Category Archives: Clinical genetics

Q&A from the VSWarehouse Launch Webcast

VSWarehouse

Yesterday, it was my pleasure to share in a live webcast our integrated solution for genetic data warehousing, VSWarehouse. If you missed the webcast live, feel free to check out the recording. Although we had a great set of questions at the end of our presentation, we didn’t have time to answer all of them, so here is a selection of… Read more »

Match Gene List algorithm not just for genes

Gene Match

The most common use of the VarSeq Match Gene List algorithm of course is to determine if the variants in your data set are contained within your genes of interest. As an example of this, say you are working with a whole exome trio and only want to consider those variants that are contained within the 56 genes recommended by… Read more »

Handling Singletons & Complex Pedigrees with Gene Count Algorithms

Complex Pedigrees

As VarSeq’s adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently. While having both parents provides the maximum power to discover de novo mutations and recessively inherited variants, it is not always possible to contact… Read more »

Tumor-normal demo project comes to VarSeq

Compound Heterozygous

With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis. This project contains an exome pair (Normal-N990005 and Tumor-T990005) from the Gastric Cancer study Exome sequencing of… Read more »

A New and Unexpectedly Powerful VarSeq Feature

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With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of marking primary, secondary or other sets of variants for a… Read more »