions.
QA and QCV values correlated highly with the severity of diabetic retinopathy, but not with the duration of diabetes. ( ClinicalTrials.gov number, NCT01546766.)
We describe a novel methodology based on the pupillary response to evaluate midperipheral and central retinal sensitivity. In diabetic subjects, the ratios of peripheral to central amplitude and constriction velocity of the pupillary response are reduced, correlating with severity of retinopathy.
doi:10.1167/iovs.12-10241
PMCID: PMC3541948  PMID: 23154459
14.  Endophenotypes for Age-Related Macular Degeneration: Extending Our Reach into the Preclinical Stages of Disease 
Journal of Clinical Medicine  2014;3(4):1335-1356.
The key to reducing the individual and societal burden of age-related macular degeneration (AMD)-related vision loss, is to be able to initiate therapies that slow or halt the progression at a point that will yield the maximum benefit while minimizing personal risk and cost. There is a critical need to find clinical markers that, when combined with the specificity of genetic testing, will identify individuals at the earliest stages of AMD who would benefit from preventive therapies. These clinical markers are endophenotypes for AMD, present in those who are likely to develop AMD, as well as in those who have clinical evidence of AMD. Clinical characteristics associated with AMD may also be possible endophenotypes if they can be detected before or at the earliest stages of the condition, but we and others have shown that this may not always be valid. Several studies have suggested that dynamic changes in rhodopsin regeneration (dark adaptation kinetics and/or critical flicker fusion frequencies) may be more subtle indicators of AMD-associated early retinal dysfunction. One can test for the relevance of these measures using genetic risk profiles based on known genetic risk variants. These functional measures may improve the sensitivity and specificity of predictive models for AMD and may also serve to delineate clinical subtypes of AMD that may differ with respect to prognosis and treatment.
doi:10.3390/jcm3041335
PMCID: PMC4284143  PMID: 25568804
age-related macular degeneration; endophenotype; genetic risk; preclinical diagnostics; retinal function; predictive modeling
15.  Identification of a Rare Coding Variant in Complement 3 Associated with Age-related Macular Degeneration 
Nature genetics  2013;45(11):1375-1379.
Macular degeneration is a common cause of blindness in the elderly. To identify rare coding variants associated with a large increase in risk of age-related macular degeneration (AMD), we sequenced 2,335 cases and 789 controls in 10 candidate loci (57 genes). To increase power, we augmented our control set with ancestry-matched exome sequenced controls. An analysis of coding variation in 2,268 AMD cases and 2,268 ancestry matched controls revealed two large-effect rare variants; previously described R1210C in the CFH gene (fcase = 0.51%, fcontrol = 0.02%, OR = 23.11), and newly identified K155Q in the C3 gene (fcase = 1.06%, fcontrol = 0.39%, OR = 2.68). The variants suggest decreased inhibition of C3 by Factor H, resulting in increased activation of the alternative complement pathway, as a key component of disease biology.
doi:10.1038/ng.2758
PMCID: PMC3812337  PMID: 24036949
16.  Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23) 
Human Molecular Genetics  2012;21(16):3647-3654.
X-linked retinitis pigmentosa (XLRP) is genetically heterogeneous with two causative genes identified, RPGR and RP2. We previously mapped a locus for a severe form of XLRP, RP23, to a 10.71 Mb interval on Xp22.31-22.13 containing 62 genes. Candidate gene screening failed to identify a causative mutation, so we adopted targeted genomic next-generation sequencing of the disease interval to determine the molecular cause of RP23. No coding variants or variants within or near splice sites were identified. In contrast, a variant deep within intron 9 of OFD1 increased the splice site prediction score 4 bp upstream of the variant. Mutations in OFD1 cause the syndromic ciliopathies orofaciodigital syndrome-1, which is male lethal, Simpson–Golabi–Behmel syndrome type 2 and Joubert syndrome. We tested the effect of the IVS9+706A>G variant on OFD1 splicing in vivo. In RP23 patient-derived RNA, we detected an OFD1 transcript with the insertion of a cryptic exon spliced between exons 9 and 10 causing a frameshift, p.N313fs.X330. Correctly spliced OFD1 was also detected in patient-derived RNA, although at reduced levels (39%), hence the mutation is not male lethal. Our data suggest that photoreceptors are uniquely susceptible to reduced expression of OFD1 and that an alternative disease mechanism can cause XLRP. This disease mechanism of reduced expression for a syndromic ciliopathy gene causing isolated retinal degeneration is reminiscent of CEP290 intronic mutations that cause Leber congenital amaurosis, and we speculate that reduced dosage of correctly spliced ciliopathy genes may be a common disease mechanism in retinal degenerations.
doi:10.1093/hmg/dds194
PMCID: PMC3406759  PMID: 22619378
17.  Complement factor H genetic variant and age-related macular degeneration: effect size, modifiers and relationship to disease subtype 
Background Variation in the complement factor H gene (CFH) is associated with risk of late age-related macular degeneration (AMD). Previous studies have been case–control studies in populations of European ancestry with little differentiation in AMD subtype, and insufficient power to confirm or refute effect modification by smoking.
