Tomi Pastinen M.D., Ph.D.
Tomi Pastinen completed his M.D., Ph.D. (2000) supervised by Leena Peltonen and Ann-Christine Syvanen at the University of Helsinki (Helsinki, Finland) with a focus on the development of array-based genotyping methods and their application to the study of complex diseases. During his postdoctoral fellowship with Thomas Hudson at McGill University, he initiated studies of allelic variation in expression in human cells. Following his appointment to the McGill faculty in the Department of Human Genetics in 2006, his laboratory has focused on genome-wide allelic assays, functional genomic and epigenomic studies and their applications to common complex disease in human. He has been author on more than 70 publications and he was awarded the Maud Menten Young Investigator Award by the Canadian Institutes of Health Research (2008-2009). He is currently an Associate Professor at the Department of Human Genetics and holds the Canada Research Chair in Human Genomics.
Since the inception of my group five years ago, I have established a vibrant environment for human functional genomics applicable to complex disease trait studies. The components of this program include:
Genome-wide characterization of regulatory variation in human cells
As opposed to widely applied methods, we have developed a niche expertise in dissecting cis-regulatory functional variants using direct detection of allelicly distinct transcripts or functional elements. We have taken a multifaceted approach to advance methods in this area ranging from collaborative efforts with Illumina to apply their platforms (Infinium BeadChips or TruSeq sequence capture) for measuring allelic activity in the human genome, to developing algorithms for calling variation in fine-mapping from next-generation sequencing (NGS), or the application of advanced analytical techniques (hidden-Markov models) for measuring the prevalence of differential expression in a non-hypothesis driven manner. Through the application of our novel tools, we have shown that heritable cis-regulatory variation is more common than estimated based on indirect methods, shows partial cell-type selectivity and only minor contribution of parent-of-origin influences are globally observable. Leveraging our ability to sensitively and specifically measure allelic changes in expression and chromatin activity in multiple cell lineages, we continue to provide functional data for the interpretation of genetic association signals observed in genome-wide association studies. Over the past 5 years, this work has contributed to understanding systemic lupus, osteoporosis, variation in human height, risk for melanoma, type I diabetes, asthma, etc. as well as some monogenic diseases. Fine-mapping efforts combined with follow-up validation experiments have provided mechanistic hypotheses for specific loci, such as the chromosome 17q locus associated with risk of asthma and multiple autoimmune diseases. These translational opportunities continue to emerge as our genomic datasets grow larger and diversify. This work is currently funded by the NIH, CIHR and FRSQ.
Human disease trait oriented population cell models
Recognizing that there existed limitations of using complex tissues and existing population cell resources, I initiated a collaboration with Swedish surgeons to establish the first genomically characterized population cell model from human bone forming cells (osteoblasts). Our work together with our collaborators to date, has shown that common skeletal disease (osteoporosis) or anthropometric traits (human height) show a predominant association to functional alleles in bone cells as opposed to cell types with less direct roles in bone development. We also have identified new functional candidates for osteoporosis. Altogether, this work has prompted us, and others to diversify functional genomics to other cellular lineages. The work is currently funded by CIHR.
Functional genomics of childhood leukemia
In collaboration with Dr. Daniel Sinnett, we are exploring the genomic characteristics of childhood acute lymphoblastic leukemia (pre-B ALL) in the French-Canadian population. My role is the assessment of genome-wide structural variation, expression variation and epigenetic variation (methylation) in both germline and “tumor” tissues (leukemic blasts). This work is supported by a CIHR Terry Fox Team Grant as well as a CIHR operating grant.
Large-scale epigenome mapping
Through our expertise in integrative regulatory genomics we were awarded Epigenome Mapping Centre (EMC) for McGill by the CIHR/CEEHRC initiative (2012-2017). EMC is one of the two national hubs providing Canadian contribution to the International Human Epigenome Consortium aiming to systematically characterize 1000 human epigenomes to enable researchers world-wide assess impact of epigenome variation in human disease. I co-lead EMC at McGill with Dr. Lathrop and run the related epigenomics platforms at the Innovation Centre.
- 2 Research associates
- 3 post-doctoral fellows
- 3 research assistants
- 3 graduate students