Cystic Fibrosis Research and Translation Center
Cystic Fibrosis Research and Translation Center
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Genomics Core

Upcoming Events

CF Seminar Series - GUEST SPEAKER Mitchell Drumm, PhD
Thursday, April 24, 2014
Location and Time TBD - Will be at UW

CF Seminar Series - Ron Gibson, MD
Thursday, May 8, 2014
4:00 pm
UW Health Sciences Building - K350

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Genomics Core Services


Genome AnalyzerThe Genomics Core provides genomics-based tools, accelerating the pace of discovery by fostering a more global molecular approach. The Genomics Core facilitates using global, highthroughput approached to support the following overall aims for the CFRTC. The core also provides data management and analysis tools and creates access platforms to integrate data from the clinical and immunology cores, for human samples and bacterial isolates. Access for CF researchers at this moment in history is especially important, as the technology is changing and advancing so rapidly. The disruptive nature of the massive increase in DNA sequencing capacity, combined with a large decrease in cost, means that global whole-genome analyses are now available to any researcher. This change fosters a much greater ability to link disease-causing characteristics of pathogens to their genome-encoded (and expressed) origins, and will allow this correlation to be made within a much greater variety of research contexts than ever before. Genetic variation of the human host has become more readily deduced with contemporary technology, including advances in Illumina proprietary technology, and contributions from major users of the technology. The purpose of the Genomics Core is to promote access to technology necessary to use these approaches, and to analyze the data they generate. The primary services of the core are:
  • Consultation and experimental design assistance for using new-generation sequencing technology.
  • Data analysis, bioinformatic support, data access and storage.
  • High throughput and new-generation whole-genome sequencing: bacterial and host.
  • RNA-seq analysis of transcriptome: bacterial and host.
  • Proteomic analysis and support for proteomic data sets.
The primary platforms for the genomics core are new-generation sequencing technology and high-throughput proteomics. Within the core we have the Illumina Genome Analyzer GAIIX sequencer, as well as a traditional ABI 3730xl capillary sequencer, an extensive array of high-throughput robotics, and extensive computational expertise to support data processing, and analysis. We use refined in-house Illumina library construction protocols to create sequence-barcoded libraries that may be combined in a single run of sequencing to maximize use of the capacity. In addition we have implemented paired-end sequencing which will accelerate analysis for insertions, deletions, and identification of novel sequences, particularly in clinical strains of bacteria. The activities supported by the core are:
  • Consultation on DNA and RNA purification techniques, including QC analysis.
  • Library preparation from user-supplied DNA or RNA.
  • Illumina Platform new-generation Sequencing.
  • Sequence data processing and storage.
  • Data analysis: SNP determination, Allele calling, Insertion / Deletion / rearrangement analysis.
  • Whole genome transcript abundance and differential regulation analysis.
  • Proteomic analysis: MS peptide analysis.
Supported by a grant from the National Institutes of Health (NIDDK P30 DK 89507). Please reference this grant number on all publications resulting from support provided by this Core Center grant.


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