Genomics & Bioinformatics Grants and Publications

Descriptions for Grant Writers 

Investigators who are writing grants can find below a description of the Genomics & Bioinformatics shared resource and its services for their grant applications. Descriptions of the overall Fred Hutchinson Cancer Research Center Shared Resources cores are available on the main Shared Resources grant information page

Examples of publications made possible by the Genomics & Bioinformatics shared resource staff are listed below.
 

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Grant Descriptions  |  Publications

Genomics & Bioinformatics Shared Resource Grant Descriptions


Short Grant Description

The Genomics & Bioinformatics shared resource has state-of-the art instrumentation and experienced staff who provide microarray, CE sequencing, next-generation sequencing, and gene modulation services. Technologies include: Illumina (microarrays); ABI/Life Technologies (CE sequencing and qPCR); Illumina NovaSeq 6000, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina MiSeq, and Pacific Biosciences Sequel (NextGen sequencing); 10x Genomics Chromium Controller (single-cell library prep technology); NanoString technologies; various shRNA and siRNA libraries from Open Biosystems, Qiagen, and Invitrogen (RNAi); and drug and compound libraries from MicroSource and ChemDiv (high-throughput screening). The resource also has sophisticated data management and analysis resources, including three dedicated bioinformaticians with the expertise to assist in data processing and analysis.

Long Grant Description 

Genomics 

The genomics team, part of the Genomics & Bioinformatics shared resource, has state-of-the art instrumentation and experienced staff who provide microarray, CE sequencing, next-generation sequencing, and high-throughput screening services. Technologies include: Illumina BeadChip (microarrays); ABI/Life Technologies (CE sequencing and qPCR); Qiagen (PyroMark sequencing); Illumina NovaSeq 6000, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina MiSeq, and Pacific Biosciences Sequel (NextGen sequencing); NanoString technologies; various shRNA and siRNA libraries from Open Biosystems, Qiagen, and Invitrogen (RNAi); and drug and compound libraries from MicroSource and ChemDiv (high-throughput screening). Partnered with genomics, the bioinformatics team has sophisticated data management and analysis capabilities, including three dedicated staff members with the expertise to assist in data processing and analysis.

Sequencing: The genomics team offers both capillary-based and next-generation sequencing services. Lab staff process sequencing reactions using a dedicated Applied Biosystems 3730xl DNA Analyzer. A second 3730xl DNA Analyzer is reserved for fragment analysis applications. Services for capillary sequencing include two sample submission options, researcher-provided DNA template or ready-to-sequence cocktail. Staff provides pre- and post-data generation consultation, performs sample preparation and processing, performs data QC, assists investigators with troubleshooting, and maintains instrumentation.

Services for next-generation sequencing include RNA-seq, ChIP-seq, whole exome sequencing, targeted resequencing, pooled CRISPR screens, and numerous unique methodologies to support researchers’ needs. In addition, the lab provides the full suite of 10x Genomics single-cell applications, including TotalSeq feature barcoding and cell hashing technologies from BioLegend. Staff provides extensive pre- and post-sequencing consultation, sample QC, library construction and QC, sequencing, data QC, assistance to investigators with troubleshooting, and equipment maintenance. Next-generation sequencing technologies include an Illumina NovaSeq 6000, an Illumina NextSeq 2000, an Illumina HiSeq 2500 system, two Illumina MiSeq systems and a PacBio Sequel. Additional equipment includes a PerkinElmer Sciclone NGSx Workstation, a 10x Genomics Chromium Controller, a Covaris LE220, two Sage Science Pippin Prep gel systems, an Agilent 4200 TapeStation, an Agilent 2200 TapeStation, a Caliper DropSense 96 spectrometer, an Invitrogen Qubit 2.0 fluorometer, and an ABI StepOne Real-Time PCR System.

Hybridization-based Technologies: Current microarray offerings through the resource consist of Illumina BeadChip technology used to support genotyping and CpG methylation and genotyping assays. The lab also houses a NanoString nCounter system and expertise to support the full suite of catalog and custom assays available through the vendor. Lab personnel perform all aspects of sample preparation and processing, as well as assistance with troubleshooting and assessment of data. Supporting equipment includes four BioRad C1000 Touch Thermal Cyclers.

qPCR: The resource also houses four user-operated ABI QuantStudio 5 Real-Time PCR Systems, two each in a 96- and 384-well configuration. Access occurs through a centralized reservation calendar via a web-based interface.

