Tag Archives: VarSeq

Using Assessment Catalogs in your VarSeq workflow

Variant Assessment Cataloug

Variant interpretation is an integral part of any workflow that results in some decisions being made about the validity and suspected functional impact of a variant in a given sample and their presenting phenotypes. The VarSeq Assessment Catalog functionality is designed to assist the VarSeq user in streamlining this process. To include this functionality in your workflow, you will first… Read more »

Case Study: Children’s Hospital Los Angeles

Laura Li

Dr. Laura Li and her colleagues at the Children’s Hospital Los Angeles (CHLA) are working to determine the underlying genetic causes of Optic Nerve Hypoplasia (ONH), which is still unclear. ONH is the absence or under-development of the optic nerve and is currently the leading ocular cause of vision impairments and blindness in young children. ONH can also be combined… Read more »

WEBCAST: CNV Analysis with VarSeq

December’s webcast will provide the Golden Helix community with a more in-depth look at CNV analysis in VarSeq. On December 7th, Dr. Nathan Fortier will discuss the challenges and metrics surrounding CNV detection and then demonstrate VarSeq’s new capability from VCF to clinical report.  Wednesday, December 7th @ 12:00 PM, EST Numerous studies have documented the role of Copy Number Variations (CNVs)… Read more »

Why Call CNVs: Getting More from your NGS Data

CNV Call

Copy Number Variants have been important to clinical genetics for quite a while now. So, what has made now the right time to be looking at calling CNVs from NGS data? Well, there are a number of good reasons. The dominant one is simply that the NGS data you are already creating for calling variants can be used in many cases… Read more »

Personalized Medicine through Tumor Sequencing

Tumor Sequencing

Join us for a guest presentation Personalized Medicine through Tumor Sequencing by Dr. Jeffrey Rosenfeld! Wednesday, September 7th 12:00 pm EDT The identification of medications that target specific gene mutations is one of the major recent advances in cancer therapy. In 2001 Gleevec was approved to treat patients with the BCR-ABL fusion in chronic myelogenous leukemia (CML). Since then many more drugs… Read more »

Finding Rare Mutations at the Center for Rare Jewish Genetic Disorders

Bonei Olam

Since 1999, Bonei Olam has been providing large-scale funding for fertility treatment and research. The non-profit’s mission is to provide whatever means or resources necessary to help childless couples achieve the dream of parenthood. Today, it is recognized in the worldwide medical arena for its leadership role at the forefront of reproductive medicine, research and technology. Specifically, Bonei Olam has… Read more »

Using Clinical Reports in a Gene Panel Pipeline

Gene Panel

Upcoming Golden Helix Webcast: Using Clinical Reports as part of a Gene Panel Pipeline Wednesday, July 13th @ 12:00 pm EDT VarSeq Reports can be used as part of an automatic pipeline to quickly list variants with information that can be used to make actionable clinical decisions in a readable HTML format. Need to further filter the variants or add interpretation… Read more »

Diagnosing Rare Disease at King Abdulaziz Medical City

King Abdulaziz Medical City

King Abdulaziz Medical City (KAMC) in Riyadh commenced its operations in May 1983. Since then, it has continued expanding, while providing services for a rapidly growing patient population in all of its catchments areas. Today, King Fahad National Guard Hospital has evolved to be part of the King Abdulaziz Medical City with many other prominent medical centers. Since its inauguration… Read more »

VSPipeline Tips and Tricks

VSPipeline Tips & Tricks

The power of VSPipeline is in it’s ability to automate VarSeq workflows. Using VarSeq to create a pipeline template is great because it allows you to dial in the applied filters as well as interactively organize the annotations and applied algorithms. Automating a workflow with VSPipeline is  straightforward when beginning with an existing project. However, there are several steps that… Read more »

CADD Scores: Rank and Filter in Harmony!

