How To’s & Advanced Workflows

Top-Quality GWAS Analysis: Part II

Jan 18, 2019

Eliminate Low-Quality Samples and Markers In Part I of this GWAS Analysis series, Dr. Eli Sward provided us with a great overview on the value SVS provides in managing the quality of your SNP or NGS data to maintain the high power and accuracy of your GWAS. He also gave…

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Considerations When Calling CNVs on Shallow Whole Genomes

Dec 20, 2018

We are happy to announce that our latest version of SVS includes the ability to call CNVs on low read depth Whole Genome Sequencing (WGS) data. Designed for calling large cytogenetic events, this algorithm can detect chromosomal aneuploidy events and other large events spanning one or more bands of a…

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VarSeq PhoRank Part: 2 Sample PhoRank Gene Ranking

Dec 18, 2018

The PhoRank tool in VarSeq is further explored in this post by looking at the sample-specific capability. VarSeq PhoRank Part: 1 Variant Phorank Gene Ranking showed how the PhoRank algorithm could be applied to all the variants in a VarSeq project, regardless of the number of (or difference in) samples.…

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VarSeq PhoRank Part 1: Variant PhoRank Gene Ranking

Dec 13, 2018

One of the main goals of clinical genomics labs is to identify problematic variants in affected individuals. One tool to assist in this search is the phenotype driven variant ontological re-ranking tool in VarSeq called PhoRank. A common situation facing clinicians is sorting through thousands of variants provided by an…

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VSClinical Best Practice Workflows: Part II

Nov 15, 2018

In part one of this series, we discussed how the ACMG Classifier can be implemented in your filter chain to support a best practice workflow. To continue our discussion on best practices of VSClinical, this blog will shed light on other attributes of VSClinical that can add support to your…

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VSClinical Best Practice Workflows: Part I

Nov 13, 2018

VSClinical is our most recent product that allows users to evaluate variants according to the ACMG guidelines. As with any tertiary analysis, there is a need to implement best practices into your workflow and using VSClinical for the ACMG guidelines is no exception. That said, we have put together a…

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Accessing your VSWarehouse Browser

Oct 23, 2018

In the first two parts of this blog, we presented examples of how to leverage Warehouse-stored VSClinical and CNV assessment catalogs in the VarSeq project. Now we are going to explore the Warehouse interface a bit more and show how to query on stored variant data. To access Warehouse from…

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VSClinical and VSWarehouse – Leveraging Consistent Clinical Interpretations

Oct 22, 2018

Part 1 of this blog series was focused on new capabilities in Warehouse to store your CNV results. We explored some approaches of how to utilize assessment catalogs of cohort and known pathogenic events. What makes Warehouse so useful in this application is that the catalog is accessed from one…

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Using the GRCh38 Reference Assembly for Clinical Interpretation in VSClinical – Webcast Recap

Oct 2, 2018

Even though GRCh37 is currently the most widely used human genome assembly, GRCh38 provides a more complete human reference genome, offers more accurate genomic analysis, and includes centromere and mitochondrial information. However, we’re getting ahead of ourselves. Perhaps start with how we got here. The Human Genome Project started this…

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Getting Started Guide for Sentieon – Part II

Sep 25, 2018

Creating Custom Scripts The first part of the Getting Started Guide for Sentieon described the steps for downloading the Sentieon tools, acquiring a license file, and running the example script/pipeline to generate the VCF and BAM files. This blog will cover some custom script changes users can make to add…

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Getting Started Guide for Sentieon

Sep 21, 2018

Sentieon; your swift secondary analysis solution. Golden Helix’s software solutions present a reputable and top-quality analysis of your NGS data. Looking at this process from a 30,000 ft view, the annotation and filtering of variants in your vcf files and discovery of CNVs based coverage data in the bam file…

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GWAS Quality Control Within SVS

Aug 23, 2018

Genome-wide association studies (GWAS) are useful in genetics as they test for the association of a phenotype with common genetic variants. GWAS is “hypothesis-free” and does not require prior knowledge of a gene’s biological impact on a trait. The catch though is that this leads to analyzing hundreds to thousands…

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CNV Setup & Quality Assessment: Part 2

Aug 7, 2018

With this two-part blog series, users should now be able to perform CNV analysis using their data, set up basic quality filter standards to isolate high-quality events and utilize annotations to hone in on publicly known events as well as in-house recorded CNVs from previous projects.

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CNV Setup & Quality Assessment: Part 1

Jul 26, 2018

2017 was a busy year regarding the development of our CNV tools. Since the release of the CNV caller, we have produced quite a bit of content tailored to assist our users with getting started. Here are some links: Robarts Research Institute CNV analysis on patients with familial hypercholesterolemia CNV…

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VSClinical: The details you should know

Jul 19, 2018

The recent release of VSClinical gives users the ability to evaluate variants based on the 33 criteria according to the American College of Medical Genetic and Genomics (ACMG) guidelines. This feature leverages a variety of variant sequencing evidence including population data, functional data, and computational predictions while providing rich visualizations…

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Top Webcasts of 2017

Jan 9, 2018

2017 was an incredibly prosperous year for Golden Helix; we released a handful of new features, announced new partnerships and completed our end-to-end architecture for clinical testing labs. Our webcast series has become a very popular way for our community to stay up-to-date with our new capabilities and best practices…

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VSWarehouse Updates with the Power of VarSeq 1.4.7

Nov 30, 2017

With the recent release of VarSeq 1.4.7, we have expanded the concepts of our popular assessment catalog to include CNV and other region-based records and not just variants. To match these capabilities, we have made a major update to VSWarehouse that supports these new record types in the centrally hosted…

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Annotation Education Series: Clinical Assessment Tracks

Sep 21, 2017

Clinical Assessment Tracks Golden Helix provides a large catalog of annotation sources for our research and clinical clientele. Making these public data repositories available to all our users is no easy task. As Cody Sarrazin mentioned in his blog post, annotation curation is a complex data science pipeline. This process…

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Upcoming Webcast: Comprehensive Clinical Workflows for Copy Number Variants in VarSeq

Sep 14, 2017

September 27, 2017 12:00 PM, EDT While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants. Golden Helix has developed and validated with our…

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Frequently Asked Questions: CNV analysis in VarSeq

Jul 20, 2017

The support team at Golden Helix is always here to help with your SVS and VarSeq needs. Often, we receive some excellent questions that should be shared with the rest of our users. This blog will answer some common questions we’ve been seeing lately regarding VarSeq CNV. I’ve noticed there is a version 2…

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