March 13, 2018

Combining CNV and SNV Analysis for Genomic Diagnostics on a Single Sample and Platform

Genome Webinar

Laboratory Specialist, Clinical Genetics, University Medical Center Utrecht (UMCU)


This webinar shares how clinical genetics labs can integrate cytogenetics and molecular data to assess abnormalities using a single sample on a single workflow platform.

The current standard of care in genomics diagnostics laboratories is advancing toward array testing and whole exome sequencing on a single sample. Additionally, labs are shifting to the analysis of all molecular events for a patient sample – whether structural (CNVs, deletions, duplications, LOH regions, translocations) or molecular (SNPs, insertions, deletions). Labs do this because they are confident the diagnostic yield of combined CNV / NGS analysis exceeds that of each individual assay type, making 1+1=3.

Moreover, historically, the cytogenetics lab and the molecular lab were separate domains, within different groups at the lab or hospital. Cartagenia Bench Lab software, which was acquired by Agilent in 2015, catered to these different customer types with separate applications. While labs that did both arrays and sequencing could make the modules talk together and collaborate, they were not tightly integrated.

Today, with Alissa Interpret, the next evolution of Cartagenia Bench Lab recently released by Agilent, array data and WES data can now be integrated for a single patient sample, allowing for combined CNV/SNV analysis on a single workflow platform.

In this webinar, Ellen van Binsbergen, a laboratory specialist in clinical genetics at the University Medical Center Utrecht (UMCU) in The Netherlands, shares how Alissa Interpret was used in a case of multiple skeletal abnormalities to assess data from CNV analysis via SNP array and from WES analysis. By jointly triaging, classifying, and curating molecular and structural variants, she shows how UMCU was able to pinpoint variants inherited from the father AND deletions in the maternal allele – all yielded from a single sample, on one platform.

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