Using the GRCh38 reference assembly for clinical interpretation in VSClinical

Editor's Notes

• #3: The ACMG guidelines provide a set of criteria to score variants and place them into one of five classification tiers. Following the guidelines requires diving into the annotations, genomic context and existing clinical assertions about every variant. VSClinical provides a tailored workflow to score each relevant criterion, while also providing all the bioinformatic literature and evidence from clinical knowledgebases. This includes population frequencies, functional prediction scores, conservation scores, and effect prediction. Through standardized questions, automatically computed evidence, and historical context, VSClinical provides clinicians with everything they need to reach a final classification consistently and reproducibly, thereby reducing the subjectivity of the variant classification process. While a final classification of a variant requires the manual inspection of the sample’s clinical details, published literature and the content of existing related clinical interpretations, many criteria from the ACMG guidelines can be automatically computed with bioinformatic algorithms and specially curated annotation sources.  The work done in your lab to classify variants will be automatically included in future analyses. As the number of samples processed increases, the number of variants requiring classification will be reduced, along with sample turn-around time. Previously classified variants will be marked with their last evaluation date, allowing them to be accepted in the context of the current sample without extra analysis time. Look at 16 and 12
• #5: Golden Helix is a bioinformatic software and analytics company seeking to promote the genetic research and translational genomics community by creating high quality software to analyze large genomic datasets The company was founded in 1998 and was developed from the founders early work in pharmacogenomics at GlaxoSmithKline, who is still a key investor and solid partner to this day. Our earliest developed software HelixTree eventually evolved into our powerful research application software SVS. SVS provides a large collection of great analytical tools for GWAS, Genomic Prediction, and Large N studies just to name a few. Eventually, there was clearly a need to develop a clinical software solution for efficient, repeatable and most importantly accurate variant interpretation. With this concept in mind, VarSeq was created. With VarSeq, users have the ability to not only streamline their variant interpretation workflows but also automatically create customizable clinical reports from the results. It was no surprise then, that with increased workflow efficiency and the ever increasing amount of genomic data, a data storage solution was also needed. With our server based Warehouse solution we offer additional power in organizing projects in a central repository, sharing all the collected data and projects easily, and a simple but powerful querying ability from multiple elements of your variant analysis.
• #6: Our software has been very well received by the industry. We have been cited in over 1000 peer-reviewed publications and that’s a testament to our customer base.
• #7: Another is that we have customers in over 350 organizations globally. This includes clinics such as Sick Kids, or Cincinnati Childrens, top tier institutions including Stanford and UCLA, Genetic testing labs with Prevention Genetics and LineaGen, pharmaceutical companies such as Bayer, and Govt institutions like USDA.
• #8: One point that cant be stressed enough is that our software has become the quality product it is thanks to high usage and scrutiny from our users. Through this feedback and consideration from our users, we have developed the trust and experience necessary to support our claim of our high quality software. Not only do we rely on feedback from our users, but we also strive to be on the leading edge when considering both industry and community needs. This coupled with our desire to provide innovative, customizable, and quick solutions only reinforces that not only are you getting a quality product, but also software that remains cutting edge. Most importantly though, is the support you receive when using Golden Helix software. We do not hand you this software and let you free wishing you the best of luck. With the software comes the reassurance that users will have access to prompt support whether it is a simple question about installation or you would like training, we at Golden Helix are here to support our customers whole heartedly.
• #12: For the vast majority of clinical genetics, we care about genes, not genomes.
• #27: The ACMG guidelines provide a set of criteria to score variants and place them into one of five classification tiers. Following the guidelines requires diving into the annotations, genomic context and existing clinical assertions about every variant. VSClinical provides a tailored workflow to score each relevant criterion, while also providing all the bioinformatic literature and evidence from clinical knowledgebases. This includes population frequencies, functional prediction scores, conservation scores, and effect prediction. Through standardized questions, automatically computed evidence, and historical context, VSClinical provides clinicians with everything they need to reach a final classification consistently and reproducibly, thereby reducing the subjectivity of the variant classification process. While a final classification of a variant requires the manual inspection of the sample’s clinical details, published literature and the content of existing related clinical interpretations, many criteria from the ACMG guidelines can be automatically computed with bioinformatic algorithms and specially curated annotation sources.  The work done in your lab to classify variants will be automatically included in future analyses. As the number of samples processed increases, the number of variants requiring classification will be reduced, along with sample turn-around time. Previously classified variants will be marked with their last evaluation date, allowing them to be accepted in the context of the current sample without extra analysis time. Look at 16 and 12
• #28: Golden Helix is a bioinformatic software and analytics company seeking to promote the genetic research and translational genomics community by creating high quality software to analyze large genomic datasets The company was founded in 1998 and was developed from the founders early work in pharmacogenomics at GlaxoSmithKline, who is still a key investor and solid partner to this day. Our earliest developed software HelixTree eventually evolved into our powerful research application software SVS. SVS provides a large collection of great analytical tools for GWAS, Genomic Prediction, and Large N studies just to name a few. Eventually, there was clearly a need to develop a clinical software solution for efficient, repeatable and most importantly accurate variant interpretation. With this concept in mind, VarSeq was created. With VarSeq, users have the ability to not only streamline their variant interpretation workflows but also automatically create customizable clinical reports from the results. It was no surprise then, that with increased workflow efficiency and the ever increasing amount of genomic data, a data storage solution was also needed. With our server based Warehouse solution we offer additional power in organizing projects in a central repository, sharing all the collected data and projects easily, and a simple but powerful querying ability from multiple elements of your variant analysis.