Over the past 3 years, Golden Helix has analyzed dozens of public and customer whole-genome and candidate gene datasets for a host of studies. Though genetic research certainly has a number of complexities and challenges, the number one problem we encounter, which also has the greatest repercussions, is born of problematic experimental design. In fact, about 95% of the studies… Read more »
How much fun is a person allowed to have when going to a conference? That kind of sums up my personal experience going to the first ever Capita Selecta in Complex Disease Analysis (bi-annual) conference in Leuven, Belgium. Not only was it fun, but the conference program was packed with interesting talks and short courses. Dr. Kristel van Steen and… Read more »
In the ongoing quest to empower our customers with the latest in genetic analysis methods, we are continually releasing new functionality for SNP & Variation Suite 7 in the form of add-on scripts. Add-on scripts are written in Python, a clear and powerful object-oriented programming language similar to Java or Perl. Python provides fully-programmatic access to most aspects of the… Read more »
We’re inspired by significance. Every tool we develop and every service we deliver is designed to help our customers achieve significance in their research. Not only statistical, but scientific and personal significance as well. The icing on the cake is being able to share what our customers do and discover with others in the scientific community. We applaud each author… 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 »
Including the completion of the Human Genome Project in 2003, scientists have created whole genome sequence maps for over 1,000 species. From maize to oysters, the quest to investigate different species’ genetic code continues. Mapping is the “first step” that provides a baseline for further study into differences between species, the occurrence of certain diseases, and the prevalence of traits… Read more »
Accuracy and completeness of genotype data are among the most important factors for a successful genome-wide association study (GWAS), and must not be taken lightly. The Golden Helix team is always on the lookout for methods to improve data quality, and we have recently found the BEAGLE and BEAGLECALL software packages to be very useful in this regard. BEAGLE is… Read more »
As Andy Ferrin and I drove the five-hour car ride home from a cytogenetics conference, we had a lot of time to reflect on the persistent themes we heard in presentations and dialog among conference attendees. Taking somewhat of an outsider view, we traced each complaint, each sigh of frustration, and the unverbalized assumptions behind opposing viewpoints, and they all… Read more »
In the paper Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia, Todd Lencz, Ph.D. introduced a new way of doing association testing using SNP microarray platforms. The method, which he termed “whole genome homozygosity association”, first identifies patterned clusters of SNPs demonstrating extended homozygosity (runs of homozygosity or “ROHs”) and then employs both genome-wide and regionally-specific statistical tests… Read more »