Gene Modulation Services: The Genomics & Bioinformatics shared resource offers gene modulation services, providing libraries, robotic automation, and skilled support staff for microtiter plate-based RNAi or small molecule screens to meet the center’s varied functional genomics and drug discovery needs.

RNAi reagents consist of GIPZ lentiviral shRNA collections that include genome-wide human (155,695 clones) and mouse (57,600 clones) obtained from Thermo Scientific (formerly Open Biosystems). Clones are available to researchers through an online, searchable shRNA Storefront as either individual clones or as plasmid pools. The siRNA reagents are comprised of the Qiagen Human Transcription Factor siRNA Library (2254 genes, 4 triggers per gene), Qiagen Human Druggable Genome siRNA Library (6961, 4 triggers per gene), Ambion Silencer Select Human Kinase siRNA library (710 genes, 3 triggers per gene), a custom Qiagen Mouse Transcription Factor siRNA Library (1675, 4 triggers per gene), and Qiagen Mouse Druggable Genome siRNA Library (8353, 4 triggers per gene). Small-compound screening libraries consist of the MicroSource Spectrum Drug Library (2000 compounds) and the ChemDiv Targeted Diversity Drug Library (50,000 compounds).

In addition, the core provides consultation and custom designs for those interested in employing CRISPR-Cas9 technology into their research.

Instrumentation used to support these efforts include: a dual arm Beckman Coulter Biomek FX with an interchangeable 96 or 384-channel pipettor with optional magnetic-mount 384-well pin tool (arm 1) and vari-span 8 pipettor (arm 2), plus barcode reader; BioTek ELx405 plate washer with a 50 plate stacker; BioTek MicroFlo Select dispensing system with a 50 plate stacker; two Napco 8000DH C02 incubators; Motic AE21 inverted microscope; Molecular Devices SpectraMax Plus absorbance microplate reader; S & P Robotics Biomatrix robot for Synthetic Genetic Array screens; and Perkin Elmer EnVision Multi-label microplate reader with Enhanced Luminescence and Turbo Alpha upgrades, barcode reader, and 50 plate stacker.

Bioinformatics

The bioinformatics team of the Genomics & Bioinformatics shared resource includes three bioinformatics specialists and the resource director, who provide a wide variety of experimental design, analysis, and programming support for the genomics lab and their end users.

Most service requests to the genomics lab occur through various technology-themed modules of HutchBASE, a web-based LIMS that was developed, tested, and implemented by the resource’s staff. HutchBASE initially extended the BASE v2.6 (BioArray Software Environment, Lund University, Sweden) microarray database framework. This customized LIMS has been designed to meet the administrative, technical, and scientific needs of the Genomics & Bioinformatics shared resource and its end users. In addition to facilitating service requests, HutchBASE captures sample annotation and QC, provides sample-tracking features, manages workflows, automatically triggers data analysis pipeline protocols, produces data QC reports, affords data management capabilities, and initiates service billing reports. The database also offers the end-user electronic lab notebook capabilities for their genomics projects, through the user-defined addition of project and sample annotation fields.

A main objective for the bioinformatics staff is to support the data analysis needs of the genomics lab’s end users, with particular focus on massively parallel next-generation and third-generation sequencing. Support encompasses a wide variety of assays one might perform on a given platform including bulk and single-cell expression profiling, single-cell immune receptor sequencing, CUT&RUN, ATAC-seq, ChIP-seq, whole-exome variant calling, CNV analysis, CRISPR-Cas9 knockout analysis. The bioinformatics staff also provide analysis support for data generated in the high-throughput siRNA and small molecule screening facility. The level of support for a given project can vary greatly and may include providing programming advice, assistance with troubleshooting R or Python code, support and guidance using commercial and academic analysis tools, and implementation of a full range of data analysis strategies that encompass in-depth data QC, various statistical analyses, and generation of summary reports and figures. Interpretation of results can be augmented by gene ontology enrichment and pathway enrichment analyses using any number of approaches (e.g., Gene Set Enrichment Analysis, DAVID, Gorilla/ReviGO).

Publications by Genomics & Bioinformatics

Our team in the Genomics & Bioinformatics shared resource is proud to have contributed to major scientific advances during our years of operation. Following is a sample of the high-impact publications our work has made possible: