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Sunquest Genetics

GeneInsight at the Mount Sinai Genetic Testing Laboratory

The Challenge of Information Management with Next Generation Sequencing

Everyone is thinking about the challenges right now because tests are becoming more and more complex. I think informatics infrastructure is critically important. Since most of the higher-complexity tests are next generation sequencing (NGS)-based and usually generate large amounts of sequence data across many genes, it’s really important that the process be as automated as possible. From data generation through the pipeline, even up to the point where you’ve identified a variant and are confirming the findings – a good informatics infrastructure can streamline the process so that you don’t need to sift unnecessarily through large amounts of data.

Part of having robust informatics is building out your bioinformatics. There are some interesting tools available that aggregate information from multiple databases and provide you a score for the likelihood a variant causes disease. People are also starting to think about effectively combining those sources into one tool so you don’t have to look at five or six different databases. Having easy and centralized access to all of the relevant analysis tools, variant databases, population sequencing data and internal databases is essential; otherwise the workflow becomes very cumbersome.

Variant Information Database

VariantWire is a data sharing initiative that leverages the GeneInsight IT infrastructure and is critical for data sharing and to furthering the field of clinical genomics.  Understanding the relevance of the variants that are identified by large scale sequencing is a real challenge. Data sharing is critical to patient care because no single laboratory is going to have all of the information, especially when we move to whole exome sequencing as a first tier test. In the same respect, no individual laboratory is going to have the kind of test volume to have a large enough database to easily classify variants for every single gene. Right now, ClinVar is very helpful, we are using it all the time. It will only improve when as more information is added.

Data sharing among the VariantWire participants is going to be very helpful to the members of the network. For example, one laboratory may have a lot of data on a particular disease and group of genes and another laboratory has a different set, and together they have a great data set that’s more comprehensive. I definitely think that being part of VariantWire is beneficial to our lab.

About the Sunquest and GeneInsight collaboration

With GeneInsight and a long term collaboration with Partners, Sunquest is building a next generation genomics system that will reduce the cost and complexity of precision medicine and provide the market with an IT tool kit for implementing and integrating genomics into routine diagnostic workflows.

Lisa Edelmann

ASSOCIATE PROFESSOR, DIRECTOR, MOUNT SINAI GENETIC TESTING LABORATORY, ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI. Dr. Edelmann is the director of the Mount Sinai Genetic Testing Laboratory and associate professor at the Department of Genetics and Genomic Sciences of Icahn School of Medicine at Mount Sinai.