Allow me to introduce you to Blaine Bettinger. Blaine is a patent attorney who holds a PhD in Biochemistry with a concentration in genetics. He is also a family history enthusiast who writes the Genetic Genealogist blog, where he gives commentary on applications of genomic science for advancing personal and family history research. I first learned about Blaine last May… Read more »
The turning of the calendar from 2011 to 2012 has been a good time for me to reflect on the lessons of the year and make resolutions for the new one. It is also the opportunity to step back and look at some of the larger systemic trends in our field and think about whether we are doing as much… Read more »
Dr. Raman Babu is a Maize Molecular Breeder at the International Maize and Wheat Improvement Center (CIMMYT). Like his counterparts conducting human genetic research, Babu used to rely entirely on free, open-source tools to complete his work. Frustrated with continual crashes and technology that was developed in the pre-SNP era, Babu switched to SNP & Variation Suite (SVS) almost a… Read more »
Recently we have expanded our annotation track offerings with new human variant frequency catalogs such as the 1000 Genomes Phase 1 Data. Of course, we also curate data for plant and animal genomes – some of which are currently available in our software and some of which will be available in our next release. In this blog post, I will… Read more »
Have you ever chosen to do something yourself instead of paying money for the alternative, when, in the long run, the alternative is not really that expensive? We all have, as we all have limited budgets. One particular example comes to mind in my own life. My boyfriend, Ben, and I bought a house in April. Unfortunately, it wasn’t properly… Read more »
While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few questions about NGS – Gabe Rudy, Vice President of Product… Read more »
If you have ever worked with NGS variant data, you may have come to realize that the first task at hand is the seemingly simple categorization of your variants into two bins: known and novel. Of course, if you’ve ever worked with NGS variant data, you may have also come to the realization that this step is more complex than… Read more »
Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve in the past. Whenever I make a breakthrough in one project, I find I want to abandon the current project… Read more »
I can’t believe it’s that time again! Next week we are heading off to Montreal, Canada for the week of October 11-15 for the 2011 American Society of Human Genetics annual meeting, this year in conjunction with the 12th International Congress of Human Genetics. We are excited as ever to hear what everyone has been up to, how your studies… Read more »
httpv://www.youtube.com/watch?v=_5CUPMD0Agk On September 16-17th, I attended the Asia-Pacific Economic Cooperative (APEC) Health Systems Innovation Policy Dialog in San Francisco. It was a stimulating opportunity to look at global healthcare concerns from the perspective of developing and developed economies. There was much opportunity to dialog and frame the issues around transforming healthcare systems to meet pressing problems such as aging populations,… Read more »
Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s always too much to do. And he finds command-line tools… Read more »
Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5. Have you ever wanted to view annotation data next to marker map data? Or expand the current marker map with spreadsheet data to create a custom map? SVS 7.5 features two new functions that can accomplish these tasks. Adding Annotation Data to a… Read more »
As I’ve mentioned in previous blog posts, one of the great aspects of our scientific community is the sharing of public data. With a mission of providing powerful and accurate tools to researchers, we at at Golden Helix especially appreciate the value of having rich and extensive public data to test and calibrate those tools. Public data allow us to… Read more »
More powerful rare variant analysis and visualization techniques We are proud to unveil SNP & Variation Suite (SVS) 7.5! The fifth installment of SVS delivers the most powerful rare variant analysis tools with the latest advances in tertiary or “sense making” methods for DNA next-gen sequencing. This release also adds some cool and productive features to our popular Genome Browser…. Read more »
Golden Helix’ SNP & Variation Suite (SVS) has a Regression Module to enable researchers with varying degrees of statistical knowledge to interrogate their data using regression models to account for potential confounding effects of covariates and interaction terms. While these tools are labeled “basic”, they can be difficult to use and results hard to interpret for those who have only… Read more »
Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data. I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium. The Illumina conference was an opportunity to learn about the latest… Read more »
Ever since the release of SNP & Variation Suite (SVS) 7.4 back in January, our software engineers have been hard at work developing new functionality for the next version, to enable researchers to have even more control over their data. (Okay, well really, they started working on it before 7.4 even came out.) While the full details of 7.5 are… Read more »
The common disease-common variant hypothesis has established the foundation of SNP-basis genome-wide association studies for the last several years. However, with few strong associations found, researchers are beginning to consider the effects of rare variants through the burgeoning availability of DNA sequencing. Qianqian Zhu and Dongliang Ge, of the Center for Human Genome Variation at Duke University, and others recently… Read more »
Academic Software, Productivity, and Reproducible Research httpv://www.youtube.com/watch?v=pGMLCxKPMSE&NR=1 Do you ever feel like Dr. McCoy on Star Trek, where your job and expertise is to do x, but to achieve your goals you also have to do y and z, which you either don’t want to do or don’t have the skills to do? Genetic researchers are faced with this every… Read more »
In a series of previous blog posts, I gave an overview of Next Generation Sequencing trends and technologies. In Part Two of the three part series, the range of steps and programs used in the bioinfomatics of NGS data was defined as primary, secondary and tertiary analysis. In Part Three I went into more details on the needs and workflows… Read more »