Methods To precisely quantify the association of the single nucleotide polymorphism (SNP rs1061170, ‘Y402H’) with risk of AMD among studies with differing study designs, participant ancestry and AMD grade and to investigate effect modification by smoking, we report two unpublished genetic association studies (n = 2759) combined with data from 24 published studies (26 studies, 26 494 individuals, including 14 174 cases of AMD) of European ancestry, 10 of which provided individual-level data used to test gene–smoking interaction; and 16 published studies from non-European ancestry.
Results In individuals of European ancestry, there was a significant association between Y402H and late-AMD with a per-allele odds ratio (OR) of 2.27 [95% confidence interval (CI) 2.10–2.45; P = 1.1 x 10−161]. There was no evidence of effect modification by smoking (P = 0.75). The frequency of Y402H varied by ancestral origin and the association with AMD in non-Europeans was less clear, limited by paucity of studies.
Conclusion The Y402H variant confers a 2-fold higher risk of late-AMD per copy in individuals of European descent. This was stable to stratification by study design and AMD classification and not modified by smoking. The lack of association in non-Europeans requires further verification. These findings are of direct relevance for disease prediction. New research is needed to ascertain if differences in circulating levels, expression or activity of factor H protein explain the genetic association.
doi:10.1093/ije/dyr204
PMCID: PMC3304526  PMID: 22253316
Age-related macular degeneration (AMD); Complement factor H gene; meta-ananlysis
18.  Evidence of association of APOE with age-related macular degeneration - a pooled analysis of 15 studies 
Human mutation  2011;32(12):1407-1416.
Age-related macular degeneration (AMD) is the most common cause of incurable visual impairment in high-income countries. Previous studies report inconsistent associations between AMD and apolipoprotein E (APOE), a lipid transport protein involved in low-density cholesterol modulation. Potential interaction between APOE and sex, and smoking status, has been reported. We present a pooled analysis (n=21,160) demonstrating associations between late AMD and APOε4 (OR=0.72 per haplotype; CI: 0.65–0.74; P=4.41×10−11) and APOε2 (OR=1.83 for homozygote carriers; CI: 1.04–3.23; P=0.04), following adjustment for age-group and sex within each study and smoking status. No evidence of interaction between APOE and sex or smoking was found. Ever smokers had significant increased risk relative to never smokers for both neovascular (OR=1.54; CI: 1.38–1.72; P=2.8×10−15) and atrophic (OR=1.38; CI: 1.18–1.61; P=3.37×10−5) AMD but not early AMD (OR=0.94; CI: 0.86–1.03; P=0.16), implicating smoking as a major contributing factor to disease progression from early signs to the visually disabling late forms. Extended haplotype analysis incorporating rs405509 did not identify additional risks beyondε2 and ε4 haplotypes. Our expanded analysis substantially improves our understanding of the association between the APOE locus and AMD. It further provides evidence supporting the role of cholesterol modulation, and low-density cholesterol specifically, in AMD disease etiology.
doi:10.1002/humu.21577
PMCID: PMC3217135  PMID: 21882290
age-related macular degeneration; AMD; apolipoprotein E; APOE; case-control association study
19.  Exclusion of Positional Candidate Gene Coding Region Mutations in the Common Posterior Polymorphous Corneal Dystrophy 1 Candidate Gene Interval 
Cornea  2009;28(7):801-807.
Purpose
Posterior polymorphous corneal dystrophy (PPCD) is an autosomal dominant disorder of the corneal endothelium associated with visually significant corneal edema and glaucoma. Statistical genetic analysis of four families with PPCD has demonstrated linkage to a 2.4 cM common support interval on chromosome 20 bordered by the markers D20S182 and D20S139. We sought to identify the genetic basis of PPCD linked to chromosome 20 (PPCD1) by screening the 26 positional candidate genes between these markers in a family previously mapped to the PPCD1 region.
