When many people think of learning disabilities such as dyslexia and language impairment, they typically do not think of a biological or medical condition. Even more rarely do people think of these conditions as being the result of biological and genetic phenomena. However, that is exactly what I have thought of every day during my doctoral training in the Department… Read more »
For lead geneticist Dr. Matthew McClure, of the Irish Cattle Breeding Federation (ICBF), 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… Read more »
Philadelphia. The City of Brotherly love, home of the Philadelphia cheesesteak, and home to the Children’s Hospital of Philadelphia, who took the No. 1 spot in this year’s U.S. News & World Report’s Best Children’s Hospitals Honor Roll. We are honored (and excited!) to sponsor this year’s Mid-Atlantic Epidemiology and Statistics (MAGES) Conference at the University of Pennsylvania. MAGES will… Read more »
The developers at Golden Helix have raised the bar again with the release of GenomeBrowe 2.0. About a year and a half after the initial release, Golden Helix has expanded the functionality of GenomeBrowse to fulfill feature requests from both fundamental research investigators and translational scientists who require a visualization tool to gain key insight into their results. The Golden… Read more »
New breakthroughs are being made every day in genomics. It’s a dynamic and fascinating industry, and with exceptional growth forecast in the DNA sequencing market, a new generation of people are entering the field: future researchers, clinicians, counselors and doctors. This new generation will need to learn not only the science, but also understand how to process the massive amounts… Read more »
Today is a big day for us. Today we are announcing a major release of our flagship product, SNP & Variation Suite (SVS), to the general public. SVS 8 is a substantial improvement over the previous release in a number of dimensions (see detailed discussion on our What’s New page). We’ve come a long way. Over five years ago, in… Read more »
Dr. Bryce Christensen recently gave a webcast on Maximizing Public Data Sources for Sequencing and GWAS Studies in which he covered options for getting GWAS and sequence information online, tips for working with these datasets and what you’ll see in terms of data quality and usefulness, how to use public data sources in conjunction with your GWAS or sequence study… Read more »
Weather.com currently says it feels like -24 degrees outside (yes, that’s negative) here in Bozeman, Montana. Which is why I’m more than a little jealous of Gabe Rudy and Andreas Scherer who get to go to San Francisco and Marco Island next week, respectively, where the weather is little more… well, let’s say… reasonable. Andreas will be headed to Marco… Read more »
In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in SVS, the files had to be converted to BAMs and then merged into a single VCF file. Since many of… Read more »
At Golden Helix our number one priority is empowering genetic researchers world-wide with software tools that are as effective as they are robust. So needless to say, we are thrilled to announce a recent collaboration with the Ontario Genomics Institute (OGI), a not-for-profit organization focused on driving and catalyzing the life sciences industry in Ontario. Through this exciting partnership, we… Read more »
In a recent blog post (Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage), Autumn Laughbaum compared three imputation programs. Data can be exported from, or imported into, SVS in the standard file formats for these and other imputation programs. The goal of this blog post will be to review the different tools available to… Read more »
Last week, we presented a webcast on Workflow Automation in SVS. If you were unable to attend, a recording of it is on our website. In this post I’ll respond to some of the questions we were unable to answer within the allotted time. Will you provide a link for the software used in the webcast? I used Golden Helix’s… Read more »
Utilizing Identical Twins Discordant for Schizophrenia to Uncover de novo Mutations We are living in exciting times – the reality of high-resolution Cand individual genome sequencing now offers renewed hope in the search for the causes of complex diseases. When this technology is combined with genetic relationships, individual sequences add unrivaled proficiency. Our lab is located in London, Ontario, Canada… Read more »
Genotype imputation is a common and useful practice that allows GWAS researchers to analyze untyped SNPs without the cost of genotyping millions of additional SNPs. In the Services Department at Golden Helix, we often perform imputation on client data, and we have our own software preferences for a variety of reasons. However, other imputation software packages have their own advantages… Read more »
Humans are said to have a 0.1% rate of diversity, seemingly small, but actually quite significant when considering the future of personalized medicine. Gaining a deeper understanding of this genetic variance can help determine susceptibility to disease as well as medicinal response and outcomes. One-third of human genetic diversity can be found in a likely contender for the birthplace of… Read more »
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. States Kleta, “For rare diseases,… Read more »
Time goes by fast. With the completion of the Human Genome Project in 2003, scientists worldwide were trying to understand the cause and effect of variations in the genome as they relate to functionalities, traits and disease. Along the way, we at Golden Helix helped researchers analyze data, discover variations and draw conclusions. It turns out that the real bottleneck… Read more »
When researchers realized they needed a way to report genetic variants in scientific literature using a consistent format, the Human Genome Variation Society (HGVS) mutation nomenclature was developed and quickly became the standard method for describing sequence variations. Increasingly, HGVS nomenclature is being used to describe variants in genetic variant databases as well. There are some practical issues that researchers… Read more »
Presenter: Dr. Bryce Christensen, Statistical Geneticist and Director of Services Date: Wednesday, May 15th, 2013 Time: 12:00 pm EDT Abstract Next-Generation Sequencing analysis workflows typically lead to a list of candidate variants that may or may not be associated with the phenotype of interest. Any given analysis may result in tens, hundreds, or even thousands of genetic variants which must… Read more »
I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of thousands or even millions of candidates. When these signals sit right in the genomic “sweet spot” of mappable regions with… Read more »