Exploring Omics with CAT: A Gateway to Genomic and Spatial Insight

Join us for the inaugural session of Exploring Omics with Centre for Advanced Technologies (CAT), an exciting opportunity co-hosted by the Centre for Health Genomics and Informatics (CHGI) and Applied Spatial Omics Centre (ASOC).

This session provides an inspiring overview of genomics and spatial omics, unveiling emerging best practices, innovative analytical approaches, and the invaluable tools and resources available through CAT. Created for researchers, trainees, and principal investigators, this seminar aims to spark interdisciplinary understanding and illuminate pathways for collaboration across the dynamic landscape of omics-driven research.


Venue


Agenda

    Time Title Speaker
    09:30 - 09:40 Perspectives from the Centre for Advanced Technologies Angela Krawetz
    09:40 - 10:40 CHGI Genomics Core: A Guide to Services and Capabilities - From Project Design to Results Interpretation. Shelly Wegener and
    Paul Gordon from CHGI
    10:40 - 10:50 Coffee break  
    10:50 - 11:50 Decoding the Spatial Dimension of Gene Expression:
    A Comprehensive Introduction to Spatial Transcriptomics Platforms, Bioinformatics Analysis, and Their Applications in Biological Research.
    Bo Young Ahn and
    Heewon Seo from ASOC
    11:50 - 12:00 Q&A  


About Centre for Health Genomics and Informatics (CHGI)

    Our organization
      The CHGI lies within the Centre for Advanced Technologies (CAT) at the Cumming School of Medicine (CSM). CAT supports all of the shared resource facilities in the School of Medicine, and falls under the portfolio of the Associate Dean, Research Infrastructure.

      "Creating the future of health" is the vision for the CSM's Strategic Plan, and the Cumming School of Medicine has committed over $7M to the establishment of the CHGI since its inception. A number of other Faculties, Institutes, Centres, and stake-holders have partnered with the CSM in supporting the growth and operations of the CHGI. Currently, these include:
      • Alberta Children's Hospital Research Institute
      • Alberta Public Laboratories' Genetic and Genomics Lab
      • Arnie Charbonneau Cancer Institute
      • Energy Bioengineering and Geomicrobiology Research Group
      • Faculty of Veterinary Medicine
      • International Microbiome Centre
      • Precision Oncology and Experimental Therapeutics (POET) Group
      • Snyder Institute for Chronic Diseases

      The CHGI's services are not limited to the Cumming School of Medicine or its supporting partners, and are offered equally to all researchers associated with the University of Calgary, regardless of department or faculty. External requests from other academic, government or commercial sources may also be considered (different fees apply).

      Management of the CHGI is divided between our Lab Manager, Shelly Wegener, and our Bioinformatics Manager, Dr. Paul Gordon.

    Our history
      Core DNA facilities began at the University of Calgary as part of the UCDNA Services labs. They were established by Dr. Richard Pon, first in oligonucleotide synthesis in 1985, with the addition of Sanger DNA sequencing in 1992. Dr. Christoph Sensen developed the bioinformatics groundwork, with the creation of the Sun Centre of Excellence for Visual Genomics in 2002 and the Distributed Bioinformatics Platform for Genome Canada from 2002-2010.

      Together, Dr. Pon and Dr. Sensen (who was then the Director of the Centre for Advanced Technologies) recognized the growing need for a local next-generation sequencing facility. However, the high cost of developing a facility was a major obstacle.

      It took the leadership and vision of Dr. Brent Scott (Executive Director, Alberta Children’s Hospital Research Institute) to drive forward a plan for a joint genomics platform between the Alberta Children’s Hospital and Faculty of Medicine. In 2009, Dr. Scott obtained a five-year funding envelop, with $5.8M from the Alberta Children’s Hospital Foundation and $2M from the Faculty of Medicine (later renamed the Cumming School of Medicine in 2014). This startup funding was used to establish two lab sites. One lab was built in the University’s Health Sciences Centre to support genomics for basic and clinical research. The other site was established within the Alberta Children’s Hospital Molecular Diagnostic Laboratory for the development of next-gen genetic tests for clinical use. It has since merged with the Genetics and Genomics Laboratory. IT infrastructure from the former Genome Canada platform was re-purposed to support the bioinformatics needs of both labs.

