Golden Helix has a long history of developing a high-quality NGS-based CNV caller. This has become even more apparent with our latest publication, where we teamed up with Twist Bioscience to demonstrate VarSeq capability of calling large copy number variants utilizing their clinical whole exome sequencing data. You can access the recent publication here: Analyzing Performance of Twist Bioscience Exome… Read more »
We’re buzzing with excitement and couldn’t wait to share some groundbreaking news with our community: VarSeq 2.5.0 has officially landed, and it’s here to transform your NGS lab experience! What’s New with VarSeq 2.5.0? VarSeq has always been about innovation and pushing the boundaries, and the 2.5.0 update is no exception. We’ve listened to your feedback and supercharged VarSeq with… Read more »
Calculating Residual Risk Residual risk is the risk remaining after a negative screening test. At the core of the calculation of residual risk resides Bayes’ Theorem. This theorem is used to calculate the probability of an outcome given the probability of events required for that outcome. The probability of the required events is compounded to calculate the combined probability of… Read more »
Last month, the researchers at Google DeepMind announced the release of AlphaMissense, a new missense prediction algorithm that leverages the protein structure prediction model AlphaFold to distinguish between benign and pathogenic missense variants (Cheng et al., 2023). AlphaFold is a model for the prediction of protein structures from amino acid sequences. During the development of AlphaMissense, the AlphaFold model was… Read more »
Discover how to enhance collaboration in VSClinical by sharing variant scores and assessment catalogs through the strategic relocation of the AppData folder. A subtle but powerful utility of VSClinical concerns the ability to share variant scores between users on the same account. What I mean by that is, leveraging the location of the AppData folder, so that users are writing… Read more »
A new VSPipeline command, set_data_folder_path, designed to bolster consistent input usage. By introducing this innovative command, we aim to empower users with improved data organization, flexibility, and standardization for their clinical cases and analyses. Embracing this command will not only support reproducibility but also ensure accountability, ultimately paving the way for better-informed patient care decisions. Managing Annotations and References in… Read more »
One of the inherent realities of next-generation sequencing is the ongoing updates to the human reference genome—one of the strongest recommendations to take the original sequencing data and remap to the latest genome assembly. However, there are several reasons why remapping may be impractical. So, an alternative solution is needed to convert the data running through an initial mapping to… Read more »
Thank you to those who attended our recent webcast, “PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq”. For those who could not attend, you can find a link to the recording here. This webcast covered upcoming improvements to the PhoRank phenotype-based gene ranking algorithm based on literature published in the years since the algorithm’s development. The PhoRank Algorithm When performing… Read more »
In this blog, we will be covering new assessment catalogs and how they work to improve saving and tracking variant interpretations. VarSeq is a variant analysis tool that effectively analyzes single nucleotide (SNVs) and copy number variants (CNVs) in both cancer and germline workflows. Because VarSeq enables such diverse variant analysis, there are many research labs and institutions that evaluate… Read more »
Our latest VarSeq release is one of the largest we’ve ever had, boasting an extensive list of new features and improvements. As part of this release, we have dramatically expanded our support for splice site analysis. This includes improvements to our novel splice site algorithm and support for splice site effect prediction along with several other small improvements. Novel Splice… Read more »
The detection and interpretation of Copy Number Variants (CNVs) is vital for the clinical evaluation of individuals with a wide range of disorders. Golden Helix has remained at the forefront of CNVs in Next-Gen Sequencing (NGS) data since 2016 with the release of VS-CNV, our solution that allows you to both detect and analyze CNVs directly from NGS data. Earlier… Read more »
An under-appreciated area of complexity when looking into the field of genetics from the outside can be found in genes and transcripts. Alternative splicing allows eukaryotic species to have a wonderfully powerful genetic code, resulting in multiple protein isoforms being encoded in a single section of DNA. But when it comes to variant interpretation, different transcripts can result in widely different predicted… Read more »
ClinVar is the NCBI variant database that focuses on the categorizing of variant alleles and their interpretation from a clinical standpoint. This has made it a great resource, especially for those seeking variant allele disease correlations and pathogenicity. And this all worked fairly well, but it was changed… Previously, the ClinVar variant track annotation took some time to curate due… Read more »
We have a lot to thank the 1000 Genomes project for in the genomics community. By the collaborate efforts of many researchers and organizations, the project produced not only the first catalog of rare human variation but in the process standardized many things we take for granted, such as the VCF and BAM file formats. The variant frequencies of the… Read more »
With the recent release of VarSeq 1.4.7, we have expanded the concepts of our popular assessment catalog to include CNV and other region-based records and not just variants. To match these capabilities, we have made a major update to VSWarehouse that supports these new record types in the centrally hosted and versioned Catalogs and Reports. Review of the VSWarehouse Genomic… Read more »
September 27, 2017 12:00 PM, EDT While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants. Golden Helix has developed and validated with our clinical partners a specialized NGS-based CNV caller capable of detecting… Read more »
Earlier this year we released our own optimized and integrated BEAGLE implementation for SVS based on the BEAGLE 4.1 and optionally 4.0 algorithms. One of the commonly requested features since that released was to expand the algorithm implementation to be considerate of the parent-offspring relationship between samples to inform and improve the accuracy of the haplotype phasing. With this information,… Read more »
In our latest VarSeq release, we updated our PhoRank algorithm with the ability to specify OMIM phenotype terms not present in HPO, as well as a general update to the algorithm to improve the results. In this post, we review the fundamentals of how PhoRank determines the ranking of genes in your VarSeq projects based on your input phenotype terms… Read more »
The new Annotate and Filter algorithm is now available with the release of SVS 8.6.0, see the release notes for full details on all new and updated features. To access this new functionality, you simply need to update your SVS installation to the new version. The update can be done by clicking the Update Available link at the bottom of… Read more »
When the new human reference genome was released over two years ago, it was hailed as a significant step forward for next generation sequencing. Compared to GRCh37, the new GRCH38 reference assembly fixed gaps, repaired incorrect sequences and offered access to sections of the genome that had been previously unaccounted for. Despite these improvements, adoption of the new assembly has… Read more »
