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OMICS Technology Facility

Mission

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the investigators and collaborators of the Genetics Branch (GB).

Areas of Expertise

Genomics and other OMICS technologies are central domains of expertise in the GB and encompass both wet lab and bioinformatics activities.

Wet Lab

  • DNA Sequencing Technologies.  We provide assistance to GB investigators on their DNA sequencing needs, including whole genome, whole exome, targeted genome, short-read (Illumina) and long-read (multiple technologies) and cost-effective analysis of copy number variation of cancer cell genome.
     
  • Clinical Cancer Genomic Analysis.  We have extensive clinical trial experience in developing custom assays and in validating the assays for clinical trials. The supported areas include comprehensive analysis of cancer genomics for oncogenic drivers from noninvasive samples such as cell-free DNA from blood samples. We have also developed methods for blood-based monitoring of mutations throughout treatment cycles.
     
  • RNA Sequencing Technologies.  We support comprehensive RNA transcriptome analysis, including long-read and short-read sequencing, gene and transcript expression, alternative splicing, mutation detection, TCR and BCR analysis, deconvolution methods and detection of fusion genes.
     
  • Epigenetics.  We provide expertise in methods to detect protein DNA interactions and epigenetic assays, including HiC, HiChIP, ChIP-Seq, ATAC-Seq and Cut-&-Run and Cut-&-Tag based sequencing.
     
  • Clinical Proteomics and Clinical Biomarker Development.  We have extensive experience in developing and validating clinical biomarker assays for oncology clinical trials which meet NCI Biomarker Review Committee requirements for integrated/integral biomarkers for NCI-sponsored trials. Our capabilities include the support of pharmacokinetics of protein and antibody-based therapeutics, and pharmacodynamics including monitoring the activity of a new agent, surrogate biomarkers for clinical responses, monitoring inflammation, determining minimum residual disease and the detection of drug resistance mutations.
     
  • Other Custom-Need Assay Development.  Other potential applications would include single-cell RNA-Seq, CITE-Seq, single-cell DNA-Seq and single-cell ATAC-Seq. 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 technologies, including whole exome and genome sequencing, whole transcriptome sequencing, Chip-Seq, Cut-&-Run and Cut-&-Tag. The team is expanding its data analytics capabilities into single-cell, three-dimensional (3D) genome and spatial transcriptomics.
  • 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 oncogenomics 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 machine learning (including artificial and convolutional neural networks) to study human cancers.
  • High-performance Computing in Bioinformatics.  We enable GB researchers to effectively use high-performance computers (HPCs) such as Biowulf, AWS cloud computing and the Amazon Genomics Command Line Interface (CLI) tools in their analyses.
  • Cancer OMICS.  We jointly work with the GB OMICS wet lab group; the team aims to streamline sample management, OMICS data generation, quality control, data analysis, and delivery of the results, bringing bioinformatics and OMICS technologies to the fingertips of GB researchers.
  • Data Management.  We manage large-scale raw and processed next-generation sequencing (NGS) datasets using the NCI High-performance Computing Data Management Environment (HP DME).
  • 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.

Project Request and Analysis Management

For Wet Lab requests contact Dr. Liang Cao (caoli@mail.nih.gov)

For Bioinformatics requests contact Dr. Patrick Zhao (patrick.zhao@nih.gov) and submit at Analysis Management Portal (AMP).