Pipelines for Patient Care

Research objectives

The Molecular Diagnostics Laboratory (MDL) is dedicated to creating providing cutting-edge genomic diagnostics driving the personalized medical care of patients in the M Health Fairview system. The lab includes technologists and genetic counselors from M Health Fairview and physician faculty members from the Department of Laboratory Medicine and Pathology at the U of M. MSI is also a crucial member of this multi-disciplinary team.

MSI PIs from the Department of Laboratory Medicine and Pathology involved in this project include Associate Professors Sophia Yohe and Bharat Thyagarajan, and Assistant Professor Andrew Nelson.

How we worked with the researchers
MSI bioinformatics analysts develop Next Generation Sequencing (NGS) analysis pipelines that provide clinical-grade variant calling and copy number analysis from numerous DNA-seq platforms. They work with the clinicians to develop and validate pipelines that meet rigorous clinical testing standards and maintain these validated pipelines during routine clinical use. MSI staff in the Research Informatics Solutions (RIS) group who are working on this project in 2021 include Dr. Sarah Munro (manager, Lab Medicine and Pathology group), and Lab Medicine and Pathology bioinformatics analysts Dr. Todd Knutson, Dr. Rebecca LaRue, Dr. Christine O'Connor, and Dr. Jeffrey Miller. Edward Munsell from the Advanced Systems Operations group and Jaime Vega from the User Gateway Group are active in supporting the pipeline infrastructure. Dr. Christine Henzler (manager, RIS) and scientific computing consultant Dr. Ham Lam from the Scientific Consulting Solutions group made significant contributions to the project in their previous roles in the Lab Medicine and Pathology group.


There are currently eight active pipelines for inherited disease and oncology genetic testing and two whole-genome pipelines are in development for both sequence and structural variant calling. Both new whole-genome pipelines use high memory nodes at MSI.