CCR Sequencing Facility

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The primary mission of the Sequencing Facility (SF) at the Frederick National Laboratory (FNL) is to support and advance cancer research by leveraging high-throughput sequencing technologies, ensuring that the National Cancer Institute (NCI) remains at the forefront of next-generation sequencing innovation. The SF provides investigators from the Center for Cancer Research (CCR), NCI, and National Institute of Allergy and Infectious Diseases (NIAID) Division of Intramural Research (DIR) with access to a comprehensive suite of cutting-edge platforms, including two Illumina NextSeq 2000 systems, two state-of-the-art NovaSeq X Plus sequencers, the latest PacBio Revio system, two Oxford Nanopore PromethION P24 sequencers, Bionano Genomics optical mapping, and single-cell technologies from 10x Genomics and Mission Bio. As of July 11, 2025, the key accomplishments of the CCR Sequencing Facility (CCR-SF) included: 1) Sequenced more than 9,452 samples for 163 NIH investigators, 2) Generated and delivered over 653 trillion base pairs of high-quality sequencing data, 3) Co-authored five publications in peer-reviewed scientific journals. 4) Developed a new and improved in-house ATAC-Seq protocol; tested and validated several new library preparation kits to substantially reduce turnaround time and sequencing costs, 5) Successfully tested and implemented the NIH LabArchives Electronic Lab Notebook (ELN) system to align with NIH data management policies. Highlights of the Illumina short-read Sequencing Team included: 1) Processed a total of 9,149 samples for 134 NIH investigators, 2) Validated and implemented the Takara SMARTer Stranded Total RNA-Seq Kit v3 Pico for ultra-low input RNA samples, 3) Team members cross-trained with the Oxford Nanopore Technologies (ONT) Long-Read team to expand technical capabilities. Highlights of the Long-Read Sequencing Technology Team included: 1) Processed 303 samples for 29 NIH laboratories, 2) Successfully implemented PacBio SPRQ reagents across all applications, reducing sequencing costs and increasing throughput to 15.1 million reads per run. Highlights of the Bioinformatics (IFX) Team included: 1) Delivered platform software upgrades for NovaSeq X Plus, PacBio Revio, ONT PromethION P24, and Bionano Saphyr, 2) Completed 442 analysis requests from 226 NIH investigators, delivering over 653 trillion base pairs of data, 3) Developed 12 new data analysis pipelines to support novel sequencing protocols, 4) Collaborated with laboratory teams to design and build a new in-house Laboratory Information Management System (LIMS) to enhance data tracking, reduce operational costs, and meet NIH IT security requirements. This integrated, multidisciplinary approach allows the CCR Sequencing Facility to remain at the forefront of genomic technology, driving scientific discovery and enabling NIH researchers to address some of the most complex questions in cancer and infectious disease biology.