Aparicio Lab
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Adrian Wan
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Cynthia Ferguson
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Annelie Tam
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Dr. Samuel Aparicio (BM, BCh, PhD, FRCPath, FRSC) is the Nan & Lorraine Robertson Chair in Breast Cancer Research, holds the Canada Research Chair (Tier 1) in Molecular Oncology, and is the recipient of the 2014 Aubrey J Tingle Prize. He is also Head of the Department of Breast and Molecular Oncology at BC Cancer Research, part of the Provincial Health Services Authority, and a Professor in the Department of Pathology and Laboratory Medicine at UBC.  

Dr. Aparicio graduated in medical and natural sciences from Cambridge University (UK), clinical medicine from Oxford, and subsequently in internal medicine and pathology. After doctoral work with Sydney Brenner in Cambridge, he held a Wellcome Trust Career Development Fellowship at the Wellcome/CRUK Developmental Biology Institute. From 2000-2005 he was a senior investigator in the Department of Oncology, Cambridge. He was a co-leader of the international consortium that sequenced the genome of the pufferfish Fugu rubripes in 2002. He moved to Vancouver in 2005.

Dr. Aparicio’s research program encompasses the fields of cancer genomics, mouse genetic models, high throughput screens, small molecule chemical probes and translational breast cancer research. His most recent work on the molecular taxonomy of breast cancer led to identification of new genes that could change the way breast cancer is diagnosed, and form the basis of next-generation treatments. This discovery was preceded by another breakthrough in decoding the genetic makeup of the most-deadly form of breast cancer, known as triple negative subtype. Dr. Aparicio is also working to develop quantitative measures of clonal fitness in patients, including methods for single cell genome sequencing and PDX models of human cancer. He collaborates widely with other groups, with current projects including the genomic and biochemical analysis of lymphoma, ovarian cancer, and several rare pediatric cancers. He was a co-founder of Paradigm Therapeutics (now, Takeda Cambridge) and currently Contextual Genomics Ltd. He was elected to the Royal Society of Canada in 2016 and is honoured as a University of British Columbia Distinguished University Scholar (2017).  His contributions to academic research have been widely published in scientific and clinical journals such as Nature, Science, Cell and the New England Journal of Medicine. He is the recipient of numerous awards from academic as well as industrial institutions.

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Affiliations

Faculty member, UBC Genome Science and Technology Graduate Program 
Associate member, UBC Department of Medical Genetics 
Associate member, UBC CIHR/MSFHR Bioinformatics Program 
Associate member, Michael Smith Genome Sciences Centre

Credentials

Professor, University of British Columbia – Department of Pathology and Laboratory Medicine

Canada Research Chair in Molecular Oncology

Department Head , BC Cancer, Department of Molecular Oncology

Nan & Lorraine Robertson Chair of Breast Cancer Research, UBC/BC Cancer

Associate Member, University of British Columbia, CIHR/MSFHR Bioinformatics Program

Associate Member, BC Cancer, Genome Sciences Center

Affiliated Investigator, Vancouver Coastal Health Authority

Distinguished Scientist, BC Cancer, Department of Molecular Oncology 

PhD, University of Cambridge

Projects

Tumour heterogeneity and clonal dynamics of breast cancer

Cancer is a dynamic disease, and as a result a single tumour mass may comprise a diverse collection cancer clones with distinct phenotypes, mutations or sensitivity to treatment. Integrating deep and single cell genomic and transcriptomic sequencing with statistical modeling of clonal fitness, our lab is developing methods to study and predict the clonal dynamics of cancer in PDX and cell models, under natural and selective pressures such as drug intervention or CRISPR knockout.

Methods for studying cancers at single cell resolution

Single cell sequencing technologies allow the study of phenomena such as tumour heterogeneity, clonal dynamics, tissue microenvironments as well as the identification of novel and intermediary cell types, which may not be easily resolved with bulk sequencing strategies. Our lab has developed methods for the surveying of single cell genomics, and integrates them with methods to study the epigenome and transcriptome at single cell resolution, as well as with imaging techniques for spatial context

Selected Publications

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.