      Our Genomics and Informatics platform opened in 2011 under Dr. Scott and the Alberta Children’s Hospital Research Institute (ACHRI). The facility has operated many next-gen sequencers over the years, evolving with developments in technology. The first sequencer, a Life Technologies SOLiD 4, was soon followed by two SOLiD 5500xl instruments and an Ion Torrent PGM. In 2014 and 2015, Illumina MiSeq and NextSeq 500 sequencers were added. During this time, the platform developed as a partnership between many stakeholders who contributed financially or through in-kind donations, and helped the platform grow.

      In 2016, the ACHRI Genomics and Informatics platform officially became the Cumming School of Medicine Centre for Health Genomics and Informatics. Executive leadership was passed to Dr. Francois Bernier upon Dr. Scott’s retirement in 2018.

      ACHRI received a Canadian Foundation for Innovation (CFI) Innovation Fund award for Precision Medicine and the Genetic Diseases of Childhood in 2018. Among the many new capabilities being funded by this award is our capacity for whole human genome sequencing, which will help position the University of Calgary as a provincial leader in Precision Health.

    Our services
    1. Sanger sequencing & fragment analysis
      1. Sanger DNA sequencing
      2. Genetic Fragment analysis
    2. Next-Gen sequencing
      1. Analytical services
      2. Library preparation
      3. Next-Gen sequencing
      4. Data and Bioinformatics

    Sequencers and analytical platforms
    1. Illumina NovaSeq 6000
    2. Illumina NextSeq 2000
    3. Illumina MiSeq
    4. Illumina iSeq 100
    5. Oxford Nanopore Technologies MinION
    6. Applied Biosystems 3730xl DNA Analyzer

    Library Preparation and Quality Control
    1. 10x Genomics Chromium iX Controller
    2. Qubit Fluorometers
    3. Agilent Technologies 4200 TapeStation
    4. Applied Biosystems StepOnePlus Real-Time PCR System
    5. Hamilton Robotics Microlab Nimbus
    6. Thermo Scientific NanoDrop 2000 Spectrophotometer
    7. BioTek Synergy HTX Multi-Mode Microplate Reader
    8. Agilent Technologies 5200 Fragment Analyzer
    9. Sage Science Pippin Prep
    10. Covaris Sonicators
For more information, visit our web at cumming.ucalgary.ca/research/cat/health-genomics/.

About Applied Spatial Omics Centre (ASOC)

    Background
      ASOC is organized as a centre within the University of Calgary, Cumming School of Medicine, an interdisciplinary research institute that is driven to the future of medicine. ASOC offers Spatial Transcriptomics (ST) data analysis packages and the ASOC Web enables Scientists to browse the analysis results in one place. Users no longer need to look up or trace multi-version files in their email threads and the Web is easy to share with anyone online for collaboration within or across institutes. On the other hand, it showcases the Demo Analysis Reports using public datasets and introduces how ST works for new customers.

    Our mission
      We aim to support ground-breaking research in genetics and genomics by integrating advanced technologies. One of the most transformative is the "Spatial Transcriptomics" revolutionizing biological research in recent years. We provide a hub of expertise in advanced techniques, ensuring the upkeep of ST and accompanying genomic tools alongside comprehensive bioinformatics support. This framework empowers researchers to harness these methodologies efficiently for their scientific breakthroughs.

    Spatial omics services
    1. Study design assistance: ASOC provides consultation services, assisting researchers in formulating effective study methodologies suitable for their research objectives.
    2. Technical services for Spatial Omics: With a keen focus on precision and accuracy, ASOC delivers comprehensive analyses of RNA and protein from tissue sections, enabling a deeper understanding of spatial omics.
    3. Histology & Histochemistry: A broad range of histological services for spatial omics analysis are available to support advanced spatial transcriptomics platforms.
    4. Sample preparation for Next-Generation Sequencing (NGS): To ensure the integrity of samples, ASOC has rigorous preparation protocols to yield optimal outcomes from NGS platforms.
    5. Bioinformatics data analysis: ASOC's Bioinformatics team offers rigorous data QC, analysis, and interpretation of Spatial Omics data into meaningful insights.

    Available platforms
    1. 10X Genomics
      1. Visium Spatial Gene Expression/Visium HD with CytAssist
      2. Xenium In Situ
    2. NanoString
      1. GeoMx® Digital Spatial Profiler (DSP)
      2. CosMx™Spatial Molecular Imager (SMI)

    For more information, visit our web at ASOC.ucalgary.ca.

