Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) In it, Khanh-Nhat highlighted tools available in SVS that might be under used or were recently updated. These tools were used in his last three… Read more »
My investigation into my wife’s rare autoimmune disease I recently got invited to speak at the plenary session of AGBT about my experience in receiving and interpreting my Direct to Consumer (DTC) exomes. I’ve touched on this before in my post discussing my own exome and a caution for clinical labs setting up a GATK pipeline based on buggy variants… Read more »
In a recent GenomeWeb article by Tony Fong, “Sequenom’s CEO ‘Puzzled’ by Illumina’s Buy of Verinata, Lays out 2013 Goals at JP Morgan,” Harry Hixson, Sequenom’s CEO, expresses puzzlement over why its major supplier, Illumina, is acquiring a Sequenom competitor in Non-Invasive Prenatal Testing (NIPT), and thus apparently competing with one of its major customers. In a JP Morgan interview… Read more »
In preparation for a webcast I’ll be giving on Wednesday on my own exome, I’ve been spending more time with variant callers and the myriad of false-positives one has to wade through to get to interesting, or potentially significant, variants. So recently, I was happy to see a message in my inbox from the 23andMe exome team saying they had… Read more »
Recently, I have been spending some time analyzing real patient data. I’m preparing for a webcast I’ll be giving in which I will walk through the process of replicating the findings of Dr. Gholson Lyon‘s study on the novel disease diagnosis he named Ogden Syndrome. Being so close to data that comes directly from clinical settings got me thinking about… Read more »
Since Dr. Ken Kaufman gave his webcast on Identifying Candidate Functional Polymorphisms in SVS, we’ve been working with Dr. Kaufman to simplify and automate many of the steps in his workflow. I touched on this in my last blog post, and I’m excited to report that with Ken’s help, we’ve been able to simplify the workflow even more. In particular… Read more »
Editor’s Note by Gabe Rudy: I’ve had the chance to exchange thoughts, emails, and blog post comments for a while now with Jeff as he has written posts on NGS Leaders and engaged with me on 23andMe. He has also worked with Golden Helix software as part of Dr. Todd Lencz’s research efforts at Zucker Hillside Hospital until he recently… Read more »
It has now been about a year since Illumina and Affymetrix announced their respective exome genotyping arrays. Both products were launched with ambitious visions of how they would enable researchers to learn significantly more about the cause of human diseases. Sales of the Illumina chip exceeded expectations, and the company said that it sold enough exome chips through the first… Read more »
Dr. Ken Kaufman’s extremely popular webinar inspired us to build new tools that would simplify the process of analyzing whole-exome DNA sequencing data even further. First I’ll describe the tools showcased in the webcast. Then I’ll detail the new tools we created to allow for a revised and simplified workflow. Subset Informative Genotypes by Category The Subset Informative Genotypes by… Read more »
What prevents scientists from being more productive and if we knew, could we do anything about it? I’d like to look at an often overlooked, but huge productivity inhibitor — bad multitasking. Many people put “excellent multitasker” on their resume as a badge of honor. We laud the efficiency of a good multitasker — they are rarely idle — someone… Read more »
I recently curated the latest population frequency catalog from the 1000 Genomes Project onto our annotation servers, and I had very high hopes for this track. First of all, I applaud 1000 Genomes for the amount of effort they have put in to providing the community with the largest set of high-quality whole genome controls available. My high hopes are… Read more »
There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. You see, I lucked out. It all began two years ago on DNA day when Hacker News reported that 23andMe… Read more »
In the last couple of weeks, the SVS Script Repository has seen a handful of new additions. This blog post highlights three new scripts, but as always, we welcome you to check out our repository regularly to enjoy the new and exciting functionality made possible by our Python integration in SVS! (To get these, or any other scripts, simply go… Read more »
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 »
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 »
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 »
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 »
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 »
