Search Results for: annotation

Clinical Variant Analysis for Cancer: Part III

         June 18, 2019

Clinical Variant Analysis for Cancer – Applying AMP Guidelines to Analyze Somatic Variants As described in my eBook “Genetic Testing for Cancer,” any bioinformatic pipeline for cancer ultimately calls variants based on the aligned reads that the sequencer generated. Variant calling is the process of reviewing a sequence alignment, typically in the form of a BAM file, to identify loci… Read more »

Automating Clinical Workflows: Part III

         April 19, 2019

In the previous two articles, we explored the different steps of a clinical workflow. The first post covered the automated analysis that creates a VarSeq project. While the second post covered the interpretation steps and generation of a clinical report. These posts illustrated the ease with which these complex tasks can be carried out. Today we’ll dig a little bit… Read more »

Automating Clinical Workflows: Part II

         April 11, 2019

In the previous blog post, we covered the automated steps to create a VarSeq project. Today we will examine the active analysis steps. These are the steps that require human interpretation to analyze the clinically relevant variants. A lab tech can take the first pass at the output in the generated VarSeq project. They can perform the quality control and… Read more »

Automating Clinical Workflows: Part I

         April 3, 2019

Automating a clinical workflow creates a stable and repeatable clinical analysis. Automation reduces the potential to introduce human error, helps in regulatory compliance, and improves the precision of the clinical results. It is important to know that if you run a sample through your clinical pipeline, you are going to get the same results today as you will in 6… Read more »

How To: VarSeq VCF Import

         February 5, 2019
annotate

The Beginning of Your Tertiary Analysis VarSeq is designed to be your NGS tertiary analysis solution providing users simple but in-depth means of exploring gene panel, exome, and whole genome variants. For those not accustomed to the VarSeq software, the main import file for variant analysis is the VCF. Those who are familiar with the VCF know that there can… Read more »

New COSMIC Database for NGS Cancer Analyses – Q&A

         January 9, 2019

We had a great time showing users the new COSMIC database for future NGS cancer analyses within VarSeq. If you didn’t get a chance to join us for this live webcast, you can watch the recording below. I have summarized our live Q&A session for anyone who is curious about what others were asking. The COSMIC track is free, what… Read more »

Considerations When Calling CNVs on Shallow Whole Genomes

         December 20, 2018
CNV Annotations

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 chromosome from genomes with average coverage as low as 0.05x…. Read more »

VarSeq PhoRank Part: 2 Sample PhoRank Gene Ranking

         December 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. There is another PhoRank algorithm in VarSeq that allows the… Read more »

VarSeq PhoRank Part 1: Variant PhoRank Gene Ranking

         December 13, 2018

One of the main goals of clinical genomic 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 individual’s exome data (or possibly the individual’s nuclear family exome… Read more »

GRCh38 Liftover: Ensuring Top Quality Variant Analysis

         November 27, 2018
annotate

In a recent webcast, our VP of Product and Engineering Gabe Rudy gave us insight into the current capability and benefits to lifting over to the GRCh38 assembly. Golden Helix fully supports this transition into the most recent reference assembly and have developed our tools on both the 38 and 37 fronts. The purpose of this blog is to not… Read more »

SVS 8.8.3 Release

         November 26, 2018
gene ranking

The SVS 8.8.3 release was created to incorporate some of the CNV, genome assembly control, and splice site capabilities that are present in VarSeq, as well as clean up and streamline the GWAS workflows (like when using Mixed Linear Model algorithms) for a better user experience. New Product Add-Ons for SVS GoldenHelix SVS now includes in-silico splice site, functional prediction… Read more »

VSClinical Best Practice Workflows: Part II

         November 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 evaluation. Specifically, we will explore how VSClinical can help users… Read more »

VSClinical Best Practice Workflows: Part I

         November 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 Best Practices Blog Series, with the purpose of discussing some… Read more »

Great Time at AMP 2018

         November 6, 2018

We just got back from three busy days at the Molecular Pathology (AMP) conference in friendly San Antonio, Texas. Keeping up the Golden Helix conference momentum for the year, we had 3-4 in-booth demonstrations a day covering our CNV calling, variant interpretation, and data warehousing products for NGS-based genetic tests. And in short, NGS based tests for cancer and germline… Read more »

VarSeq Stable 2.1.0 Release Notes

         October 31, 2018
VSClinical algorithm

VarSeq Stable 2.1.0 is Ready for Clinical Validation, See it in Action Next Week This week we are happy to see the general availability of VarSeq 2.1, the culmination of the last five months of work since we launched VSClinical. We have been blown away by the adoption of VSClinical, outpacing any previous product launch in terms of the pace… Read more »

Annotating and Cataloging CNVs in Varseq – Webcast Q&A

         October 25, 2018

We love when our viewers send questions in during the webcast but unfortunately we can’t answer all of them during the time allotted!  If you asked a question see below for answers, or if after viewing, you have any questions that weren’t asked, please feel free to send those over to support@goldenhelix.com. Does this work for FFPE derived DNA or ctDNA?… Read more »

Accessing your VSWarehouse Browser

         October 23, 2018
VSWarehouse Updates

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 VarSeq, click the V Connect icon located in the top… Read more »

Optimizing your CNV Analysis in VSWarehouse

         October 16, 2018
VSWarehouse Updates

We recently hosted a webcast covering the value and application of VSWarehouse through VarSeq. Not only is VSWarehouse a solution for storing your NGS data in a central repository, but it also provides a means to enhance the tertiary analysis done in VarSeq. VSWarehouse will store all your sample/variant data but also stores your catalogs of pathogenic variants, clinical reports, and has the capability of filtering/querying on all your stored data quickly. In addition,… Read more »

Storing your Copy Number Variant & ACMG Results in VSWarehouse – Webcast Q&A

         October 11, 2018

This webcast generated some great questions! If you have any other questions for me that are not answered below, please feel free to ask those by emailing support@goldenhelix.com. To what level does the Warehouse scale? We have tested multiple instances of Warehouse in-house and on the cloud and it scales incredibly well to tens of thousands of samples and 100s… Read more »

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

         October 2, 2018
VCF file format

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 all off with the world’s largest biological collaboration project in… Read more »