Author Archives: Eli Sward

Eli Sward

About Eli Sward

Eli Sward, Ph.D is a Field Application Scientist at Golden Helix, joining the team in May of 2018. Eli graduated from Montana State University with a bachelor’s degree in Microbiology, and a doctorate’s in the Department of Immunology and Infectious Diseases. Beyond providing customer support and training at Golden Helix, Eli enjoys many outdoor activities and spending quality time with family and friends.

Clinical Validation of Copy Number Variants Using the AMP Guidelines

The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you… Read more »

Variant Interpretation with VSClinical: RET-KIF5b Gene Fusion

Gene Fusion Background Gene fusions are hybrid genes that result from translocations, interstitial deletions, or chromosomal inversions that can lead to constitutive gene activation and result in increased or abnormal protein production. Increased or abnormal protein production subsequently can play an important role in tumorigenesis and thus identifying and evaluating this type of biomarker is important in the cancer workspace…. Read more »

Variant Interpretation with VSClinical: Non-Small Cell Lung Cancer

With the increasing knowledge of mutations involved in cancer, it is imperative to have a tertiary analysis pipeline that provides users with the most up to date information on somatic mutations. VSClinical’s Cancer Add-On does just that and more; with this feature, users can investigate and report on SNVs, indels, CNVs, gene fusions, and considerations for wild type genes in… Read more »

Variant Interpretation with VSClinical: Congenital Myasthenic Syndromes (CMS)

Congenital Myasthenic Syndromes (CMS) History: Congenital Myasthenic Syndromes (CMS) are a group of rare hereditary conditions that can cause seizures, severe muscle weakness, respiratory problems, and potentially disabling weaknesses shortly after birth or early childhood (1). CMS is the result of abnormalities in acetylcholine proteins residing in the motor endplate of the neuromuscular junction (1). These abnormalities can be diagnosed… Read more »

Variant Interpretation with VSClinical: Evaluation of Hypertrophic Cardiomyopathy

Hypertrophic Cardiomyopathy History It was December 9th, 1989, when one of Loyola Marymount’s strongest inside players, Hank Gathers, collapsed during the middle of a collegiate level basketball game against UC Santa Barbara. Measuring in at 6’7” and weighing 210 pounds, Gathers was diagnosed with exercise-induced ventricular tachycardia, or in layman’s terms, an abnormal heartbeat. Even with the concerning nature of… Read more »

Variant Interpretation with VSClinical: Evaluation of an X-linked recessive mutation

Overview VSClinical enables users to evaluate variants according to the ACMG guidelines in a high-throughput fashion and obtain consistent results and accurate variant interpretations. This feature is tightly integrated into our VarSeq platform as well, and when paired together, users can evaluate NGS data and obtain clinical reports all in one suite. Coupled with the ability to find novel or… Read more »

Top-Quality GWAS Analysis: Part V

      Eli Sward    January 28, 2019    No Comments on Top-Quality GWAS Analysis: Part V

As our final part of the ‘Top-Quality GWAS Analysis’ blog series, we will be giving a summary of the values behind GWAS quality control and quality assessment. Performing GWAS can provide insight into the association of genetic variants with traits and complex disorders. Any novel insights into marker-phenotype associations need to be based on performing quality control steps. In this… Read more »

Top-Quality GWAS Analysis: Part III

      Eli Sward    January 22, 2019    No Comments on Top-Quality GWAS Analysis: Part III

Sample Relatedness Pruning your data based on Linkage Disequilibrium (LD) values and filtering for sample “relatedness” are ideal quality assurance steps following the marker and sample quality filtering described in Part II of this blog series. The value of running an Identity by Decent estimation not only allows you to factor family relatedness in your samples but makes screening for… Read more »

Top-Quality GWAS Analysis: Part I

      Eli Sward    January 16, 2019    No Comments on Top-Quality GWAS Analysis: Part I

Importance of Quality in Association Tests SVS is a research application platform provided by Golden Helix that enables an array of computational analyses including genome-wide association studies (GWAS). GWAS is an observational study that can provide insight into the association of genetic variants with traits and complex disorders. The foundation of GWAS utilizes large cohorts sequenced with single nucleotide polymorphisms… Read more »

Optimized Breeding Selection via Genomic Prediction

What is Genomic Prediction? Genomic prediction is an algorithm widely used to improve desirable phenotypic traits in agriculture. For example, the cattle industry uses genomic prediction to improve beef quality and palatability as well as improve dairy production (1,2). By using genomic prediction, researchers can minimize multiple expenses in breeding industries as well as diminish the need for performing cumbersome… Read more »

VSClinical Best Practice Workflows: Part III

This blog will conclude our VSClinical Best Practice Workflow series and focuses on one of our new reports: VSClinical ACMG Gene Panel Template. This template is valuable because it automatically enters your variant interpretation from the ACMG Guidelines into the report and eliminates the need for manual submission. I would like to explain how to properly implement this report into… Read more »

VSClinical Best Practice Workflows: Part II

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

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 »

Using VS-CNV to detect high-quality CNV events

In my recent webcast, I demonstrated how VS-CNV users can detect high-quality CNV events. If you didn’t have a chance to join, you can view the recording below! This webcast generated a lot of great questions! If you have any other questions about the content covered in this webcast that is not answered below, please feel free to reach out… Read more »

GWAS Quality Control Within SVS

      Eli Sward    August 23, 2018    No Comments on GWAS Quality Control Within SVS
SVS 8

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 of genome-wide array samples to elucidate single nucleotide polymorphisms (SNPs) associated with a specific phenotype.

VSClinical: The details you should know

ClinVar

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 and auto recommendations to help answer challenging criteria. This highly… Read more »