Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators.
Wet Lab
• Single cell isolation from fresh, frozen and FFPE tissue
• DNA/RNA extractions from fresh, frozen, FFPE tissue, and tissues preserved by other methods
• Cell free circulating DNA from plasma and serum
• Quality assessment of nucleic acids by spectrophotometry, fluorometry, qPCR, capillary electrophoresis, digital droplet PCR
• Next-generation sequencing (NGS) library preps
• Sequencing (Whole genome sequencing including low pass (WGS) and whole transcriptome sequencing (WTS), whole exome sequencing (WES), panel, low-pass WGS for copy number variations)
• ChIP-Seq, Cut&Run
• Meso scale discovery (MSD) protein detection
• Fluorescence in situ hybridization (copy number evaluation for specific genes, fusion or break-apart probes)
• miFISH (novel method to hybridize, scan and enumerate up to 35 multicolored FISH probes within the same nucleus, can evaluate hundreds to thousands of cells)
• Spectral karyotyping (SKY- visualizing each chromosome in a specific color to decipher complex karyotypes)
• Custom-Need Assay Development: Other potential applications would include single-cell RNA-Seq, CITE-Seq, single-cell DNA-Seq, and single-cell ATAC-Seq, as well as long-read WGS and WTS. There are plans to introduce new biological technologies, such as single-cell enhancer mapping combined with scRNA-Seq, and new proteomics-based assays.
Bioinformatics
• Data Analytics. Currently, we offer integrated OMICS data analytics support and facilitate the interpretation of large-scale omics data from short- and long-read NGS, including WES and WGS, WTS, ChIP-Seq, Cut&Run and Cut&Tag, and single-cell technologies. The team is expanding its data analytics capabilities into three-dimensional (3D) genome profiling and spatial transcriptomics and proteomics.
• Bioinformatics Research and Development. We conduct need-based bioinformatics research and development, such as implementing bioinformatics pipelines to meet new data analytics demands.
• Omics Data Integration and Presentation. We develop and maintain cancer genomics databases for data integration and web-based visualization. These provide biologists, physicians, and trainees with easy access to omics data.
• Big Data and Data Science. We facilitate the GB investigators’ increasing utilization of public datasets, and a future direction will include the development of deep/machine learning (including artificial (ANN) and convolutional neural networks (CNN)) to study human cancer data.
• High-performance Computing in Bioinformatics. We enable GB researchers to effectively use high-performance computing clusters (HPCs, i.e., Biowulf), AWS cloud computing, and the Amazon Genomics Command Line Interface (CLI) tools in their analyses.
• Data Management. We manage large-scale raw and processed next-generation sequencing (NGS) datasets using the NCI High Performance Computing Data Management Environment (HPC DME).
• Data Submission to Public Databases. We provide assistance to PIs to upload data to public resources such as dbGaP, GEO, Imaging Data Commons, Genomic Data Commons, Proteomic Data Commons, and others.
• Hands-on Bioinformatics Training and Consulting. We provide training for GB staff and trainees in performing their own analysis. The team also advises researchers on experimental design and recommends tools and methods for data processing and interpretation.
• SQ120-MSD protein detection (https://www.mesoscale.com/en/applications/oncology_and_cancer)
• Digital droplet generator and Digital droplet reader (BioRad QX200 Droplet Digital PCR System)
• Bioview Automated Spotcounting microscope (FISH)
• Leica ThunderImager for FISH and Brightfield
• ASI Spectral Karyotyping microscope (SKY)
• Maxwell RSC instrument
• NextSeq 500 and NextSeq 2000 Illumina sequencers
• Agilent Bioanalyzer
• Covaris Sonicator
Collaborators outside the Genetics Branch are welcome, but proposals should be collaborative with a GB PI to access the GB OMICS services.