Description of Research Expertise:
Genome wide association studies of age-related macular degeneration and glaucoma; Next-generation targeted sequencing of age-related macular degeneration in African Americans; Genetics of age-related macular degeneration in the Amish; Whole exome sequencing of families with refractive error; Zebrafish modeling of refractive error and glaucoma; Characterization of mouse models for microphthalmia.
Key Words: Fun Lab, Bioinformatics galore, espirit de corps, collegial atmosphere, challenging projects, molecular genetics.
Description of Research:
Age-related macular degeneration (AMD) in African Americans
Much work has been accomplished on the genetics of AMD in Caucasians to the point that we currently have 10 well-defined loci identified by genome-wide association studies. While we have had amazing successes in Caucasians for AMD, very little has been done in African Americans probably because the disease is much rarer in this group. A GWAS study is not plausible in African Americans because of the decreased frequency of AMD. Therefore, we are using new DNA sequencing technology to identify the reasons that AMD is less severe in African Americans. We have collected a large cohort of African American cases and controls and are currently utilizing targeted next-gen sequencing to identify protective haplotypes that might offer an explanation of resistance to AMD development in African Americans. If these protective SNPs are found, they could serve as new potential drug targets.
Expression differences between normal and AMD eyes
We have been very successful in the identification of susceptibility genes for AMD through GWAS. The next horizon is to understand the expression differences between eyes with AMD and eyes that are normal. To identify differential expression between normal and AMD eyes, we have collected a series of postmortem eyes with and without AMD. RNA and DNA has been isolated from these eyes for the purpose of RNA sequencing and genotyping. Our underlying hypothesis is that there is a difference in normal transcript expression between normal and AMD eyes or a defect in alternative splicing that predisposes to AMD. The RNA-Seq data is being analyzed for expression differences as well as for alternative splicing defects with our new algorithm developed in the lab, SplicePL. Expression will also be correlated with known AMD risk SNPs to assess SNP potential to influence expression.
Genetics of AMD in the Amish
The genetics of AMD has been well studied in unrelated case-control Caucasian cohorts. However, very little has been done to identify genes in families. To that end, we have screened 3000 Amish individuals over the age of 50 years living in Lancaster County, Pa for various eye diseases including AMD. Every subject visiting the Amish clinic received a full eye exam, an epidemiology questionnaire, and a fundus photo along with the donation of a blood sample. We currently have DNA on all these individuals. Our collected Amish cohort currently consists of 750 nuclear families and has tremendous power to identify rare variants. We are currently preparing to do whole exome sequencing in selected families for the purpose of rare variant discovery in AMD. Discovery of rare AMD variants of large effect will have potential impact in the general population.
Genetics of Refractive Error
Refractive error is an abnormality of the eye that results in myopia, hyperopia or astigmatism. It is the leading cause of blindness worldwide. Most studies to date have centered on family linkage studies. Our lab is currently leading an international consortium to identify the genes for refractive error through GWAS and next-gen sequencing. We have just completed a GWAS of 7000 individuals with a few significant hits. We now seek to understand how these significant GWAS SNPs lead to the development of refractive error. We are currently utilizing bioinformatic tools to characterize the function of these SNPS and will move to functional studies in zebrafish after exhausting our bioinformatic tools. In addition, we have collected DNA from large families transmitting myopia and are preparing to perform whole exome sequencing to identify rare variants in these families.
Modeling of Human Disease in Zebrafish
We have developed a system in the lab to assess the refractive error phenotype in zebrafish embryos. Current experiments include knockdown and overexpression of various potential refractive error genes as a validation to the GWAS hits we have identified. Validated results in a zebrafish model will be followed by RNA-Seq of the mutants to provide a framework for a systems biology approach to understanding refractive error.
Characterization of Mouse Models for Microphthalmia
Over the past few years we have been characterizing a mouse model for microphthalmia (Tcm), a phenotype identified in a colony of X-ray irradiated mouse. Genetic mapping refined the causative locus to a 1.3Mb region on mouse Chromosome 4 which contains 5 genes. Further molecular characterization is underway in our lab to identify the founder mutation responsible for the microphthalmic phenotype.
Common techniques in the lab include bioinformatics, DNA cloning, PCR, agarose gel electrophoresis, in situ hybridization, DNA sequencing and library screening.
Sardell Rebecca J, Nittala Muneeswar G, Adams Larry D, Laux Reneé A, Cooke Bailey Jessica N, Fuzzell Denise, Fuzzell Sarada, Reinhart-Mercer Lori, Caywood Laura J, Horst Violet, Mackay Tine, Dana Debbie, Sadda SriniVas R, Scott William K, Stambolian Dwight, Haines Jonathan L, Pericak-Vance Margaret A: Heritability of Choroidal Thickness in the Amish. Ophthalmology 123 (12): 2537-2544,2016.
