ASHG 2016 is in our rear mirror. Again, it was bigger and better than the previous year. The conference hosted over 9,000 visitors from 66 countries. This gave the event a level of vibrancy that was evenly matched by the wonderful ambiance of the city of Vancouver. Nestled in between the two conference centers was a little pier offering spectacular views.
For us as a company, the conference was a success. Our booth was well attended over the three days, and we had four demos every day on various topics such as:
- Genetic Data Warehousing
- Copy Number Variation Analysis
- Clinical Reporting
- Genome-Wide Association Studies
- Premium Annotation Sources in SVS
Genetic Data Warehousing
Genetic data warehousing is becoming more important as Next-Generation Sequencing is taking off in the clinic, creating significant data management issues for clinicians, scientists and IT professionals alike. How can we retain the massive amounts of data coming out of clinical pipelines in a way that enables labs to systematically build a knowledge base, capturing the insights clinicians gain on a day to day basis while analyzing the genetic information of their patients? What infrastructure is required to alert medical personnel to new research that could potentially alter medical decisions? And how can we embed the work that is being done in the labs into general hospital workflows? Golden Helix’s VSWarehouse is a pivotal technology that can help in all of these areas.
Copy Number Variation Analysis
Copy Number Variations (CNVs) play an important role in human health and disease, and the detection of CNVs in clinical samples has the potential to improve clinical diagnoses and inform treatment decisions. Yet until now, if you wanted to have CNVs on your targeted gene samples, you would need an alternative assay such as Chromosomal Microarrays (CMAs). In our in-booth demo, we showed how to conduct CNV analysis with VarSeq:
- Designed specifically for targeted gene panels and exomes
- Builds on and goes beyond best practices of existing NGS calling methods
- Has the precision to detect events ranging from a single-target to a whole chromosome
- Takes advantage of the variants in target regions and their allele frequencies
- Designed and being validated in partnership with a clinical lab on clinical samples
- Integrates seamlessly with the VarSeq interpretation workflow and visualization
Via VSReports, VarSeq has the ability to generate clinical-grade reports. These reports are fully customizable and contain focused and actionable data. VSReports ships with report templates that are modeled off of the ACMG guidelines, the de-facto gold standard for clinical reporting. Templates for both hereditary and cancer analysis are included free of charge.
Genome-Wide Association Studies
SVS offers a powerful and straightforward way of testing for genotypic association against either dichotomous or quantitative traits using one or more statistical measure under any one of several genetic model assumptions. These tests can be run individually or simultaneously while also correcting for stratification and applying multiple testing corrections (including permutation testing). Supported genetic models include allele comparison, genotype comparison, and the additive, dominant and recessive genetic models. Test statistics include the correlation/trend test, the Armitage trend test (including the exact Armitage trend test), Pearson’s chi-squared test, Fisher’s exact test, Odds Ratio with confidence intervals, analysis of deviance (ANODEV), the F-test and linear or logistic regression.
Premium Annotation Sources in SVS
During the week of ASHG 2016 we also released SVS 8.6.0. This new version of SVS comes with an updated Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Now, annotations can be run against gene, interval, variant and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters. While our public annotation repository has been previously available in SVS, they are now more powerfully integrated with more advanced filter and annotation control.
It was a true pleasure meeting with existing clients and partners. Also, we saw a lot of new faces visiting the Golden Helix booth. It was a wonderful experience to come to Vancouver. We hope to see everybody next year again at ASHG 2017 in Orlando, Florida.