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You are here: Home / Faculty / Dr. Robert Holt, PhD

Dr. Robert Holt, PhD

Head of Sequencing, Michael Smith Genome Sciences Centre, BC Cancer Agency
Professor, Molecular Biology & Biochemistry, Simon Fraser University
Professor, Department of Medical Genetics, University of British Columbia

Phone 604-675-8165
Fax 604-675-8178


B.Sc.  - Biology, University of British Columbia, 1992
Ph.D.  - Pharmacology, University of Alberta, 1998

Applications are welcome from prospective Post-Doctoral Fellows



T-cells circulating in blood are the key players in your adaptive immune system and are particularly important in recognizing and killing other cells that are infected with viruses, or that carry cancer causing mutations.  Because there are a vast number of different infectious agents or cancer causing mutations possible, a vast number of T-cell variants are required to recognize them. The component of the T-cell responsible for this recognition is the T-cell receptor, and the variation required for recognition is generated mainly by shuffling the large number of short DNA segments that comprise T-cell receptor genes.  Although the central importance and T-cell receptor in adaptive immunity is well established, the actual number and diversity of T-cells that exist in an individual (ie. the T-cell repertoire), how this changes in response to immune challenge, and how it varies from one individual to the next, remains unknown.  We have used the latest DNA sequencing technologies to develop an approach for examining the T-cell repertoire in a given blood sample by directly sequencing T-cell receptor genes.  We are using this method to explore T-cell repertoires in healthy individuals, and in instances of immune challenge, such as cancer, infectious disease, vaccination and transplantation.  We are also developing novel methods for identifying antigens recognized by T cell receptors.

Metagenomics - Infectious agents in Cancer

A large proportion (at least 15%) of the global cancer burden is attributable to known infectious agents, such as HPV, HBV and H. pylori.  It is possible that infectious agents may have a still greater role in cancer etiology, but traditional methods for finding them have limited sensitivity.  As an alternative approach we are using deep metagenomic sequencing of tumours to find microbial signatures associated with various types of cancer.  Linking of an infectious agent to cancer is useful because is leads to the possibility of prevention and/or intervention by vaccination or antibiotic therapy.

Cancer Genomes

We are using deep sequencing to identify the spectrum of somatic mutations in various cancers, with a particular focus on the identification of mutational epitopes for cancer vaccines.


The causes of disorders such as schizophrenia and bipolar disorder remain unknown. We are using DNA sequence analysis and IP/MS to explore candidate genes for these and other disorders.  We also have ongoing projects in the genetics of cognitive evolution, and we are part of the Pleiades Promoter Project ( and related projects, where the aim is to develop synthetic human promoter systems suitable for driving gene expression in specific brain regions of therapeutic interest.

Synthetic Biology

There has been spectacular success reading genetic code. In contrast, progress made in writing genetic code and building genomes has been extremely limited. The new field of synthetic biology explores these possibilities. Our current work in synthetic biology focuses on developing laboratory methods for constructing large DNA molecules, engineering whole microbial genomes and exploring microbial genome interaction.

DNA Sequencing

The Sequencing Group at BCGSC provides an efficient, flexible, reliable high throughput platform to support collaborative research related to human disease, model organisms, and organisms of industrial importance in Canada. Laboratory and informatics technology development is ongoing.


Select Publications

The Cancer Genome Atlas Network.  Comprehensive molecular portraits of human breast cancer tumours. Nature. 2012 Oct 4;490(7418):61-70.

Castellarin M, Milne K, Zeng T, Tse K, Mayo M, Zhao YJ, Webb JR, Watson PH, Nelson BH, Holt RA.  Clonal evolution of high-grade serous ovarian carcinoma from primary to recurrent disease.  Journal of Pathology. Epub ahead of print, 21 September 2012

Reinke SN, Resch L, Maingat F, Branton W, Jackson A, Saxinger L, Holt RA, Slupsky C, Marrie T, Sykes BD, Power C.  Metagenomic and metabolomic characterization of rabies encephalitis – new insights into the treatment of an ancient disease.  Journal of Infectious Diseases. Epub ahead of print, 21 August 2012

Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Aug 2; 488(7409):49-56.

The Cancer Genome Atlast Network.  Comprehensive molecular characterization of human colon and rectal cancer.  Nature.  2012 Jul 18; 478(7407):330-7.

Schmouth JF, Banks KG, Mathelier A, Gregory-Evans CY, Castellarin M, Holt RA, Gregory-Evans K, Wasserman WW, Simpson EM.  Retina restored and brain abnormalities ameliorated by single-copy knock-in of human NR2E1 in null mice.  Molecular Cell Biology.  2012 Apr;32(7):1296-311.

Castellarin M, Warren RL, Freeman D, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res doi: 10.1101/gr.126516.111.

Moore RA, Warren RL, Freeman JD, Gustavsen JA, Chenard C, Friedman JM, Suttle CA, Zhao Y, Holt RA. The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissues.  PLoS One. 2011;6(5):e19838. Epub 2011 May 13.

Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T- cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Research. 21(5):790-7. 2011 May.

Gardy JL et al. Whole Genome Sequencing and Social Network Analysis of a Tuberculosis Outbreak. New England Journal of Medicine. 364(8):730-9. 24 February 2011

Portales-Casamar E, et al. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proceedings of the National Academy of Sciences. 21;107(38):16589-94. 2010 September

Zhou W et al. BACE1 Gene Promoter Single-Nucleotide Polymorphisms in Alzheimer's Disease.  Journal of Molecular Neuroscience. 42(1):127-133. 2010 Sep

Jones SJM et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 9;11(8):R82. 2010 Aug.

Mead CL et al.  Cytosolic protein interactions of the schizophrenia susceptibility gene dysbindin. Journal of Neurochemistry. 113(6):1491-1503. 2010 Jun

Warren RL and Holt RA.  A census of predicted mutational epitopes suitable for immunologic cancer control.  Human Immunology. 71(3):245-254. 2010 Mar.

Holt RA. Reflections on a prosthetic genome. Journal of Cosmology. Vol 8. 2010.

Shah SP et al. Mutational evolution and RNA editing in a lobular breast tumour profiled at single nucleotide resolution. Nature. 461:809-813. 2009.

Pel J et al.  Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules. Proceedings of the National Academy of Sciences. 1;106(35):14796-14801. 2009.

Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research. 19(10):1817-18124. 2009.

Holt RA and Jones SJM.  The new paradigm of flow cell sequencing. Genome Research. 18:839-846. 2008.

Holt RA et al. Rebuilding microbial genomes. Bioessays. 29: 580-590. 2007.

Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23: 500-501. 2007.

Missirlis PI, Smailus DE and Holt RA. A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination.  BMC Genomics. 7:73. 2006.

Wilson GE, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG and Holt RA. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla.  Genome Research. 16:173-181. 2006.

Marra MA,  et al. The Genome Sequence of the SARS-Associated Coronavirus.  Science. 300:1399-1404. 2003.

Holt RA,  et al. The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 298:129-149. 2002.

Venter JC et al. The Sequence of the Human Genome. Science. 291:1304-1351. 2001.

Robert Holt's complete publications list including selected links to full text articles.