VSClinical algorithm

There used to be much energy expended at conferences, bioinformatics forums and even publications about what was the better strategy for interpreting variants of clinical significance: Rule-based filtering and classification mechanisms or rank-based prioritization through all-encompassing “pathogenicity” scores. Both have shown to be effective. Rule-based systems, as exemplified in this filtering diagram in Baylor’s ground-breaking paper on clinical whole-exome sequencing… Read more »

Customizing Workflows for Family Structure

family structure

During the webcast yesterday, I demonstrated a few ways of customizing de Novo Candidate and Compound Heterozygous Candidate workflows to consider family structure that was slightly different from the default trio workflow. The families included additional affected and unaffected siblings added to a trio as well as looking at what could be done if there were only two affected siblings… Read more »

N-of-One Integration comes to VSReports

Submit directly to N-of-One from VarSeq If you or your lab uses N-of-One solutions for clinical annotations, here’s some good news: You can now submit directly to N-of-One from VarSeq! N-of-One’s set of preferred transcripts may differ from those outputted by our algorithms in VarSeq, so our solution was built with that in mind. Our slick, easy to use, and… Read more »

Custom Family Workflows featured in May Webcast

Wednesday, May 11th 12:00 pm EDT VarSeq contains default workflows for Trio analysis which include filter chains for identifying de Novo and Compound Heterozygous variants, but what if you have data for a full Quad or even just a few siblings? How could your VarSeq workflow be adjusted to handle this custom family structure?In this presentation we will demonstrate how… Read more »

Case Study: Clinical Testing at the University of Iowa

Dr. Benjamin Darbro

Benjamin Darbro, MD, PhD at the University of Iowa, uses VarSeq® software for Clinical Testing Founded by Hans Zellweger in the 1960’s, The Shivanand R. Patil Cytogenetics and Molecular Lab at the University of Iowa has a long history of clinical testing, seeing 45 years of advancements. Today, the lab is mainly focused on oncology, pre and post-natal genetics testing… Read more »

Cancer Workflows in VarSeq

      Delaina Hawkins    February 19, 2016    No Comments on Cancer Workflows in VarSeq
VCF file format

Wednesday, March 2nd 12:00 pm EST Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go… Read more »

Quality Assurance Sample Statistics Added To VarSeq

VarSeq

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 and sequencing problems are difficult to detect through the analysis… Read more »

Scaling is in our DNA: Making Genomics Accessible

Scalable Data

Scaling is in our DNA: Making Genomics Accessible One of the things I absolutely love about the work we do at Golden Helix is keeping up with the changes in data analysis driven by the iterative and generational leaps in technology. But one thing has always been a constant since day one: we break preconceived notions of what scale of… Read more »

Genetic Data Warehousing e-Book

      Andreas Scherer    February 10, 2016    No Comments on Genetic Data Warehousing e-Book
Genetic Data Warehouse

Genetic Data Warehousing e-Book In our webcast last week, we announced the upcoming release of VSWarehouse, a scalable genetic data warehouse for VarSeq. Genetic data warehousing becomes more important as Next-Generation Sequencing is taking off in the clinic, creating significant data management issues for clinicians, scientists and IT professionals alike. How can we retain the massive amounts of data coming out… Read more »

Compound Heterozygous Workflows: Including a 2nd Affected Child

VarSeq

Compound Heterozygous Workflows: Including a 2nd Affected Child Looking for Compound Heterozygous regions for a trio is fairly straight forward in VarSeq, we include this workflow in our shipped Exome Trio Template. An example of which is included with our Example Projects which can be found by going to File > Example Projects > Example YRI Exome Trio Analysis. But… Read more »

Announcing VSWarehouse – Golden Helix’s Data Warehouse Solution for genomic data

VSWarehouse Updates

So, why are we launching a new data warehouse product? Why did we build VSWarehouse? According to Grand View Market Research, the next generation sequencing (NGS) market size was $2.0 billion (USD) globally in 2014. This number is expected to grow from 2015 to 2022 at an annual rate of about 40%. What drives this phenomenon is the increasing number… Read more »