McCarthy Shane, Das Sayantan, Kretzschmar Warren, Delaneau Olivier, Wood Andrew R, Teumer Alexander, Kang Hyun Min, Fuchsberger Christian, Danecek Petr, Sharp Kevin, Luo Yang, Sidore Carlo, Kwong Alan, Timpson Nicholas, Koskinen Seppo, Vrieze Scott, Scott Laura J, Zhang He, Mahajan Anubha, Veldink Jan, Peters Ulrike, Pato Carlos, van Duijn Cornelia M, Gillies Christopher E, Gandin Ilaria, Mezzavilla Massimo, Gilly Arthur, Cocca Massimiliano, Traglia Michela, Angius Andrea, Barrett Jeffrey C, Boomsma Dorrett: A reference panel of 64,976 haplotypes for genotype imputation. Nature genetics 48 (10): 1279-83,2016.
Das Sayantan, Forer Lukas, Schönherr Sebastian, Sidore Carlo, Locke Adam E, Kwong Alan, Vrieze Scott I, Chew Emily Y, Levy Shawn, McGue Matt, Schlessinger David, Stambolian Dwight, Loh Po-Ru, Iacono William G, Swaroop Anand, Scott Laura J, Cucca Francesco, Kronenberg Florian, Boehnke Michael, Abecasis Gonçalo R, Fuchsberger Christian: Next-generation genotype imputation service and methods. Nature genetics 48 (10): 1284-7,2016.
Draper Erin M, Feng Rui, Appel Sarah D, Graboyes Marcy, Engle Erin, Ciner Elise B, Ellenberg Jonas H, Stambolian Dwight: Low Vision Rehabilitation for Adult African Americans in Two Settings. Optometry and Vision Science 93 (7): 673-82,2016.
Hughes Anne E, Bridgett Stephen, Meng Weihua, Li Mingyao, Curcio Christine A, Stambolian Dwight, Bradley Declan T: Sequence and Expression of Complement Factor H Gene Cluster Variants and Their Roles in Age-Related Macular Degeneration Risk. Investigative ophthalmology & visual science 57 (6): 2763-9,2016.
Fan Qiao, Verhoeven Virginie J M, Wojciechowski Robert, Barathi Veluchamy A, Hysi Pirro G, Guggenheim Jeremy A, Höhn René, Vitart Veronique, Khawaja Anthony P, Yamashiro Kenji, Hosseini S Mohsen, Lehtimäki Terho, Lu Yi, Haller Toomas, Xie Jing, Delcourt Cécile, Pirastu Mario, Wedenoja Juho, Gharahkhani Puya, Venturini Cristina, Miyake Masahiro, Hewitt Alex W, Guo Xiaobo, Mazur Johanna, Huffman Jenifer E, Williams Katie M, Polasek Ozren, Campbell Harry, Rudan Igor, Vatavuk Zoran, Wilson James F, Joshi Peter : Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error. Nature communications 7 : 11008,2016.
Szymczak Silke, Holzinger Emily, Dasgupta Abhijit, Malley James D, Molloy Anne M, Mills James L, Brody Lawrence C, Stambolian Dwight, Bailey-Wilson Joan E: r2VIM: A new variable selection method for random forests in genome-wide association studies. BioData mining 9 : 7,2016.
Fritsche Lars G, Igl Wilmar, Bailey Jessica N Cooke, 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 : A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. Nature genetics 48 (2): 138-143,2016.
Cuellar-Partida Gabriel, Lu Yi, Kho Pik Fang, Hewitt Alex W, Wichmann H-Erich, Yazar Seyhan, Stambolian Dwight, Bailey-Wilson Joan E, Wojciechowski Robert, Wang Jie Jin, Mitchell Paul, Mackey David A, MacGregor Stuart: Assessing the Genetic Predisposition of Education on Myopia: A Mendelian Randomization Study. Genetic epidemiology 40 (1): 66-72,2016.
Sadigh Sam, Luo Xunda, Cideciyan Artur V, Sumaroka Alexander, Boxley Stacy L, Hall Laura M, Sheplock Rebecca, Feuer William J, Stambolian Dwight S, Jacobson Samuel G: Drusen and photoreceptor abnormalities in African-Americans with intermediate non-neovascular age-related macular degeneration. Current eye research 40 (4): 398-406,2015.
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