Golden Helix Blog

The State of NGS Variant Calling: DON’T PANIC!!

Mar 25, 2013

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…

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Population Structure + Genetic Background + Environment = Mixed Model

Mar 22, 2013

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg.  Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems…

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Follow Along on an Analyst’s Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

Mar 14, 2013

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…

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Meet Andrew Jesaitis: Software Engineer

Mar 7, 2013

In 2011, I was looking for my next move and happened to attend a lecture given by Gabe Rudy at Montana State University. I was immediately struck by his passion and intelligence about the field of bioinformatics. He ended his talk by mentioning that Golden Helix was hiring, and I…

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Is Illumina Aiming to Compete with its Customers?

Feb 12, 2013

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…

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Three New Scripts and Two Updated Ones

Jan 16, 2013

We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed…

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Meet Autumn Laughbaum: Biostatistician

Jan 9, 2013

As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company.  I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented…

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New Plant and Animal Genomes and Tracks Now Available!

Jan 3, 2013

Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition…

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SVS 7.7 is here!

Nov 19, 2012

After much anticipation, we are excited to announce that SVS 7.7 is available! It’s been a lot of work, but we are pleased with the result and know you will be too! SVS 7.7 includes: Improved RNA-Seq Analysis Package for mRNA Expression Profiling Import tabularized quantification data from the Golden…

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Golden Helix Leaves Its Fingerprint on the Cure with EA at ASHG

Oct 31, 2012

Golden Helix is proud to announce our participation in EA’s 2012 “Leave Your Fingerprint on the Cure.” This event will be taking place at ASHG 2012 in San Francisco at the Moscone Center on November 7th. The fifth annual “Leave Your Fingerprint on the Cure” was designed by EA to…

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Dr. Folefac Aminkeng Saves Time and Increases Productivity with SVS to Study the Pharmacogenomics of Adverse Drug Reactions in Cancer Therapy

Oct 17, 2012

Dr. Folefac Aminkeng is a Postdoctoral Fellow at The Centre for Molecular Medicine and Therapeutics (CMMT) at the University of British Columbia in Vancouver, BC, Canada. He utilizes GWAS studies to identify single-nucleotide polymorphisms (SNPs) that might be associated with serious adverse drug reactions (ADRs) in cancer therapeutics. The field…

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Streamlined Workflow for Identifying Candidate Functional Polymorphisms

Oct 4, 2012

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…

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Guest Post: Next Generation Variant Calling

Sep 26, 2012

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…

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GenomeBrowse is here!

Sep 13, 2012

Golden Helix announced it would offer a complimentary genome browser for visualizing DNA and RNA-Seq data back in October of 2011; however no release date was disclosed at that time. Well, after much blood, sweat, and tears, we are VERY excited to announce that GenomeBrowseTM is here! GenomeBrowse raises the…

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New Tools to Simplify the Workflow for Identifying Candidate Functional Polymorphisms in SVS

Sep 5, 2012

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.…

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Peter K. Gregersen, MD Puts Analytical Power in the Hands of the Biologist with SVS

Aug 21, 2012

Dr. Peter K. Gregersen, head of the Robert S. Boas Center for Genomics and Human Genetics at the Feinstein Institute for Medical Research, utilizes GWAS, targeted arrays, and sequencing technologies to identify genes associated with human autoimmune disorders. The arrival of the GWAS platform in the mid-2000’s greatly accelerated the…

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Learning vs. Doing (or why that Ph.D. took 10 years)

Aug 15, 2012

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…

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A Conversation with 1000 Genomes Analysis Group Member: Jeffrey Rosenfeld

Aug 14, 2012

After my latest blog post, Jeffrey Rosenfeld reached out to me. Jeff is a member of the Analysis Group of the 1000 Genomes Project and shared some fascinating insights that I got permission to share here: Hi Gabe, I saw your great blog post about the problems in the lack…

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Dr. Ken Kaufman’s Webcast on Exome Sequencing Wildly Successful

Aug 9, 2012

Thank you to everyone who joined us yesterday for a webcast by Dr. Ken Kaufman of Cincinnati Children’s Hospital: “Identification of Candidate Functional Polymorphism Using Trio Family Whole Exome DNA Data.” Over 750 people registered for this event and 430 attended – a new Golden Helix record! If you missed…

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Announcing Technical Support Bulletins

Jul 20, 2012

Last month I was inspired to create a new way to keep our customers apprised of the latest information on Golden Helix software without cluttering inboxes and overwhelming our blog. I happened to receive a link to an article for one of Illumina’s bulletins and realized that was exactly what…

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