In advance of the Plant & Animal Genome conference in January in San Diego, CA, it made sense to showcase those working in Agrigenomics in the December Customer Success blog post! The published works this month also perfectly illustrate how SVS software can generate valuable GWAS and Genomic Prediction data for the agricultural industry. We look forward to seeing you… Read more »
Genetic testing labs deal with personal data in categories with the highest level of security requirements: personal identity and medical records. Given the liability and risk associated with a breach of this secure information, it is not surprising that many labs and institutes that aggregate genomic data prefer, if not require, on-premise analysis and storage solutions. Golden Helix is in… Read more »
As clinical genetic tests have been adopted as a critical enabler of precision medicine, the number of tests offered by clinical labs and the volume of tested patients has grown by orders of magnitude in the past five years. The Gene Testing Registry, managed by the NIH, documented a rise from 13,000 to 60,000 tests offered in the US market… Read more »
Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted. Although CNV events are rare in the human population, constituting approximately 10% of the human genome, they are also associated with being causal mutations for disease phenotypes. Because of this, it is important for clinical and research settings to identify… Read more »
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 »
The first two blogs in this series covered Sentieon’s somatic variant calling from Tumor with Normal (Part I) and Tumor without Normal (Part II). In addition to providing multiple somatic variant calling processes, users also have access to high-sensitivity scripts and full support for the GRCh38 reference assembly. Without going into excessive detail, this final blog of the series will… Read more »
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 »
If you have watched this blog over time, it would be no surprise that Golden Helix invests a lot in curating genomic annotations for use with our clinical and research analysis products. Often, we spend considerable time on the attention to detail necessary to ensure the best experience for any data source by cleaning, normalizing, documenting and then distributing it through our data annotation server. Many annotations… Read more »
November is the month where we pause to reflect on what we are thankful for. At Golden Helix, we are thankful for the many dedicated scientists and practitioners who are tirelessly working on new discoveries to enhance the lives of humans and preserve our food supply in the face of ever-changing conditions in agriculture. As always, we are proud to… Read more »
Our tutorials are a popular resource for prospective users. We have added a tutorial to help introduce customers to the ease and utility of the ACMG Guidelines incorporated in VSClinical. The ACMG Guidelines are a collection of 33 criteria that are used to determine a variant’s level of pathogenicity. VSClinical and VarSeq make it easy for users to sort and… Read more »
To recap what we have covered in this blog series thus far, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Part I of this series covered the variant calling workflow for tumors with matching normal samples. However, a common situation would be to call variants for a tumor sample without the normal…. Read more »
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 »
Our team has returned from the annual meeting of the Association of Molecular Pathology (AMP 2019), and, as always, I am grateful for all the wonderful experiences we are bringing back with us. The plenary sessions and talks were bountiful, and we were very impressed with the well-organized exhibition. Hats off to everyone involved in planning this great event! Innovation… Read more »
We have recently added a tutorial to help introduce customers to the ease and utility of the AMP Guidelines incorporated in VarSeq’s VSClinical package. The AMP Guidelines allow users to sort through available clinical evidence in a streamlined fashion to arrive at final classification and interpretation and then transfer that information into a clinical report. And the AMP Guidelines also… Read more »
As I mentioned in the first part of this series, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Utilization of a Tumor-Normal Workflow In addition to the fundamental process of alignment and variant calling, there are a few more steps that will improve the quality of your secondary analysis. Figure 1 (below)… Read more »
With October being recognized as Breast Cancer Awareness Month, the team at Golden Helix thought it would be appropriate to pay tribute to some of the publications that over the years, have contributed to the many discoveries made in breast cancer diagnosis, prediction, underlying causes, and case management. We are very proud to be a part of cancer research and… Read more »
Golden Helix works to keep incorporating and updating great somatic annotation catalogs for our VSClinical users. We currently have the updated version of one of the largest cancer databases from the International Cancer Genome Consortium, or ICGC. Version 28 has been improved by integrating ClinVar and CIViC clinical annotations, and as always, increasing the number of mutations listed. The current… Read more »
VarSeq 2.2.0 was released today and this a stable release full of upgrades and polishes. Some of the newer features include the ability to store and include AMP Cancer assessment catalogs on VSWarehouse, quicker accessibility to common annotations plotted in GenomeBrowse, and the addition of all of our standard templates for the GRCh38 genome assembly. Many of the polishes were… Read more »
As our team returns from another successful ASHG conference, I would like to reflect on the great memories, connections, and future plans that were made at this meeting. First, I will start by thanking everyone involved with the superb planning and execution of the conference. We are thankful to have this opportunity to connect with our customers, partners, and friends… Read more »
Our team is getting ready to head to Houston, Texas for the American Society of Human Genetics Annual Meeting (ASHG) 2019. We are looking forward to spending the week discussing genetics with new and familiar faces! If you are planning on attending, please stop by our booth and say hello! You will find the Golden Helix team in booth 601…. Read more »
