From research genomics to clinical genetics: Insourcing next generation sequencing in a pediatric and women’s hospital

Abstract

Abstract Introduction/Objective The Sidra Medicine Clinical Genomics Laboratory (CGL) offers rapid and cost-effective next- generation sequencing (NGS) solutions such as Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) which support various research initiatives in Qatar. With the current worldwide trend in precision and personalized medicine, the Pathology Genetics (PG) division is required to provide in-house diagnostic genetic testing to clinical patient groups. The main objective of this quality initiative project is to decrease the cost of NGS send-out tests and to perform patient testing in-house. The CGL NGS workflow and processes must be validated to comply with the clinical accreditation requirements of the College of American Pathologists (CAP). Methods/Case Report Assay performance metrics are considered for the validation of the Illumina NovaSeq 6000 NGS platform. Sample library preparation is performed in PG while sequencing and data analysis is based in CGL. NGS quality assurance in CGL involves the use of Illumina PhiX control mixed with the pooled library. To maintain the high throughput and low-cost NGS approach, Illumina S4 flow cells are used with efficient library pooling techniques. The TAT of clinical samples for WES and WGS analysis in CGL is around 14 days which includes sequencing, data conversion, and bioinformatics. Results (if a Case Study enter NA) A Service Level Agreement (SLA) between Sidra Research and Sidra Pathology was created to define the workflow and services provided by both departments with clear lines of responsibility and accountability. A quality manual is also written to describe the QMS of the genomics laboratory and outlines the various NGS services offered. CGL protocols are transferred to CAP-approved SOP templates for standardization with pathology documentation. For quality improvement, the NGS workflow in CGL is continuously developed to improve the data produced and TAT. Conclusion The collaboration between the two departments maximized the available infrastructures of Sidra Medicine, saved costly send-out tests, improved the TAT of genetic analysis, and most importantly enhanced healthcare outcomes and related clinical diagnostics in alignment with the National Health Strategy (NHS) of the country. Accreditation propels good QMS in laboratory services hence this quality initiative fulfills Sidra Medicine’s vision to provide total precision diagnosis and personalized medicine leading to the delivery of exceptional care to rank amongst the top medical centers internationally.