Clinical Interpretation of Genomic Variants from Large Next-Generation Panel (NGS), Whole Exome Sequencing and Whole Transcriptome Sequencing

The firm-fixed-price purchase order was not awarded competitively. UNIQUE QUALIFICATIONS OF THE CONTRACTOR This purchase order builds on prior purchase orders to N-of-One and then Qiagen, who acquired N-of-One in 2019. Qiagen is the primary name referred to throughout this justification. Under previous purchase orders, Qiagen, in collaboration with NCI, CCR, LP, provided a software system to meet the analysis requirements and needs for clinical reporting. Implementation of the current system has been ongoing for over a year and as a result, Qiagen has helped analyze and produce reports for over 289 cases. In meeting LP’s clinical needs, Qiagen’s Knowledge Base (database) has provided a breadth of the biology and chemical knowledge, accuracy, and structure of content. The Qiagen Knowledge Base also curates’ drug-labels, clinical case counts, and clinical trials and currently has over 4,100,000 human phenotype-associated findings. The knowledge acquisition and extraction process for the Qiagen Knowledge Base is protected by multiple US Patents, has been operational for over 18 years, and is recognized as an industry standard. Continued support by Qiagen is required to tailor reporting to clinical needs and shorten reporting turnaround times. If the laboratory were to switch to a different vendor, there would be a complete breakdown of the reporting workflow currently in place, leading to negative clinical effects. The existing tools and user interface have been customized by Qiagen to fit into the laboratory’s pipeline. This allows staff to upload data files from LP’s laboratory equipment directly into the Qiagen database. The new requirement will be facilitated using the same methodology and expertise to ensure consistency with reporting and timely delivery. Any efforts to identify a different vendor and tool would pose additional costs to the government, significant delays in the workflow, and risk the overall work performed by NCI, CCR, LP.