Golden Helix Blog

Comparing Meta-Analysis Methods: A Meta Examination

May 5, 2015

Meta-analysis is an important tool to have in the bioinformatics toolbox. The numbers alone speak for themselves. It is the fourth most requested feature for SVS, and a simple google scholar search for 2014 and 2015 find 17,300 results for genetics + meta-analysis. There are several meta-analysis utilities out there…

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Cross-Validation for Genomic Prediction in SVS

Apr 28, 2015

The SNP and Variation Suite (SVS) software currently supports three methods for genomic prediction: Genomic Best Linear Unbiased Predictors (GBLUP), Bayes C and Bayes C-pi. We have discussed these methods extensively in previous blogs and webcast events.  Although there are extensive applications for these methods, they are primarily used for…

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Precision Medicine – Part III – Tailoring Diagnostic and Therapeutic Strategies

Apr 23, 2015

Tailoring diagnostic and therapeutic strategies Many have called Sir William Osler (1849-1910) the “Father of Modern Medicine”. He was one of the four founding professors of Johns Hopkins Hospital where he was instrumental in creating the first residency program for the specialty training of physicians. He brought medical students from…

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VarSeq as a Clinical NGS Platform Q&A

Apr 21, 2015

Our VarSeq as a Clinical Platform webcast last week highlighted some recent updates in VarSeq that support gene panel screenings and rare variant diagnostics. The webcast generated some good questions, and I wanted to share them with you. If the questions below spark new questions or need clarification, feel free…

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Visually Filtering Data in GenomeBrowse

Apr 16, 2015

Over 650 GenomeBrowse licenses have been registered and downloaded since the beginning of 2015, and with so many people enjoying the utility of this freeware program, I wanted to showcase some advanced tips and tricks so you can get more out of GenomeBrowse! Under the Controls panel, when you’re clicked…

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Precision Medicine Part II – Reimbursement and Cost

Apr 14, 2015

Reimbursement and Cost – Precision Medicine Part II The promise of precision medicine is to leverage highly targeted therapies for the benefit of the patient. By understanding better what makes us unique and leveraging our genetic make up, we hope to improve the outcome for the individual. Now, this blog…

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Unique Labs, Common Tool: Making VarSeq Ready for Clinical Workflows

Apr 9, 2015

As VarSeq has been evaluated and chosen by more and more clinical labs, I have come to respect how unique each lab’s analytical use cases are. Different labs may specialize in cancer therapy management, specific hereditary disorders, focused gene panels or whole exomes. Some may expect to spend just minutes…

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Precision Medicine – Part I

Apr 7, 2015

Precision Medicine Initiative On January 30, 2015, the Precision Medicine Initiative was announced by President Obama. Many in our field, researchers and clinicians alike, recognize that such a program would bring additional funding into our space to design, develop and implement new diagnostic tests that are aiding physicians in their practice of precision medicine. Here…

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Q&A Surrounding the Molecular Sciences Made Personal Webcast

Mar 26, 2015

This week, Dr. Jeffery Moore presented a webcast on the Molecular Sciences Made Personal. The webcast delved into Dr. Moore’s attempts to transform how they teach chemistry at the University of Illinois and demonstrated how he uses VarSeq with his students to examine exome data. The following are the questions…

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Supercentenarian Variant Annotation: Complex to Primitive

Mar 19, 2015

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genome sequencing data of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering. Well, we just published the…

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Question and Answers: Cancer Gene Panels Webcast

Mar 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”. We had some excellent questions which we answered during the webcast and a few more that we didn’t get to in the allotted time. Please find answers to those questions here: 1. Are Cancer Gene Panels just another stepping stone on…

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Analyzing a Unique Family Structure in VarSeq 1.1.1

Mar 12, 2015

I am constantly on the lookout for fun or interesting datasets to analyze in SVS or VarSeq and recently came across a study looking into inherited cardiac conduction disease in an extended family (Lai et al. 2013). The researchers sequenced the exomes from five family members including three affected siblings…

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Final thoughts on AGBT 2015

Mar 5, 2015

It was a great trip down to Florida this year. AGBT 2015 was an exciting event with lots of great presentations. For us in this tightly-knit community it is an excellent networking opportunity to catch up with existing clients and partners, but also to make new connections. Now, it is…

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Introducing Phenotype Gene Ranking in VarSeq

Mar 3, 2015

Personal genome sequencing is rapidly changing the landscape of clinical genetics. With this development also comes a new set of challenges. For example, every sequenced exome presents the clinical geneticist with thousands of variants. The job at hand is to find out which one might be responsible for the person’s illness. In…

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Golden Helix and Fluxion Biosciences Join in a Global, Value-Added Reseller Agreement

Feb 16, 2015

Today, Golden Helix and Fluxion Biosciences announced a collaboration in a value-added reseller relationship. The relationship will bring the VarSeq software application to Fluxion’s global client base providing them with a method to study tumor DNA in the circulation. Fluxion is proud to offer the capability as it helps move them…

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Q&A from our December Genomic Prediction webcast

Feb 12, 2015

Our Genomic Prediction webcast in December discussed using Bayes-C pi and Genomic Best Linear Unbiased Predictors (GBLUP) to predict phenotypic traits from genotypes in order to identify the plants or animals with the best breeding potential for desirable traits. The webcast generated a lot of good questions as our webcasts…

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Tri-Con 2015 – just 5 days away!

Feb 10, 2015

In just 5 days, the 22nd International Molecular Medicine Tri-Conference (Tri-Con) will kick off in San Francisco. This year, Tri-Con will offer over 3,000 attendees 6 symposia, over 20 short courses, and 17 conference programs focused on drug discovery, genomics, diagnostics, and information technology surrounding, molecular medicine. Both Dr. Andreas Scherer, CEO…

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PreventionGenetics to Use Golden Helix’s VarSeq for Dx Test Offering

Feb 9, 2015

Today, we at Golden Helix announced our collaboration with PreventionGenetics as they prepare to implement the VarSeq software into their exome sequencing pipeline. The VarSeq software will allow PreventionGenetics to offer an exome test by dramatically speeding up the analysis process. VarSeq will narrow down sequence data into gene(s) of interest…

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To Impute, or not to Impute

Feb 5, 2015

Genotype imputation is a statistical technique for estimating sample genotypes at loci that were not directly assayed by sequencing or microarray experiments.  There are several reasons why you might want to use imputation in a research study.  For example: These are all important applications for imputation technology and can make…

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SVS, Population Genetics, and 1000 Genomes Phase 3

Jan 27, 2015

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes…

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