Clinical Genetics

Quality Assurance Sample Statistics Added To VarSeq

Feb 18, 2016

As VarSeq continues its adoption amongst clinical labs and researchers looking for reproducible workflows for variant annotation, filtering and interpretation, we have continued to prioritize the addition of features to assess the quality of the upstream data at a variant, coverage and now sample level. The  Importance of Quality Assurance Sample prep…

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Q&A from the VSWarehouse Launch Webcast

Feb 4, 2016

Yesterday, it was my pleasure to share in a live webcast our integrated solution for genetic data warehousing, VSWarehouse. Although we had a great set of questions at the end of our presentation, we didn’t have time to answer all of them, so here is a selection of the remaining representative…

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Match Gene List algorithm not just for genes

Dec 17, 2015

The most common use of the VarSeq Match Gene List algorithm of course is to determine if the variants in your data set are contained within your genes of interest. As an example of this, say you are working with a whole exome trio and only want to consider those…

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Handling Singletons & Complex Pedigrees with Gene Count Algorithms

Dec 3, 2015

As VarSeq’s adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently. While having both parents provides the maximum power to discover de novo mutations and…

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Tumor-normal demo project comes to VarSeq

Dec 1, 2015

With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis. This project contains an exome pair…

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A New and Unexpectedly Powerful VarSeq Feature

Nov 17, 2015

With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of…

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New VarSeq Demo Projects

Nov 12, 2015

As VarSeq gains in popularity, we want to give Viewers and customers alike the opportunity to look at projects that are completed from start to finish. To this end, VarSeq (and VarSeq Viewer!) currently comes with two demonstration projects, Example TruSight Cardio Gene Panel and Example YRI Exome Trio Analysis. To…

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Analyzing a Single Sample Exome in VarSeq

Oct 22, 2015

While VarSeq comes with a number of starter workflows that are stored as templates, customers also have the option of creating filter chains from scratch; analyzing a single exome may require you to do exactly that. In this blog, I’ll go through analyzing a single exome and generating a list…

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Precision Medicine e-Book

Sep 15, 2015

Precision Medicine e-Book “It’s far more important to know what person the disease has than what disease the person has.” – Hippocrates (460 BC – 370 BC) Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century we take the understanding of…

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Top 5 things you need to know about VSPipeline

Jul 14, 2015

Recently, Golden Helix, Inc. announced the addition of VSPipeline to our VarSeq software suite. VSPipeline is a command-line interface that will allow high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command line context, including existing bioinformatics pipeline. So,…

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The Clinical Genome Conference 2015 Highlights

Jun 30, 2015

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of the conference from my perspective: Talking about clinical genomics is…

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Partnership with MedGenome

Jun 17, 2015

Just a few weeks ago we announced our partnership with MedGenome. The news was covered by a number of outlets including: Financial Express Pharmabiz Let me expIain the importance and impact of this announcement. Since Varseq was released, we have received strong interest from testing labs that are leveraging our product…

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Baby Genes is raising the bar for Newborn Screening

May 28, 2015

Today we wanted to share a recent client case study to demonstrate how VarSeq has been implemented in a CLIA certified clinical laboratory. Please feel free to contact us if you have questions or if you would like to discuss VarSeq further at [email protected]. It is standard practice for newborns to…

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What’s in a Name: The Intricacies of Identifying Variants

May 26, 2015

There’s a strong desire in the genetics community for a set of canonical transcripts. It’s a completely understandable and reasonable thing to want since it would simplify many aspects of analysis and especially the downstream communicating and reporting of variants. Unfortunately, biology isn’t so tidy as to provide a clear…

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Precision Medicine – Part VII – Regulatory Issues

May 21, 2015

Regulatory Issues Regulatory bodies such as the Federal Drug Administration (FDA) already have a full plate. In the US, FDA-regulated products account for 20 percent of each dollar spent by American consumers each year. More specifically, the work of the regulatory authorities include the following: Carefully considering benefits and risks when evaluating…

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Precision Medicine – Part VI – The Educational Challenge

May 14, 2015

The Educational Challenge Precision medicine will fundamentally change how health care is practiced. Of course, we have a long way to go. For most practitioners today, their knowledge of the human genome was established many years ago. However, new therapies and diagnostic methods are pouring in on a daily basis.…

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Precision Medicine – Part V – Bioinformatics Pipelines and Systems Infrastructure

May 7, 2015

Bioinformatics Pipelines and Systems Infrastructure The genetics industry is undergoing a fundamental shift from a clinical science focus to a bioinformatics focus. Genetic services require a greater level of data analytics sophistication than is required for other laboratory testing. Currently, data generated by new tests overwhelms current information technology systems…

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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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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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