Methods
The coding regions of the 26 positional candidate genes mapped to the common PPCD1 support interval were amplified and sequenced in affected and unaffected individuals from a family previously linked to the PPCD1 locus. Nine other genes positioned just outside of the common PPCD1 support interval but within the autosomal dominant congenital hereditary endothelial dystrophy (CHED1) interval were also screened.
Results
Four DNA sequence variants in three of the positional candidate genes demonstrated complete segregation with the affected phenotype: p.Thr109Thr (rs6111803) in OVOL2, p.Arg56Gln (novel variant - RPSnovel) in RPS19P1, and p.Thr85Thr (rs1053834) and p.Pro99Ser (rs1053839) in C20orf79. Each of these four sequence variants demonstrated significant linkage with the affected phenotype in this family (p-value = 2.5 × 10−7 for RPSnovel, rs1053834 and rs1053839; p-value = 8.6 × 10−7 for rs6111803). However, we also identified each of these four sequence variants in ≥ 9% of unaffected control individuals. The haplotype upon which the disease causing mutation is segregating was found to have a population frequency of 4.2% in the CEPH HapMap trios. While a number of other previously described and novel SNPs were identified in the 35 positional candidate genes located within the PPCD1 and CHED1 intervals, none segregated with the affected phenotype.
Conclusions
We report the absence of a presumed pathogenic coding region mutation in the common PPCD1 support interval. Although minor alleles of four SNPs were identified that segregated with the affected phenotype, the relatively high frequency of each minor allele in the general population indicates that none is a candidate for the causal variant for PPCD. Instead, the causal variant is most likely a coding region deletion or a variant in a non-coding region of the PPCD1 common support interval.
doi:10.1097/ICO.0b013e31819672fb
PMCID: PMC2714875  PMID: 19574904
Posterior polymorphous corneal dystrophy; Candidate gene screening; Linkage; Congenital hereditary endothelial dystrophy
20.  Molecular diagnosis of putative Stargardt disease probands by exome sequencing 
BMC Medical Genetics  2012;13:67.
Background
The commonest genetic form of juvenile or early adult onset macular degeneration is Stargardt Disease (STGD) caused by recessive mutations in the gene ABCA4. However, high phenotypic and allelic heterogeneity and a small but non-trivial amount of locus heterogeneity currently impede conclusive molecular diagnosis in a significant proportion of cases.
Methods
We performed whole exome sequencing (WES) of nine putative Stargardt Disease probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Follow-up dideoxy sequencing was performed for confirmation and to screen for mutations in an additional set of affected individuals lacking a definitive molecular diagnosis.
Results
Whole exome sequencing revealed seven likely disease-causing variants across four genes, providing a confident genetic diagnosis in six previously uncharacterized participants. We identified four previously missed mutations in ABCA4 across three individuals. Likely disease-causing mutations in RDS/PRPH2, ELOVL, and CRB1 were also identified.
Conclusions
Our findings highlight the enormous potential of whole exome sequencing in Stargardt Disease molecular diagnosis and research. WES adequately assayed all coding sequences and canonical splice sites of ABCA4 in this study. Additionally, WES enables the identification of disease-related alleles in other genes. This work highlights the importance of collecting parental genetic material for WES testing as the current knowledge of human genome variation limits the determination of causality between identified variants and disease. While larger sample sizes are required to establish the precision and accuracy of this type of testing, this study supports WES for inherited early onset macular degeneration disorders as an alternative to standard mutation screening techniques.
doi:10.1186/1471-2350-13-67
PMCID: PMC3459799  PMID: 22863181
Stargardt Disease; Macular Degeneration; Exome; Mutation Screening; Molecular Diagnostics; ABCA4; PRPH2
21.  Variations in Apolipoprotein E Frequency With Age in a Pooled Analysis of a Large Group of Older People 
American Journal of Epidemiology  2011;173(12):1357-1364.
Variation in the apolipoprotein E gene (APOE) has been reported to be associated with longevity in humans. The authors assessed the allelic distribution of APOE isoforms ε2, ε3, and ε4 among 10,623 participants from 15 case-control and cohort studies of age-related macular degeneration (AMD) in populations of European ancestry (study dates ranged from 1990 to 2009). The authors included only the 10,623 control subjects from these studies who were classified as having no evidence of AMD, since variation within the APOE gene has previously been associated with AMD. In an analysis stratified by study center, gender, and smoking status, there was a decreasing frequency of the APOE ε4 isoform with increasing age (χ2 for trend = 14.9 (1 df); P = 0.0001), with a concomitant increase in the ε3 isoform (χ2 for trend = 11.3 (1 df); P = 0.001). The association with age was strongest in ε4 homozygotes; the frequency of ε4 homozygosity decreased from 2.7% for participants aged 60 years or less to 0.8% for those over age 85 years, while the proportion of participants with the ε3/ε4 genotype decreased from 26.8% to 17.5% across the same age range. Gender had no significant effect on the isoform frequencies. This study provides strong support for an association of the APOE gene with human longevity.
