Genomic Technologies

The central mission of the Genomic Technologies Department is to develop and effectively apply genomic technologies to accelerate DOE users’ science.  Our primary product continues to be robust sample management & library construction coupled to state-of-the-art high throughput DNA sequencing and analysis.  In addition, our group has also diversified to explore new opportunities for technological access to our user services (including single cell genomics and DNA synthesis).  Our Department serves at the interface between the Project Management Office which initiates and communicates projects with external and internal scientific users and the Scientific Programs which provide secondary analysis and sophisticated web-based hosting of genomic data generated at the JGI.  The Genomic Technologies Department is divided into six Groups to effectively delegate activities among a complementary set of scientific managers and their associated staff.

Groups

Sequencing Technologies

Sequencing Technologies Group provides end-to-end support for the DOEJGI production sequencing activities. Our group applies state-of-the-art automation-based processing technologies coupled with high throughput sequencing operation to support our global DOE research community. Our user community and scientific projects include sequencing needs from the Bioenergy Research Centers (BRCs) and Community Science Program (CSP) submissions.

Our group is organized into three functionally discrete but highly-interactive units. These include nucleic-acid based Sample Management, large-scale and high quality Library Construction and various second and third generation DNA sequencing platforms. These functional units are connected through an extensive workflow management effort to ensure high productivity, efficiency and tractability.

Beside standard genome (DNA) and transcriptome (RNA) analysis, we are also aggressively committed to continuous research and development efforts to stay competitive. Our technology development efforts focus on new sequencing technologies and innovate functional genome analysis methods to interrogate genomic and epigenomic elements pertinent to genome function and biology. Using Chlamydomonas algae as a biofuel model organism, our group implements a series of advanced sequencing-based genomic technologies and initiates an “algal systems biology” project to examine regulatory pathways and key lipid trigger directing biofuel precursor synthesis.

Sequencing Informatics

The Sequencing Informatics group maintains, extends, and supports the software systems for production sequencing activities, from the point where material arrives on-site, through the completion of a variety of post-sequencing quality control checks. The Sequencing Informatics group is organized into four subgroups:

Production Process Support (PPS):  This team maintains and extends the software systems used by the Sequencing Technology group.  This includes Sample Management, Molecular Cloning, and Sequencing Operations.  This covers an existing set of systems that are in maintenance mode, as well as the replacements currently being developed as part of the overall Integrated Tracking System (ITS) effort.

Sequence Data Management (SDM):  This team is responsible for the systems that convert raw sequence data into forms suitable for downstream analysis and NCBI SRA submission.  The systems are based on vendor-provided pipelines, wrapped with in-house software to allow integration with the rest of the JGI’s infrastructure.  This team is also responsible for the maintenance of the master sequence data repository, and for providing basic tools to allow users to access sequence data on demand.

Automated Analysis Pipelines:  This team primarily provides support for the QA/QC and Genome Assembly groups.  Their work is centered on the Rolling QC system, a framework for triggering standard analysis pipelines as sequence data becomes available.  A web-based user interface is also provided, allowing analysts in the QA/QC group to review the results of sequence QC analyses and record results.

Shared Components (SC):  This team is responsible for developing and maintaining the infrastructure shared across the other Sequencing Informatics teams.  This includes the shared database and web application servers used by the overall group.

Quality Control & Assurance

The central goal of Quality Control and Assurance group is to ensure that the Genomic Technologies Department delivers high quality data to the JGI’s scientific programs, users, and partner institutions.  To this end, the group provides laboratory quality control and supply chain management of reagents, as well as bioinformatic data analysis and pipeline automation support for sequence generated by the Sequencing Technologies Group.

Quality Control:  The quality control team orders, manages and tracks reagents for all high volume sequencing technologies.  We work closely with the Project Management Office to generate reagent forecasts needed to support sequencing operations for JGI’s projects.  Once acquired, reagents are inventoried and stored in a secure location.  In addition to physical security measures, a reagent request and tracking system was implemented to improve accountability for reagent usage and inventory monitoring.  This system has enhanced the JGI’s ability to maintain low reagent inventories while remaining adequately supplied with critical reagents to ensure uninterrupted operation of our sequencers.

Quality Assurance:  The quality assurance team provides general statistical and bioinformatic data analysis support for projects initiated by the Scientific Programs.  We perform sequence QA analyses which function as a checkpoint to measure progress against goals prescribed by the Project Management Office at the beginning of each project.  Sequence QA analyses result in recommendations to the sequencing coordinator and project managers on data types and sequencing effort needed to reach project goals.  Since we are the first to analyze data coming off of the JGI’s sequencers, we are the first to recognize and provide feedback on quality issues which impact our ability to successfully complete projects.  In addition to JGI’s programmatic microbial, fungal, plant, and metagenome projects, we provide ad hoc data analysis support for laboratory R&D, process improvement, and new product development projects for internal laboratory scientists.

Genome Analysis

Our responsibilities lie in three major areas.  First, we provide support for the department to adopt new sequencing technologies.  This includes analysis support for new experimental protocol development and support for new sequencing instruments.  Second, we provide data analysis as an evolving service to internal and external users to deliver on JGI products.  This includes implementing or developing data analysis workflows and software algorithms, researching and developing tools that can take advantage of the latest high performance computing capabilities, and engineering an integrated data analysis framework to streamline our data analysis service.  Finally, we actively participate in JGI’s ongoing flagship and grand challenge projects to lead JGI users by providing cutting edge examples of novel genomic approaches as technological accomplishments continue to materialize.

Advanced Sequencing

The primary focus of the Advanced Sequencing Group is to explore technologies on the mid- to long- range horizon to facilitate the JGI in maintaining state of the art capabilities.  Their responsibilities include assessing, developing and implementing the most desirable technologies to continue to enable DOE-relevant science. During the past three years, new commercially available sequencing technologies have emerged and existing vendors have further evolved their sequencing products in an impressive fashion.  The JGI continues to obtain early access to nascent technologies and to determine their strengths and weaknesses compared to existing platforms.

Functional Genomics

This is a new group that was formed in April 2011.  It consists of two subgroups: Micro-scale Applications and Synthetic Biology.  The goal of this group is to expand the JGI technological capabilities in these two areas for application to outstanding questions in biology.  The former group is focused on single cell related technology while the latter is using DNA synthesis as a method to build constructs as reagents for downstream studies.

Micro-scale Applications: Single cell genomics and transcriptomics is an emerging field that provides powerful means to study genomes and expression activities of the vast majority of unculturable organisms at the single cell resolution.  The JGI has developed a single cell genomics pipeline by integrating several high throughput instruments including a fluorescent activated cell sorter (FACS), a liquid handling robot, and a LightCycler to perform single cell isolation, lysis, MDA amplification, and real-time 16S PCR in 384-well plates.  This pipeline has significantly enhanced the ability of users to perform studies of complex genomes of high impact science.

Synthetic Biology:  Massive production of sequence data has resulted in the identification of millions of novel predicted genes, many with potential application as biocatalysts for DOE mission relevant biological and biochemical processes.  Translating the sequence data into experimentally validated functions and applications at scale is challenging largely due to the lack of focused efforts and tools.  Although individual users can purchase synthesized genes from commercial vendors, we believe that our strengths in data mining combined with the gene synthesis and downstream functional analyses provide a powerful tool for large-scale characterization of genes and regulatory sequences.  Giving access of this tool to users has been identified as a high priority area for developing new capability in the JGI strategic vision.