Using linkage and association studies to better understand the genetic mechanisms of inherited eye disease at the NIH - NEI
Dr. James Fielding Hejtmancik and his team at the National Eye Institute’s Ophthalmic Genetics and Visual Function branch, use linkage and association studies to better understand the genetic mechanisms of inherited eye disease. The team investigates both Mendelian and complex diseases as well as functional work with a focus on cataracts, retinal degenerations, myopia and corneal dystrophies. “If it effects vision, we pretty much study it,” commented Dr. Hejtmancik, the lab's director.
With uncertain funding levels, the small lab has created strong collaborations across the globe with other centers and labs studying eye disease. Their collaborations provide access to larger data sets which in turn allow for more broad analysis. Currently, the lab is completing and publishing five to ten studies a year with a focus on linkage analysis and candidate gene studies.
Founded by Hans Zellweger in the 1960’s, The Shivanand R. Patil Cytogenetics and Molecular Lab at the University of Iowa has a long history of clinical testing, seeing 45 years of advancements. Today, the lab is mainly focused on oncology, pre and post-natal genetics testing and serves the University of Iowa Hospitals and Clinics as well as the University of Iowa Stead Family Children’s Hospital. In last year alone they have performed over 5,500 clinical tests.
When the lab’s director, Dr. Benjamin Darbro purchased Illumina’s NextSeq 500, he did so with the vision of being able to offer phenotype-focused gene sequencing panels. Darbro knew this goal would require an informatics pipeline with the same level of sophistication the lab developed for their research side, but one that would fit within the framework required of clinical testing.
Scott Diehl, a professor and geneticist at Rutgers School of Dental Medicine, performs family studies, association studies and gene mapping to discover the genetic causes of periodontal diseases. Originally, Diehl had a large team of bioinformaticians in the lab to help with his analyses, but the high cost of such personnel created the need for another solution. With Golden Helix’s SVS software, Diehl and his small lab team are able to rapidly conduct a wide range of statistical analyses on their data without having to spend all their time bogged down in difficult command language.
Much of Diehl’s work is focused on periodontal diseases and tooth decay, two conditions with substantial heritability. The main goal of the lab is to find the specific genetic variants that underlie the heritability to understand the diseases’ mechanisms.
Rick Kittles, PhD Uses Golden Helix® Software to Identify Novel Genetic Variations for Complex Diseases that Disproportionately Impact African-American and Hispanic Populations
Dr. Rick Kittles, Director of the Institute of Human Genetics at the University of Illinois at Chicago, investigates the genetics of complex diseases that disproportionately impact people of color. Well known for his research in this field, Kittles has been featured in the PBS series African American Lives, in two BBC Two films, and on 60 Minutes. With SNP & Variation Suite (SVS), Kittles can quickly interpret his data with ease. "We just did a GWAS with 2 ½ million SNPs in minutes with SVS. It's impressive," said Kittles.
Dr. Peter K. Gregersen, Head of the Center for Genomics and Human Genetics at the Feinstein Institute for Medical Research, utilizes GWAS, targeted arrays, and sequencing technologies to identify genes associated with human autoimmune disorders. An increasing number of projects generated the need for an analytical tool that would allow the biologists to find significant data quickly. "I have always thought that putting the analytic power in the hands of the biologists who are thinking about the disease is really important," says Gregersen. With SNP & Variation Suite™ (SVS) software, Gregersen can do just that.
One-third of human genetic diversity can be found in a likely contender for the birthplace of mankind: Southern Africa. Africa as a whole boasts over 2,000 distinct languages and cultures. The magnitude of ethnic diversity was a signal for Dr. Vanessa Hayes, Dr. Desiree Petersen, and their team at the J. Craig Venter Institute. For that reason, it has been their mission to make sure that African genomes are examined and represented sufficiently in databases worldwide.
"Easy-to-Use" SNP & Variation Suite Assists John Curtin, PhD in Uncovering Genetic Associations for Asthma and Allergies
Dr. John Curtin is a Lecturer in Functional Genomics at the University of Manchester where he works with a large team studying the development of asthma in a birth cohort: the Manchester Asthma and Allergy Study (MAAS). Dr. Curtin has been conducting genome-wide association studies to uncover the genetic variation(s) that may underlie the risk and development of asthma and its intermediate phenotypes. To perform the analyses, he and his team use SNP & Variation Suite. Dr. Curtin concludes: "Basically SVS is just easy to use."
