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Ioannis Ragoussis

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Ioannis Ragoussis

Head of Genome Sciences
Professor, Department of Human Genetics

Email: ioannis.ragoussis@mcgill.ca
Phone: (514) 398-6508

740 Dr Penfield Ave
Montréal, Québec, Canada, H3A 0G1

Professor Ioannis (Jiannis) Ragoussis has studied Biochemistry at the University of Tuebingen, Germany, where he obtained his PhD. He did his postdoctoral studies as EMBO fellow with J. Trowsdale at the Imperial Cancer Research Fund Laboratories in London, UK. Subsequently he became Lectures and then Senior Lecturer at the Division of Medical and Molecular Genetics at Guy’s Hospital, then Guy’s and now King’s Medical School. In 2001 he moved to the University of Oxford as Head of Genomics and in 2013 to McGill University where he is Head of Genome Sciences at the McGill University Genome Center and Professor in Human Genetics at the Department of Human Genetics. He is also affiliated with the Department of Bioengineering and Visiting Professor at the University of Thessaly, Greece. He has developed expertise in all fields of genomics and functional genomics. His main interest is developing state-of-the art NGS based approaches to disease gene identification, as well as functional genomics approaches for the identification of prognostic markers and associated pathways in gynecological cancers and brain cancer.

As head of Genome Sciences, he is responsible for the Genomic Platform Development within the McGill Genome Centre. He has established the Center’s high-though put nucleic extraction facility, genotyping facility, long read sequencing technology and single cell genomics.  He has responsibility for the scientific oversight of the MAGIC production platform, new technology evaluation and integration. As chair of the McGill Genome Center’s Technology Development and Head of the Advanced Genomic Technologies Laboratory, which includes the Single Cell Genomics Lab of the McGill Genome Center, he works on technical developments related to single cell genomics as well as long read sequencing technologies. In 2019 he introduced a PromethION instrument at the Center and works on applications of this technology in population studies and transcriptomics. Supported by CFI the lab includes a Fluidigm BioMark HD instrument, a 10X Genomics Chromium instrument, Nanopore Sequencers (MinION and PromethION), a PacBio Sequel instrument, as well as low volume liquid handling instruments.

The Ragoussis lab is a member of McGill’s Integrative and Quantitative Biology Initiative, lead by Prof. Jacalyn Vogel at the Department of Biology. The lab is responsible for single molecule sequencing using PacBio Sequel technology.

The laboratory is developing genomic tools as part of the international effort to develop Sterile Insert Techniques (SIT) in collaboration with The International Atomic Energy Authority. As part of this work it has contributed to the groundbreaking discovery of the maleness on the Y (MoY) factor in tephretidae published in Science: https://science.sciencemag.org/content/early/2019/08/28/science.aax1318

The laboratory plays a key role in SRAS-COV-2 genome sequencing as part of the Canadian effort on Host and Virus genome sequencing, CanCOGEn, funded by Genome Canada, where Ragoussis chairs the virus genome sequencing committee.

The Single Cell Genomics Laboratory is open to Investigators from McGill University and for collaborations with any other Institute, offering single cell expression profiling and DNA analysis, as well as TCR profiling and ATAC-seq. For enquiries on single cell technology, 10X Genomics and single molecule long read sequencing please email: ioannis.ragoussis@mcgill.ca

Teaching:

Ragoussis coordinates two courses at the Department of Human Genetics:

Graduate course HGEN 400, Genetics in Medicine and the postgraduate course HGEN 676, Laboratory Course in Genomics.

For enquiries please email: ioannis.ragoussis@mcgill.ca

Advanced Genomic Technologies Laboratory

Projects:

  1. Single Cell Genomics: The Laboratory is part of the CRUK Grant Challenge program STORMing Cancer in collaboration with Lorenzo Ferri at MGH. It also collaborates with Professors Morag Park (Tumor Heterogeneity and Microenvironment) Richard Kremer (Circulating Tumor Cells), Guillaume Bourque, and Kevin PetreccaJack Antel, Gustavo Turecki, and Nada Jabado on pediatric and adult brain cancer as well multiple sclerosis and depression. Technical developments include single cell tagging in collaboration with Claudia Kleinman and Santiago Constantino supported by a Genome Canada Disruptive Technologies award.
  2. Genome Canada LSARP Project “Tackling childhood brain cancer”: Work with Nada Jabado’s group at MUHC and Michael Taylor’s group on novel long read and linked read approaches for the genomic and transcriptomic analysis of childhood brain tumours..
  3. Inherited Ovarian Cancer project in collaboration with Patricia Tonin: Discovering new high-risk ovarian cancer predisposing genes through targeted genetic analyses of a Canadian founder population, as well as interrogating large available biobank data from defined cohorts to investigate a moderately infrequent, functionally aberrant and potentially actionable proposed new cancer predisposing alleles, all funded by CIHR.
  4. Methodologies for the highly sensitive detection of both somatic as well as germline mutations: Collaboration with Will Foulkes (Inherited Breast Cancer, DICER1 Syndrome), Lucy Gilbert (Endometrial Cancer) & Bert Vogelstein (Johns Hopkins).
  5. The laboratory is also taking part in the Genome Canada LSARP project CanPrevent, working on the development of long read single molecule sequencing based methodologies and diagnostic tests in collaboration with Paul Keown (UBC), Ruth Sapir Pichadze and Cheelong Shaw (MUHC).
  6. High Throughput Whole Genome Genotyping using Affymetrix Axiom technology is performed as part of Canada’s Longitudinal Study of Aging (CLSA).
  7. The laboratory is part of the Canadian COVID-19 Genomics Network (CanCOGeN), a Genome Canada led network created to coordinate and fund SARS-CoV-2 and host genome sequencing efforts and support the sharing of resultant data. The Network includes two projects, the Host Genome Sequencing Project and the Virus Genome Sequencing Project, to provide essential information for tracking and managing SARS-CoV-2 as well as inform our understanding of the variable clinical response of patients to COVID-19. In the Quebec, the virus genome sequencing effort called Coronavirus Sequencing in Québec (CovSeQ), aims to sequence the viral genomes of Québec patients with COVID-19 disease, and is led by the Institute national de santé publique (INSPQ), the Quebec public health institute and its diagnostic lab, the Laboratoire de santé publique du Québec (LSPQ), in partnership with The McGill University’s Genome Centre (https://www.mcgillgenomecentre.ca/covid-19-research/sars-cov-2-sequencing).