Exploring Omics with CAT: A Gateway to Genomic and Spatial Insight

Join us for the inaugural session of Exploring Omics with Centre for Centre for Advanced Technologies (CAT), an exciting opportunity co-hosted by the Centre for Health Genomics and Informatics (CHGI) and Applied Spatial Omics Centre (ASOC).

This session provides an inspiring overview of genomics and spatial omics, unveiling emerging best practices, innovative analytical approaches, and the invaluable tools and resources available through CAT. Created for researchers, trainees, and principal investigators, this seminar aims to spark interdisciplinary understanding and illuminate pathways for collaboration across the dynamic landscape of omics-driven research.



Venue


Agenda

    Time Title Speaker
    09:30 Perspectives from the Centre for Advanced Technologies Angela Krawetz
    09:40 CHGI Genomics Core: A Guide to Services and Capabilities - From Project Design to Results Interpretation. Shelly Wegener / Paul Gordon
    10:40 Coffee break  
    10:50 Decoding the Spatial Dimension of Gene Expression: A Comprehensive Introduction to Spatial Transcriptomics Platforms, Bioinformatics Analysis, and Their Applications in Biological Research. Bo Young Ahn / Heewon Seo
    11:50 Q&A  


About Centre for Health Genomics and Informatics (CHGI)

    Our organization
      The CHGI lies within the Centre for Advanced Technologies (CAT) at the Cumming School of Medicine (CSM). CAT supports all of the shared resource facilities in the School of Medicine, and falls under the portfolio of the Associate Dean, Research Infrastructure.

      "Creating the future of health" is the vision for the CSM's Strategic Plan, and the Cumming School of Medicine has committed over $7M to the establishment of the CHGI since its inception. A number of other Faculties, Institutes, Centres, and stake-holders have partnered with the CSM in supporting the growth and operations of the CHGI. Currently, these include:
      • Alberta Children's Hospital Research Institute
      • Alberta Public Laboratories' Genetic and Genomics Lab
      • Arnie Charbonneau Cancer Institute
      • Energy Bioengineering and Geomicrobiology Research Group
      • Faculty of Veterinary Medicine
      • International Microbiome Centre
      • Precision Oncology and Experimental Therapeutics (POET) Group
      • Snyder Institute for Chronic Diseases

      The CHGI's services are not limited to the Cumming School of Medicine or its supporting partners, and are offered equally to all researchers associated with the University of Calgary, regardless of department or faculty. External requests from other academic, government or commercial sources may also be considered (different fees apply).

      Management of the CHGI is divided between our Lab Manager, Shelly Wegener, and our Bioinformatics Manager, Dr. Paul Gordon.

    Our history
      Core DNA facilities began at the University of Calgary as part of the UCDNA Services labs. They were established by Dr. Richard Pon, first in oligonucleotide synthesis in 1985, with the addition of Sanger DNA sequencing in 1992. Dr. Christoph Sensen developed the bioinformatics groundwork, with the creation of the Sun Centre of Excellence for Visual Genomics in 2002 and the Distributed Bioinformatics Platform for Genome Canada from 2002-2010.

      Together, Dr. Pon and Dr. Sensen (who was then the Director of the Centre for Advanced Technologies) recognized the growing need for a local next-generation sequencing facility. However, the high cost of developing a facility was a major obstacle.

      It took the leadership and vision of Dr. Brent Scott (Executive Director, Alberta Children’s Hospital Research Institute) to drive forward a plan for a joint genomics platform between the Alberta Children’s Hospital and Faculty of Medicine. In 2009, Dr. Scott obtained a five-year funding envelop, with $5.8M from the Alberta Children’s Hospital Foundation and $2M from the Faculty of Medicine (later renamed the Cumming School of Medicine in 2014). This startup funding was used to establish two lab sites. One lab was built in the University’s Health Sciences Centre to support genomics for basic and clinical research. The other site was established within the Alberta Children’s Hospital Molecular Diagnostic Laboratory for the development of next-gen genetic tests for clinical use. It has since merged with the Genetics and Genomics Laboratory. IT infrastructure from the former Genome Canada platform was re-purposed to support the bioinformatics needs of both labs.