For 10 Years Julia Pinsonneault, PhD Relies on SVS to Find Pharmacogenetic Associations for Central Nervous System Disorders
Over the past decade, Dr. Juila Pinsonneault has worked with numerous human cohorts in analyzing genetic susceptibility and drug response to complex diseases. Her focus is central nervous system disorders such as post-partum depression, bipolar disorder, and other disorders affected by the dopamine transporter and estrogen receptor alpha, for example. Clinicians from around the continent send Pinsonneault their cohort samples so that targeted SNPs can be genotyped by restriction fragment length polymorphism (RFLP) analysis and other methods.
Sander van der Laan, a doctoral candidate at the Interuniversity Cardiology Institute Netherlands based at the University Medical Center Utrecht performs genomic association studies with the goal of uncovering biomarkers and drug targets for atherosclerosis. Upon initiating his PhD work, van der Laan realized that he needed an analytical tool that was better suited to the manipulation of large-scale genomic data than open-source off erings. Van der Laan found SNP & Variation Suite suited his research needs exactly. "With Golden Helix, my frustration went out the door," he says.
Robert Kleta, MD, PhD and His Newly-Formed Team Publish in The New England Journal of Medicine in a Few Short Months with SVS
Thirteen years ago, Dr. Robert Kleta had never heard of a genome-wide association study (GWAS), let alone considered doing one. Now, Dr. Kleta and his colleagues at the University College of London regularly publish articles in The New England Journal of Medicine and other journals on the genetics of rare diseases and their associated phenotypes using SVS. "I am a geneticist and a pediatrician, but at the end of the day, I'm a clinical scientist. SVS is so good that I, myself, without being a computer scientist, could upload the data and actually do a GWAS myself."
Dr. Folefac Aminkeng Saves Time and Increases Productivity with SVS to Study the Pharmacogenomics of Adverse Drug Reactions in Cancer Therapy
Dr. Folefac Aminkeng is a Postdoctoral Fellow at The Centre for Molecular Medicine and Therapeutics at the University of British Columbia in Vancouver, BC, Canada. He utilizes GWAS studies to identify single-nucleotide polymorphisms that might be associated with serious adverse drug reactions in cancer therapeutics. For Aminkeng the use of SNP & Variation Suite (SVS) is vital for efficient and meaningful analyses of large datasets. With SVS, he has seen a tremendous improvement in terms of the speed with which projects are completed.
The International Maize and Wheat Improvement Center's (CIMMYT) mission is "To sustainably increase the productivity of maize and wheat systems to ensure global food security and reduce poverty." To accomplish this task, one area of focus for the CIMMYT is genetic research and molecular marker technology to improve certain traits of maize and wheat, such as drought tolerance, resistance to disease, and amino acid balance. In this case study, Dr. Raman Babu describes his experience using SVS to analyze model populations in order to predict certain traits at CIMMYT.
Agrigenomic Researcher at U.C. Davis, Gonzalo Rincon, DVM, and Colleagues Publish 14 Articles and Obtain 2 Patents Using SVS
Gonzalo Rincon, DVM is a Project Scientist in the Medrano Lab, part of the Department of Animal Science, at the University of California, Davis. While the lab works on several different species including canine and ovine, the main focus is bovine research. Rincon is in charge of the analysis, and his goal is to find SNP and CNV variations that affect phenotypes such as the quality of milk and beef. Through the use of tools from Golden Helix, Rincon and his colleagues have been able to publish 14 papers and obtain 2 patents, three-to-four times faster than they would have been able to.
For lead geneticist Dr. Matthew McClure, of the Irish Cattle Breeding Federation, finding a software program that could handle massive amounts of data as well as more than the standard twenty-three pairs of chromosomes found in humans was a challenge. McClure says, "Agriculture often feels like the black sheep of the genomics industry. The majority of current genetic analysis programs are written for humans and do not know what to do with those extra chromosomes found in animals and plants."
For PhD graduate student Xin Geng, conducting Genome Wide Association Study (GWAS) to uncover the quantitative trait loci (QTL) controlling disease resistance in catfish was not just an interesting study, but potentially the start of finding a way to improve the economics of the aquaculture industry in the United Sates and China. Before coming to the United States as a graduate exchange student, Xin Geng graduated from Ocean University, which boasts one of the top agricultural programs in China.
Dr. Heather Huson is a Professor of Dairy Cattle Genetics at Cornell University, where she works with a team studying genetic improvement and diversity in livestock. Over the course of her career, Huson has used a number of different analysis tools in her research, but has found the ease of use and efficiency of Golden Helix's SNP & Variation Suite (SVS) to be instrumental in her research as well as teaching genetic analysis to her students.