The scientists in the Molecular Genetics Laboratory at Cincinnati Children’s Hospital Medical Center understand the importance of high-quality interpretation tools. After all, as a CAP- and CLIA-certified facility, they deliver results back to physicians which can be used to help guide patient diagnosis and treatment. So when they added whole exome sequencing to the lab’s service repertoire, the scientists chose Ingenuity® Variant Analysis™ from QIAGEN to perform trusted interpretation and filtering of the data.
Ammar Husami, genomic systems analyst at the Molecular Genetics Laboratory, set up the original sequencing analysis pipeline using an in-house variant filtering and classification method. Now that exome sequencing has been incorporated into his purview, he makes routine use of Ingenuity Variant Analysis — today, he has run variants from some 200 exomes through the application. Husami says that setting up Variant Analysis was simple. “Within a few minutes of data transfer and annotation, I started to interpret and confirm possible genotype-phenotype associations,” he says.
Since joining the lab full-time in 2009, Husami has focused on providing medical insights to physicians treating children with immunodeficiencies and other inherited disorders, such as hearing loss, metabolic diseases, and skin disorders. His tools include tried-and-true single gene tests as well as gene panel tests, which offer answers to the majority of cases that come his way.
But for more complex cases, or for those in which gene panels do not reveal an answer, he has begun to use exome sequencing to help track down the causal genetic variation that might explain an unknown medical condition. “Chances are if we don’t find it with gene panels, we’ll find it with exome sequencing,” says Husami, whose background is in biomedical engineering.
The Molecular Genetics Laboratory is outfitted with both high-throughput and benchtop sequencers, and Husami expects the facility will eventually perform whole-genome sequencing for hospital patients. As genetic analysis has expanded beyond screens for individual genes, more hospital investigators have taken an interest in the lab’s rapidly growing capabilities. “We collaborate with other departments here, such as rheumatology and immunology,” Husami says. “With the launch of whole exome sequencing, we’ve really expanded and started to work with more departments in the hospital.”
Need For Knowledge
Getting ready for clinical exome sequencing meant that Husami required an interpretation tool that could handle more information than the lab’s custom-built data set, which was developed for single-gene or gene panel tests. “I realized very quickly the importance of having a knowledge base, especially for whole exome sequencing,” he says. “Having all of that information available is key for making an interpretation.”
“There’s so much information — how the analysis was performed, how many variants were filtered, the different flow — and the fact that [Variant Analysis] provides a summary that is easy to interpret is a big advantage.”
Husami was already familiar with Ingenuity products, having previously used Ingenuity Pathway Analysis (IPA). He brought in Variant Analysis to test and confirm predicted associations for whole exome sequencing results; Husami compared findings to those generated by in-house variant filtering tools to make sure he felt completely confident in the results.
Without Variant Analysis, Husami says he would have to perform countless time-consuming queries of various databases to try to gain this level of confidence. As he is often using the tool to try to deliver a diagnosis for a patient with an unknown disease, “saving time is a key advantage,” he says.
Context is Key
Husami has come to rely on the Ingenuity Knowledge Base that powers these interpretation products. “The redundancy of representation in Ingenuity Knowledge Base provides for very flexible testing,” he says.
By working closely with requesting physicians, he can incorporate their knowledge about the disorder into the analysis, using that information to direct his attention for “which pathways, proteins, and biological entities are more relevant in the context of what I’m looking for,” he says.
When following up on variants and checking into pathways, he says, “The Ingenuity Knowledge Base provides the link that sometimes is not easily accessible.” Because the repository is phenotype-based and easy to query, he adds, the tool allows him to make sense of complex biological associations from exome sequencing variant results.
Using Variant Analysis also makes life easier when delivering results. “The best advantage that I’ve found is that it’s really useful for being able to communicate the results to a physician or investigator who can go through the findings, interpret them, and send me some feedback,” Husami says. “There’s so much information — how the analysis was performed, how many variants were filtered, the different flow — and the fact that it provides a summary that is easy to interpret is a big advantage.”
Patients and families from around the world come to Cincinnati Children’s Hospital Medical Center to seek treatment for rare pediatric diseases. Husami plays an important role in that process by incorporating the best possible tools for analyzing and interpreting whole exome sequencing data.