The lab collaborates with companies such as Oxford Nanopore, Agilent, 10X Genomics, SAGE Biosciences and PacBio with further support from Genome Canada, Compute Canada, CFI,  CIHR,  and others.

Recent Publications

  • Bayega, A, Oikonomopoulos, S, Gregoriou, ME, Tsoumani, KT, Giakountis, A, Wang, YC et al.. Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest. Sci Rep. 2021;11 (1):7878. doi: 10.1038/s41598-021-86753-7. PubMed PMID:33846393 PubMed Central PMC8042104.
  • Bayega, A, Djambazian, H, Tsoumani, KT, Gregoriou, ME, Sagri, E, Drosopoulou, E et al.. De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly. BMC Genomics. 2020;21 (1):259. doi: 10.1186/s12864-020-6672-3. PubMed PMID:32228451 PubMed Central PMC7106766.
  • Bayega, A, Fahiminiya, S, Oikonomopoulos, S, Ragoussis, J. Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing. Methods Mol Biol. 2018;1783 :209-241. doi: 10.1007/978-1-4939-7834-2_11. PubMed PMID:29767365 .
  • Bayega, A, Wang, YC, Oikonomopoulos, S, Djambazian, H, Fahiminiya, S, Ragoussis, J et al.. Transcript Profiling Using Long-Read Sequencing Technologies. Methods Mol Biol. 2018;1783 :121-147. doi: 10.1007/978-1-4939-7834-2_6. PubMed PMID:29767360 .
  • Savage, P, Blanchet-Cohen, A, Revil, T, Badescu, D, Saleh, SMI, Wang, YC et al.. A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer. Cell Rep. 2017;21 (5):1140-1149. doi: 10.1016/j.celrep.2017.10.015. PubMed PMID:29091754 .
  • Gao, B, Shao, Q, Choudhry, H, Marcus, V, Dong, K, Ragoussis, J et al.. [Corrigendum] Weighted gene co-expression network analysis of colorectal cancer liver metastasis genome sequencing data and screening of anti-metastasis drugs. Int J Oncol. 2017;50 (1):339. doi: 10.3892/ijo.2016.3722. PubMed PMID:27748802 PubMed Central PMC5182005.
  • Lopez, JP, Diallo, A, Cruceanu, C, Fiori, LM, Laboissiere, S, Guillet, I et al.. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics. 2015;8 :35. doi: 10.1186/s12920-015-0109-x. PubMed PMID:26130076 PubMed Central PMC4487992.
  • Ragoussis, J. Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet. 2009;10 :117-33. doi: 10.1146/annurev-genom-082908-150116. PubMed PMID:19453250 .
  • Ragoussis, J, Elvidge, GP, Kaur, K, Colella, S. Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. PLoS Genet. 2006;2 (7):e100. doi: 10.1371/journal.pgen.0020100. PubMed PMID:16895448 PubMed Central PMC1523240.
  • Ragoussis, J. Genotyping technologies for all. Drug Discov Today Technol. 2006;3 (2):115-22. doi: 10.1016/j.ddtec.2006.06.013. PubMed PMID:24980397 .
Search PubMed

Author/co-author in >200 peer reviewed publications, see: https://www.ncbi.nlm.nih.gov/myncbi/1DoXiQngOkzcu9/bibliography/public/

Lab members:

Yu Chang Wang: Lab Manager, Single Cell Genomics
Corinne Zwaig: Research Assistant (DNA extraction and Genotyping)
Nimara Asbah: Research Assistant
Fadi Alkayal: Research Assistant
Setor Amuzu: PhD student, Queen Elizabeth II scholar
Anthony Bayega: PhD student, Queen Elizabeth II scholar
Melissa Zwaig: PhD student in Human Genetics
Maria Sotiropoulou: MSc student in Human Genetics
Sarah Reiling: Research Associate in Nanopore technology
Anne-Marie Roy: Research Assistant in Advanced Genomics
Haig Djambazian: Academic Research Associate
Dunarel Badescu: Research Associate in Bioinformatics
Rui Wang: Research Associate in Bioinformatics and Statistics
Timothee Revil: Research Associate, Mutation detection 
Spyridon Oikonomopoulos: Research Associate, Long read technologies
Julian Willet: PhD student