doi:10.1093/aje/kwr015
PMCID: PMC3145394  PMID: 21498624
aged; apolipoprotein E2; apolipoprotein E3; apolipoprotein E4; apolipoproteins E; longevity; meta-analysis; multicenter study
22.  Variants of the Adenosine A2A Receptor Gene Are Protective against Proliferative Diabetic Retinopathy in Patients with Type 1 Diabetes 
Ophthalmic Research  2010;46(1):1-8.
Aims
The adenosine A2A receptor (ADORA2A) may ameliorate deleterious physiologic effects associated with tissue injury in individuals with diabetes. We explored associations between variants of the ADORA2A gene and proliferative diabetic retinopathy (PDR) in a cohort of patients with type 1 diabetes (T1D).
Methods
The participants were from the Pittsburgh Epidemiology of Diabetes Complications prospective study of childhood-onset T1D. Stereoscopic photographs of the retinal fundus taken at baseline, then biennially, for 10 years were used to define PDR according to the modified Airlie House system. Two tagging single nucleotide polymorphisms (tSNPs; rs2236624-C/T and rs4822489-G/T) in the ADORA2A gene were selected using the HapMap (haplotype map) reference database.
Results
A significant association was observed between SNP rs2236624 and PDR in the recessive genetic model. Participants homozygous for the T allele displayed a decreased risk of developing prevalent PDR (odds ratio, OR = 0.36; p = 0.04) and incident PDR (hazard ratio = 0.156; p = 0.009), and for all cases of PDR combined (OR = 0.23; p = 0.001). The protective effect of T allele homozygosity remained after adjusting for covariates. Similarly, for SNP rs4822489, an association between PDR and T allele homozygosity was observed following covariate adjustment (OR = 0.55; 95% CI: 0.31–0.92; p = 0.04).
Conclusion
Genetic variants of ADORA2A offer statistically significant protection against PDR development in patients with T1D.
doi:10.1159/000317057
PMCID: PMC2997447  PMID: 21088442
Diabetes; Diabetic retinopathy; Single nucleotide polymorphism; Adenosine receptor
23.  Associations between Genetic Polymorphisms of Insulin-like Growth Factor Axis Genes and Risk for Age-Related Macular Degeneration 
This paper provides the first epidemiological evidence that IGF axis genes may be involved in the pathogenesis of advanced AMD and that IGF1R may predispose obese people to higher risk.
Purpose.
To investigate whether insulin-like growth factor (IGF) axis genes, together with a novel dietary risk factor, the dietary glycemic index (dGI), and body mass index (BMI) affect the risk for age-related macular degeneration (AMD).
Methods.
This case–control study involved 962 subjects originally recruited through the Age-Related Eye Disease Study (AREDS) Genetic Repository. After those with missing covariates or invalid calorie intake (n = 23), diabetes (n = 59), and non-Caucasian race (n = 16) were excluded, 864 participants were used, including 209 AREDS category 1 participants (control group), 354 category 2 or 3 participants (drusen group), and 301 category 4 participants (advanced AMD group). A total of 25 single-nucleotide polymorphisms (SNPs) selected from IGF-1 (n = 9), IGF-2 (n = 1), IGF binding protein 1 (IGFBP1; n = 3), IGFBP3 (n = 3), acid-labile subunit of IGFBP (IGFALS; n = 2), IGF1 receptor (IGF1R; n = 4), and IGF2R (n = 3) were genotyped. SNP-AMD associations were measured with genotype, allele χ2 tests and Armitage's trend test. Odds ratios (OR), 95% confidence intervals (CIs), and SNP-exposure interactions were evaluated by multivariate logistic regression.
Results.
One SNP (rs2872060) in IGF1R revealed a significant association with advanced AMD (P-allele = 0.0009, P-trend = 0.0008; the significance level was set at 0.05/25 = 0.002 for multiple comparisons). The risk allele (G) in the heterozygous and homozygous states (OR, 1.67 and 2.93; 95% CI, 1.03–2.71 and 1.60–5.36, respectively) suggests susceptibility and an additive effect on AMD risk. Further stratification analysis remained significant for both neovascularization (OR, 1.49 and 2.61; 95% CI, 0.90–2.48 and 1.39–4.90, respectively) and geographic atrophy (OR, 2.57 and 4.52; 95% CI, 0.99–6.71 and 1.49–13.74, respectively). The G allele interaction analysis with BMI was significant for neovascularization (P = 0.042) but not for geographic atrophy (P = 0.47). No significant interaction was found with dGI.