Cell, 2019
Laks, Emma, McPherson, Andrew, Zahn, Hans, Lai, Daniel, Steif, Adi, Brimhall, Jazmine, Biele, Justina, Wang, Beixi, Masud, Tehmina, Ting, Jerome, Grewal, Diljot, Nielsen, Cydney, Leung, Samantha, Bojilova, Viktoria, Smith, Maia, Golovko, Oleg, Poon, Steven, Eirew, Peter, Kabeer, Farhia, Ruiz de Algara, Teresa, Lee, So Ra, Taghiyar, M Jafar, Huebner, Curtis, Ngo, Jessica, Chan, Tim, Vatrt-Watts, Spencer, Walters, Pascale, Abrar, Nafis, Chan, Sophia, Wiens, Matt, Martin, Lauren, Scott, R Wilder, Underhill, T Michael, Chavez, Elizabeth, Steidl, Christian, Da Costa, Daniel, Ma, Yussanne, Coope, Robin J N, Corbett, Richard, Pleasance, Stephen, Moore, Richard, Mungall, Andrew J, Mar, Colin, Cafferty, Fergus, Gelmon, Karen, Chia, Stephen, , , Marra, Marco A, Hansen, Carl, Shah, Sohrab P, Aparicio, Samuel
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Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses.

Genome biology, 2019
O'Flanagan, Ciara H, Campbell, Kieran R, Zhang, Allen W, Kabeer, Farhia, Lim, Jamie L P, Biele, Justina, Eirew, Peter, Lai, Daniel, McPherson, Andrew, Kong, Esther, Bates, Cherie, Borkowski, Kelly, Wiens, Matt, Hewitson, Brittany, Hopkins, James, Pham, Jenifer, Ceglia, Nicholas, Moore, Richard, Mungall, Andrew J, McAlpine, Jessica N, , , Shah, Sohrab P, Aparicio, Samuel
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CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.

Nature communications, 2017
Xu, Hong, Di Antonio, Marco, McKinney, Steven, Mathew, Veena, Ho, Brandon, O'Neil, Nigel J, Santos, Nancy Dos, Silvester, Jennifer, Wei, Vivien, Garcia, Jessica, Kabeer, Farhia, Lai, Daniel, Soriano, Priscilla, Banáth, Judit, Chiu, Derek S, Yap, Damian, Le, Daniel D, Ye, Frank B, Zhang, Anni, Thu, Kelsie, Soong, John, Lin, Shu-Chuan, Tsai, Angela Hsin Chin, Osako, Tomo, Algara, Teresa, Saunders, Darren N, Wong, Jason, Xian, Jian, Bally, Marcel B, Brenton, James D, Brown, Grant W, Shah, Sohrab P, Cescon, David, Mak, Tak W, Caldas, Carlos, Stirling, Peter C, Hieter, Phil, Balasubramanian, Shankar, Aparicio, Samuel
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CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Nature communications, 2017
Funnell, Tyler, Tasaki, Shinya, Oloumi, Arusha, Araki, Shinsuke, Kong, Esther, Yap, Damian, Nakayama, Yusuke, Hughes, Christopher S, Cheng, S-W Grace, Tozaki, Hirokazu, Iwatani, Misa, Sasaki, Satoshi, Ohashi, Tomohiro, Miyazaki, Tohru, Morishita, Nao, Morishita, Daisuke, Ogasawara-Shimizu, Mari, Ohori, Momoko, Nakao, Shoichi, Karashima, Masatoshi, Sano, Masaya, Murai, Aiko, Nomura, Toshiyuki, Uchiyama, Noriko, Kawamoto, Tomohiro, Hara, Ryujiro, Nakanishi, Osamu, Shumansky, Karey, Rosner, Jamie, Wan, Adrian, McKinney, Steven, Morin, Gregg B, Nakanishi, Atsushi, Shah, Sohrab, Toyoshiba, Hiroyoshi, Aparicio, Samuel
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Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

