GWAS became possible about 10 years ago as the result of several scientific advances. Since then, GWAS has continually developed as a primary method for identification of disease susceptibility genes in humans and other organisms. At Golden Helix we are proud of our history in supporting GWAS analysis from its inception. Our software was used to analyze whole-genome data from… Read more »
Recently, customer Xin Geng of Auburn University published a paper using SVS, and we wanted to share his story with you. Please feel free to contact us if you have questions or if you would like to learn more about SVS at info@goldenhelix.com. For PhD graduate student Xin Geng, conducting Genome Wide Association Study (GWAS) to uncover the quantitative trait… Read more »
Genotype imputation is a statistical technique for estimating sample genotypes at loci that were not directly assayed by sequencing or microarray experiments. There are several reasons why you might want to use imputation in a research study. For example: Improve call rates in GWAS by imputing sporadic missing genotypes Harmonize the data content from different GWAS genotyping platforms so that… Read more »
There is a lot we can be grateful for at Golden Helix. The past year was marked by two major breakthrough launches. Earlier in 2014, we shipped SVS 8 which unified SVS with our GenomeBrowse product. We were able to improve SVS’ data management and visualization capabilities. In addition we added a number of new methods in SVS, such as SKAT-O, MM-KBAC, and various genomic prediction algorithms.
Tutorials are ever-present in the world today, and for good reason. Why struggle through a complicated process yourself, when there is already a guide established to assist? While no one would suggest that a tutorial is the only way to complete a project, it is certainly a nice starting point. This rings true with genetic software as well. There are… Read more »
Genomic research is exploding. There is a plethora of new methods and workflows for research and clinical use. While we are a software company at heart, we find ourselves in the role of educators. Our customer interactions are about informing, teaching, and consulting. A few years back, we started with regular webcasts that took this idea to the next level…. Read more »
For the SVS 8.2 release we decided to improve upon the existing ROH feature. The improvements include new parameters to define a run and a new clustering algorithm to aide in finding more stringent clusters of runs. The improvements were motivated by customer comments and a recent research paper by Zhang 2013, “cgaTOH: Extended Approach for Identifying Tracts of Homozygosity,”… Read more »
Genetic improvement in livestock, particularly dairy cattle, has been a priority for both industry and researchers for nearly a century. While the animal itself is the foundation for improvement, our research and the implementation of improvement has progressed with developing technologies and priorities. In terms of genetics, we have evolved from basic measures of heritability to identifying specific mutations and… Read more »
Join us tomorrow, July 9th at 12PM EDT, for Ashley Hintz’s webcast on GWAS in a Model Organism: Arabidopsis Thaliana. Joining the Golden Helix team as a Field Application Scientist in April of 2014, Hintz is the perfect candidate to present on Arabidopsis Thaliana given her background in zoology and phylogenetics of planigales.
Type 2 Diabetes, Rheumatoid Arthritis, Obesity, Chrohn’s Diseases and Coronary Heart Disease are examples of common, chronic diseases that have a significant genetic component. It should be no surprise that these diseases have been the target of much genetic research. Yet over the past decade, the tools of our research efforts have failed to unravel the complete biological architecture of… Read more »
“Where is the missing heritability?” is a question asked frequently in genetic research, usually in the context of diseases that have large heritability estimates, say 60-80%, and yet where only perhaps 5-10% of that heritability has been found. The difficulty seems to come down to the common disease/common variant hypothesis not holding up. Or perhaps more accurately, that the frequency… Read more »