      Our Genomics and Informatics platform opened in 2011 under Dr. Scott and the Alberta Children’s Hospital Research Institute (ACHRI). The facility has operated many next-gen sequencers over the years, evolving with developments in technology. The first sequencer, a Life Technologies SOLiD 4, was soon followed by two SOLiD 5500xl instruments and an Ion Torrent PGM. In 2014 and 2015, Illumina MiSeq and NextSeq 500 sequencers were added. During this time, the platform developed as a partnership between many stakeholders who contributed financially or through in-kind donations, and helped the platform grow.

      In 2016, the ACHRI Genomics and Informatics platform officially became the Cumming School of Medicine Centre for Health Genomics and Informatics. Executive leadership was passed to Dr. Francois Bernier upon Dr. Scott’s retirement in 2018.

      ACHRI received a Canadian Foundation for Innovation (CFI) Innovation Fund award for Precision Medicine and the Genetic Diseases of Childhood in 2018. Among the many new capabilities being funded by this award is our capacity for whole human genome sequencing, which will help position the University of Calgary as a provincial leader in Precision Health.

    Our services
    1. Sanger sequencing & fragment analysis
      1. Sanger DNA sequencing
      2. Genetic Fragment analysis
    2. Next-Gen sequencing
      1. Analytical services
      2. Library preparation
      3. Next-Gen sequencing
      4. Data and Bioinformatics

    Sequencers and analytical platforms
    1. Illumina NovaSeq 6000
    2. Illumina NextSeq 2000
    3. Illumina MiSeq
    4. Illumina iSeq 100
    5. Oxford Nanopore Technologies MinION
    6. Applied Biosystems 3730xl DNA Analyzer

    Library Preparation and Quality Control
    1. 10x Genomics Chromium iX Controller
    2. Qubit Fluorometers
    3. Agilent Technologies 4200 TapeStation
    4. Applied Biosystems StepOnePlus Real-Time PCR System
    5. Hamilton Robotics Microlab Nimbus
    6. Thermo Scientific NanoDrop 2000 Spectrophotometer
    7. BioTek Synergy HTX Multi-Mode Microplate Reader
    8. Agilent Technologies 5200 Fragment Analyzer
    9. Sage Science Pippin Prep
    10. Covaris Sonicators
For more information, visit our web at cumming.ucalgary.ca/research/cat/health-genomics/.

About Applied Spatial Omics Centre (ASOC)

    Background
      ASOC is organized as a centre within the University of Calgary, Cumming School of Medicine, an interdisciplinary research institute that is driven to the future of medicine. ASOC offers Spatial Transcriptomics (ST) data analysis packages and the ASOC Web enables Scientists to browse the analysis results in one place. Users no longer need to look up or trace multi-version files in their email threads and the Web is easy to share with anyone online for collaboration within or across institutes. On the other hand, it showcases the Demo Analysis Reports using public datasets and introduces how ST works for new customers.

    Our mission
      We aim to support ground-breaking research in genetics and genomics by integrating advanced technologies. One of the most transformative is the "Spatial Transcriptomics" revolutionizing biological research in recent years. We provide a hub of expertise in advanced techniques, ensuring the upkeep of ST and accompanying genomic tools alongside comprehensive bioinformatics support. This framework empowers researchers to harness these methodologies efficiently for their scientific breakthroughs.

    Spatial omics services
    1. Study design assistance: ASOC provides consultation services, assisting researchers in formulating effective study methodologies suitable for their research objectives.
    2. Technical services for Spatial Omics: With a keen focus on precision and accuracy, ASOC delivers comprehensive analyses of RNA and protein from tissue sections, enabling a deeper understanding of spatial omics.
    3. Histology & Histochemistry: A broad range of histological services for spatial omics analysis are available to support advanced spatial transcriptomics platforms.
    4. Sample preparation for Next-Generation Sequencing (NGS): To ensure the integrity of samples, ASOC has rigorous preparation protocols to yield optimal outcomes from NGS platforms.
    5. Bioinformatics data analysis: ASOC's Bioinformatics team offers rigorous data QC, analysis, and interpretation of Spatial Omics data into meaningful insights.

    Available platforms
    1. 10X Genomics
      1. Visium Spatial Gene Expression/Visium HD with CytAssist
      2. Xenium In Situ
    2. NanoString
      1. GeoMx® Digital Spatial Profiler (DSP)
      2. CosMx™Spatial Molecular Imager (SMI)

    For more information, visit our web at ASOC.ucalgary.ca.