Fred Hutch, Seattle Cancer Care Alliance, and UW Medicine Complete Restructure of Partnership

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Data Analysis and Consultation

Data Analysis Support

Our team of bioinformatics specialists provide support in experimental design, data analysis and programming. We take a customer-centered approach, whether advising a new user learning an unfamiliar assay or supporting an established researcher who is developing new cutting-edge methods. 

Our data analysis and consultation team members are available to engage during all experimental phases, from planning to implementation, and can discuss technology selection, experimental design and choice of data analysis strategies. We also perform data analysis using reproducible workflows. 

We work closely with other Fred Hutch shared resources, including the Cellular Imaging and Proteomics & Metabolomics cores. To ensure an appropriate experimental design is in place prior to seeking bioinformatics support, we strongly encourage researchers to consult with a bioinformatics specialist in a project’s earliest stages. 

Schedule With Us

To schedule consultation or data analysis services with the Hutch Data Core, or to get more information about how we can work with you, contact the data analysis and consultation team lead:

Matt Fitzgibbon
Bioinformatics Manager

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Bioinformatics

Our dedicated bioinformatics staff have deep expertise in a broad range of sequence-based assays. We tailor our level of engagement to each project’s needs, from helping to troubleshoot code to collaborating on development of complex novel workflows. Our team helps scientists tackle projects of varying complexity, from small pilot runs to surveys of hundreds of specimens analyzed via multiple assays.

Typical supported workflows include whole exome sequencing, targeted amplicon sequencing, somatic variant calling, CRISPR/Cas9 knockout analysis, bulk RNA-seq expression profiling, single-cell expression profiling, and single-cell immune repertoire sequencing. We also analyze epigenomic profiling data and can help users compare these profiles with RNA-seq expression data when available. For more information about our standard workflows, please consult the bioinformatics services of the Genomics & Bioinformatics shared resource.

In addition to focused, shorter-duration projects, we often work with researchers to bring new techniques to the center and to engage in longer-term collaborative work. Larger specialized projects we have contributed to recently include: 

  • Development of neoantigen-profiling workflows
  • Assembly of a large, disease-specific, gene expression compendium 
  • Long-range haplotype phasing
  • Development of new methods to profile translational control
  • De novo assembly of small viral genomes

For further information about the bioinformatics services we offer, or to schedule a consultation, please email bioinformatics@fredhutch.org.

Morphometrics and Image Analysis

Modern imaging systems provide an unprecedented capability to observe biological structures, but the size, depth and complexity of these image datasets challenge even top-rated commercial image analysis software. 

Our dedicated scientific staff can assist in developing customized image analysis pipelines and algorithms. Our expertise allows us to create the flexible, sophisticated and high-throughput analysis workflows needed to analyze rich imaging datasets by combining data I/O, image pre-processing, image segmentation and feature extraction, metrics collection, display and export.

We also provide consultation to help select the most appropriate imaging techniques and to plan post-acquisition analyses. We work closely with colleagues in the Cellular Imaging shared resource throughout planning and image acquisition to ensure a seamless transfer of data from instruments to our analysis resources. 

We perform analysis on a wide range of data types generated by light or electron microscopy, including 2D images, 3D stacks and time series. Example metrics for which we have developed versatile quantitative pipelines include cell/object counting, subcellular localization, signal colocalization, cell tracking and spatial distribution, including crowding or neighbor occupancy. Please see the Cellular Imaging shared resource’s image analysis page for more information.

For further information or to schedule consultation please contact Dr. Julien Dubrulle, image analysis staff scientist in the Cellular Imaging core.

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Single cell tracks. Each cell track is depicted in a different color with the starting point defined by a black dot. Data courtesy of the Hatch Lab, Fred Hutch
Dynamics of wound healing in a Drosophila syncytial embryo. Left panel: Time-lapse movie of wound-induced epithelial layer of an embryo labeled with fluorescent actin protein. Right panel: Processed data showing the hole extent in green and the actin ring in magenta. Video by Dr. Mitsutoshi Nakamura, Parkhurst Lab, Fred Hutch
Proteomics

Our bioinformatics staff have considerable experience analyzing proteomics data and are available to assist with downstream analysis for various mass spectrometry-based techniques. In close partnership with members of the Proteomics & Metabolomics shared resource, bioinformatics staff have developed custom deconvolution methods for labeled peptides, helped identify long-lived proteins in yeast through analysis of metabolically labeled peptides, searched for specific secondary structure motifs in the proteomes of non-model organisms, and taught introductory courses on the interpretation of tandem mass spectra.

For assistance analyzing proteomics data please contact Dr. Chenwei Lin, staff scientist in the Proteomics & Metabolomics core.

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Volcano plot showing magnitude and significance of protein differences in a two-condition LC-MS/MS experiment using label-free quantification. Image courtesy of Dr. Chenwei Lin, Proteomics & Metabolomics shared resource Click for high-resolution image
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Questions about our data analysis and consultation services or how to schedule with us?

Last Modified, September 21, 2021