Tag Archives: SVS

Off to PAG XXVIII!

      Delaina Hawkins    January 7, 2020    No Comments on Off to PAG XXVIII!

We’re packing our bags and getting ready to head out to San Diego, CA for the International Plant & Animal Genome XXVIII meeting (or PAG 2020). This is the largest ag-genomics meeting in the world, bringing together over 3,000 leading genetic scientists and researchers in plant and animal research, and over 120 exhibits, 140+ workshops, 1000+ posters, and 1700+ abstracts. We… Read more »

Using the K-Fold Cross-Validation Statistics to Understand the Predictive Power of your Data in SVS

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Using the K-Fold Cross-Validation Statistics to Understand the Predictive Power of your Data in SVS In cross-validation, a set of data is divided into two parts, the “training set” and the “validation set”. A model for predicting a phenotype from genotypic data and (usually) some fixed effect parameters is “trained” using the training set—that is, the best value(s) of the… Read more »

GWAS & Genomic Prediction Webcast Q&A

Thank you all for tuning in to yesterday’s webcast, “Simplify Your GWAS & Genomic Prediction with SVS”. I hope you all enjoyed it as much as I did! If you didn’t get a chance to join us for this live webcast, you can watch the recording below. We covered a lot of topics in so little time, but you all… Read more »

Simplify Your GWAS & Genomic Prediction with SVS

Genome-Wide Association Studies

SVS is a project-oriented program that manages and analyzes genomic datasets. This webcast statistically and visually explores the relationships among genetic variants within a cattle dataset. Even further, this webcast evaluates genotypes with corresponding phenotypes to assess how well a model can predict a phenotype of interest. Starting with genotypic data from the microarray and the recorded phenotypic data for… 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 IV

Population Stratification This article is going to cover how to factor for population stratification in your association test to continue our blog series on top quality GWAS analysis (additional articles for this series are located at the bottom of this blog). Quality control steps up to this point have included assessing sample and marker statistics, LD pruning on markers, and… 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 II

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 a snapshot of what a typical genotype spreadsheet may look… Read more »

SVS 8.8.3 Release

      Cody Sarrazin    November 26, 2018    2 Comments on SVS 8.8.3 Release
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 »

GWAS Quality Control Within SVS

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

Third-Place Abstract Competition Winner

I would like to congratulate our third and final winner of the 2017-18 Abstract Competition, Suxu Tan, a current PhD Student at Auburn University. Our first and second place winners, Michael Iacocca and Nicole Weaver, performed their research using VarSeq. Suxu, however, used SVS to conduct the research in his paper ‘GWAS analysis of QTL for resistance against Edwardsiella ictaluri in… Read more »

Genomic Prediction Methods in SVS Q&A

VS-CNV Annotations

Yesterday’s webcast, Genomic Prediction Methods in SVS, gave attendees a chance to see how the principles of genomic prediction are applied within SVS, predicting phenotypes for both plant and animal species. You can find a recording of the webcast on our site here should you be interested in checking it out or sharing with a colleague! The webcast garnered a… Read more »

End of Year VarSeq Bundles

      Delaina Hawkins    November 28, 2017    No Comments on End of Year VarSeq Bundles

This week we’re featuring several VarSeq bundles that are part of our end of year pricing specials! VarSeq CNV PowerPack – $15,995 We’ve made tremendous progress integrating CNV analytics capabilities into VarSeq this year. The PowerPack bundle is a great solution for those who are interested in combining SNV and CNV analysis. SVS-VarSeq Bundle – $7,995 If you’re a researcher or… Read more »

Our End of Year Bundles Are Back!

In case you haven’t heard the big news … our end of year bundles are back by popular demand! There’s a little something for everyone so if you’ve had your eye on one of our products now is the time to buy! SVS Single-User License – $2,995 Wouldn’t it be great to be able to easily perform complex analyses and visualizations on… Read more »

Customer Publications From Around the Globe

customer

It’s fascinating to hear the various ways our products are being used by customers all around the world. This month we’re featuring publications citing VarSeq, SVS and HelixTree which cover studies from Schizophrenia, Multiple Sclerosis and more. We hope you enjoy! Exome sequencing in schizophrenic patients with high levels of homozygosity identifies novel and extremely rare mutations in the GABA/glutamatergic pathways This… Read more »

GWAS Workflows with SVS webcast Q & A

VS-CNV Annotations

In case you missed our live event yesterday, I wanted to share a link to the webcast recording: New Enhancements: GWAS Workflows with SVS. There were several questions asked, so we’ve also shared the Q & A session below! Question: Are these enhancements priced as a separate feature?  Answer: No, SVS is a constantly evolving platform, so everything you see in this webcast is… Read more »

Webcast: New Enhancements – GWAS Workflows With SVS

genetic variants

We are dedicating our August webcast to explain the latest and greatest enhancements with GWAS workflows in SVS. Below you can find further details and registration information. We hope you can attend! Wednesday, August 9th, 2017 12:00 PM EST In this webcast, we will focus on the recent improvements to our research product SNP & Variation Suite. Over the past… Read more »

Understanding Your GWAS Signal with LD Scores

Genome-Wide Association Studies

When studying complex diseases that may have multi-genic contributions from across the genome, it is not uncommon to see what may appear like elevated correlation between your trait or other test variable and the SNPs across the genome. The problem is at first glance you won’t be able to tell if this is due to a population structure in your… Read more »

Recent Customer Success

      Delaina Hawkins    May 30, 2017    No Comments on Recent Customer Success

As usual, we would like to share some of the articles that our clients have published recently citing our software. These articles are incredibly diverse and interesting, and we hope you enjoy browsing through them. Fielding Hejtmancik and Lin Li of the NIH-NEI and colleagues published Homozygosity Mapping and Genetic Analysis of Autosomal Recessive Retinal Dystrophies in 144 Consanguineous Pakistani… Read more »