The Comprehensive Genomics shared resource offers a full portfolio of translational research services including sample preparation and extraction, genetic and genomic analytical services (gene expression profiling, genotyping, and next-generation sequencing), and bioinformatics/analysis services. Genomics is located within RUCDR on the Piscataway campus of Rutgers University in over 45,000 sq. ft. of laboratory, storage, and office space.
Staff review the experimental design with investigators, including sample preparation and quality, optimal sequencing platforms, issues regarding breadth and depth of sequencing, and choice of analytic pipelines. Genomics staff members, often in coordination with staff from the Biomedical Informatics Shared Resource, are engaged in all stages of experimental design, data acquisition, processing, and analysis.
Sample Prep and Extraction
Preparation, tracking and processing of blood, tissue, and other sample types to support laboratory and diagnostic analyses are offered through a variety of semi- and fully-automated processing methods tailored to sample type, collection vessels, and project criteria. Genomics uses QIAgen technology for extraction services, preparing DNA, RNA, and miRNA for downstream processing in a highly automated format. Extracted samples are purified and normalized to optimum concentrations specific for the intended service. Genomics has the capability of extracting high-quality nucleic acids from a number of different sources including whole blood, plasma, buffy coat, fresh frozen tissue, formalin-fixed paraffin-embedded tissue and cell pellets. Multiple solutions for the robust amplification of precious nucleic acid samples, as well as restoration of degraded or compromised material, are available. Whole-genome and whole-transcriptome amplification chemistries enable highly uniform and unbiased enrichment, preserving relative abundance and allelic balance for downstream genetic analysis.
Genomics offers state-of-the-art technologies to support the processing, tracking, and analysis of research samples. RUCDR-Infinite Biologics provides a Laboratory Information Management System (LIMS) which tracks the life cycle of the sample as it moves through each stage of a service workflow within the laboratory and automatically updates sample information to provide a fully integrated individual sample tracking system across bioprocessing services. A document management system, Qualtrax, is used to monitor and standardize protocols for sample processes, as well as personnel training and certification documents.
Genomics provides massively parallel next-generation sequencing services, whole genome sequencing, whole exome sequencing, RNA-Seq, ChIP-Seq, small RNA-Seq, and targeted sequencing (amplicon based on capture baits) using Ion Torrent, Illumina MiSeq, HiSeq2500 and NextSeq platforms. Comprehensive service bundles include nucleic acid extraction, integrated sample quality control, and construction of sequencing libraries. Whole transcriptome amplification services are available for limited amounts of starting RNA. Sample preparation for next-generation sequencing platforms, including library preparation and emulsion PC, are performed according to strict protocols to ensure adequate sequence reads.
For analysis of DNA methylation, services include whole genome bisulfite sequencing and reduced representation bisulfite sequencing. CHiP-seq experiments are also supported, and protocols and workflows are provided to help investigators planning such experiments.
Comprehensive analysis of RNA, including small/micro RNA species, is supported on multiple platforms. In addition to the next-generation sequencing platforms described above, RT-PCR, digital-droplet-PCR, Fluodigm single cell analysis, and microarray platforms are also available.
Clinical Grade Tumor Sequencing
Rutgers Clinical Genomics Laboratory (RCGL) is a partnership between CINJ, RUCDR, and the RWJMS Department of Pathology. RCGL is CLIA-certified, accredited by the College of American Pathologists, and is licensed by the State of New Jersey under the Clinical Laboratory Improvement Services (CLIS) program. RCGL currently offers two next-generation sequencing panels from RainDance Technologies™: The ThunderBolts™ Cancer Panel for solid tumors and the ThunderBolts™ Myeloid Panel for myeloid malignancies and related disorders. Both panels are based on the RainDance droplet PCR technology and sequencing is done on the Illumina MiSeq platform. These platforms, used by physicians for clinical care, are available for research use by investigators.
Data Processing and Transfer
Raw data from a sequence analysis are pre-processed to ensure quality control and transferred to the Biomedical Informatics shared resource for detailed analysis (including functional analysis) to elucidate the underlying biological processes giving rise to the observed data. Processed data are stored on one terabyte external hard drives provided to the investigators.
Last updated 05/14/2020