Conclusions.
These data suggest a role of IGF1R on the risk for advanced AMD in this group of subjects.
doi:10.1167/iovs.11-7782
PMCID: PMC3231967  PMID: 22058336
24.  Dissection of Chromosome 16p12 Linkage Peak Suggests a Possible Role for CACNG3 Variants in Age-Related Macular Degeneration Susceptibility 
Through extensive linkage and association analyses in multiple independent datasets, this study identified CACNG3 as the most likely AMD susceptibility gene on 16p12.
Purpose.
Age-related macular degeneration (AMD) is a complex disorder of the retina, characterized by drusen, geographic atrophy, and choroidal neovascularization. Cigarette smoking and the genetic variants CFH Y402H, ARMS2 A69S, CFB R32Q, and C3 R102G have been strongly and consistently associated with AMD. Multiple linkage studies have found evidence suggestive of another AMD locus on chromosome 16p12 but the gene responsible has yet to be identified.
Methods.
In the initial phase of the study, single-nucleotide polymorphisms (SNPs) across chromosome 16 were examined for linkage and/or association in 575 Caucasian individuals from 148 multiplex and 77 singleton families. Additional variants were tested in an independent dataset of unrelated cases and controls. According to these results, in combination with gene expression data and biological knowledge, five genes were selected for further study: CACNG3, HS3ST4, IL4R, Q7Z6F8, and ITGAM.
Results.
After genotyping additional tagging SNPs across each gene, the strongest evidence for linkage and association was found within CACNG3 (rs757200 nonparametric LOD* = 3.3, APL (association in the presence of linkage) P = 0.06, and rs2238498 MQLS (modified quasi-likelihood score) P = 0.006 in the families; rs2283550 P = 1.3 × 10−6, and rs4787924 P = 0.002 in the case–control dataset). After adjusting for known AMD risk factors, rs2283550 remained strongly associated (P = 2.4 × 10−4). Furthermore, the association signal at rs4787924 was replicated in an independent dataset (P = 0.035) and in a joint analysis of all the data (P = 0.001).
Conclusions.
These results suggest that CACNG3 is the best candidate for an AMD risk gene within the 16p12 linkage peak. More studies are needed to confirm this association and clarify the role of the gene in AMD pathogenesis.
doi:10.1167/iovs.09-5112
PMCID: PMC3101690  PMID: 21169531
25.  Linkage of Posterior Amorphous Corneal Dystrophy to Chromosome 12q21.33 and Exclusion of Coding Region Mutations in KERA, LUM, DCN, and EPYC 
Genomewide linkage analysis has identified a chromosomal locus for posterior amorphous corneal dystrophy at 12q21.33, though no mutations were identified in the positional and functional candidate genes KERA, LUM, DCN, and EPYC.
Purpose.
To identify the genetic basis of posterior amorphous corneal dystrophy (PACD) segregating in a large pedigree.
Methods.
The authors performed clinical evaluation of a previously unreported pedigree with PACD, light and electron microscopic examination of an excised corneal button, genomewide linkage analysis, fine mapping linkage and haplotype analysis, and screening of four candidate genes (KERA, LUM, DCN, and EPYC).
Results.
Twenty-one participants were determined to be affected based on the presence of characteristic clinical features of PACD; 15 affected and 39 unaffected individuals from a single pedigree enrolled in the study and provided DNA for analysis. Histopathologic examination of an excised corneal specimen from an affected individual demonstrated disorganized stromal lamellae and stromal staining with colloidal iron. Genomewide analysis demonstrated significant evidence of linkage to chromosome region 12q21.33 and evidence suggestive of linkage to chromosome region 8q22.3. Fine mapping of the chromosome 12 locus confirmed significant linkage; the largest multipoint log odds ratio score was 5.6 at D12S351. The linkage support interval was approximately 3.5 Mb (3.5 cM) in length between flanking markers D12S1812 and D12S95, roughly the entire chromosome band 12q21.33. No coding region mutations were identified in four candidate genes—KERA, LUM, DCN, EPYC—located in the chromosome 12 linkage support interval.
Conclusions.
Linkage and haplotype analyses identified 12q21.33 as a locus for PACD. However, no mutations were identified in the candidate genes (KERA, LUM, DCN, EPYC) within this region.
doi:10.1167/iovs.09-4067
PMCID: PMC2910638  PMID: 20357198

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