Nature genetics, 2016
McPherson, Andrew, Roth, Andrew, Laks, Emma, Masud, Tehmina, Bashashati, Ali, Zhang, Allen W, Ha, Gavin, Biele, Justina, Yap, Damian, Wan, Adrian, Prentice, Leah M, Khattra, Jaswinder, Smith, Maia A, Nielsen, Cydney B, Mullaly, Sarah C, Kalloger, Steve, Karnezis, Anthony, Shumansky, Karey, Siu, Celia, Rosner, Jamie, Chan, Hector Li, Ho, Julie, Melnyk, Nataliya, Senz, Janine, Yang, Winnie, Moore, Richard, Mungall, Andrew J, Marra, Marco A, Bouchard-Côté, Alexandre, Gilks, C Blake, Huntsman, David G, McAlpine, Jessica N, Aparicio, Samuel, Shah, Sohrab P
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The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Nature, 2012
Shah, Sohrab P, Roth, Andrew, Goya, Rodrigo, Oloumi, Arusha, Ha, Gavin, Zhao, Yongjun, Turashvili, Gulisa, Ding, Jiarui, Tse, Kane, Haffari, Gholamreza, Bashashati, Ali, Prentice, Leah M, Khattra, Jaswinder, Burleigh, Angela, Yap, Damian, Bernard, Virginie, McPherson, Andrew, Shumansky, Karey, Crisan, Anamaria, Giuliany, Ryan, Heravi-Moussavi, Alireza, Rosner, Jamie, Lai, Daniel, Birol, Inanc, Varhol, Richard, Tam, Angela, Dhalla, Noreen, Zeng, Thomas, Ma, Kevin, Chan, Simon K, Griffith, Malachi, Moradian, Annie, Cheng, S-W Grace, Morin, Gregg B, Watson, Peter, Gelmon, Karen, Chia, Stephen, Chin, Suet-Feung, Curtis, Christina, Rueda, Oscar M, Pharoah, Paul D, Damaraju, Sambasivarao, Mackey, John, Hoon, Kelly, Harkins, Timothy, Tadigotla, Vasisht, Sigaroudinia, Mahvash, Gascard, Philippe, Tlsty, Thea, Costello, Joseph F, Meyer, Irmtraud M, Eaves, Connie J, Wasserman, Wyeth W, Jones, Steven, Huntsman, David, Hirst, Martin, Caldas, Carlos, Marra, Marco A, Aparicio, Samuel
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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Nature, 2012
Curtis, Christina, Shah, Sohrab P, Chin, Suet-Feung, Turashvili, Gulisa, Rueda, Oscar M, Dunning, Mark J, Speed, Doug, Lynch, Andy G, Samarajiwa, Shamith, Yuan, Yinyin, Gräf, Stefan, Ha, Gavin, Haffari, Gholamreza, Bashashati, Ali, Russell, Roslin, McKinney, Steven, , , Langerød, Anita, Green, Andrew, Provenzano, Elena, Wishart, Gordon, Pinder, Sarah, Watson, Peter, Markowetz, Florian, Murphy, Leigh, Ellis, Ian, Purushotham, Arnie, Børresen-Dale, Anne-Lise, Brenton, James D, Tavaré, Simon, Caldas, Carlos, Aparicio, Samuel
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The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.

Nature communications, 2016
Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M, Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A, Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W Y, Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F, Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R, McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R, Ellis, Ian O, Purushotham, Arnie, Pinder, Sarah E, Børresen-Dale, Anne-Lise, Earl, Helena M, Pharoah, Paul D, Ross, Mark T, Aparicio, Samuel, Caldas, Carlos
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