The Aparicio lab studies the genomic and phenotypic behaviour of breast and other cancers. Integrating leading edge technologies with patient-derived xenograft models of cancer, this research is working to better understand how cancer clones evolve and to identify novel strategies for cancer treatment and predictors of response.   

Dr. Aparicio’s research program encompasses the fields of cancer genomics, cancer evolution, single cell biology, mouse genetic models, high throughput screens, small molecule chemical probe development and translational breast cancer research. His 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 (TNBC). 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.

Members

Faculty/Leaders

Staff

Cherie Bates

Leader, Breast Cancer Provincial Clinical Research Program

Sean Beatty

Bioinformatics Scientist

Justina Biele

Research Assistant

Viviana Cerda Llanos

Research Assistant

Cynthia Ferguson

Research Projects and Operations Leader

Dr. Takako Kono

Visiting Research Fellow

Daniel Lai

Senior Bioinformatics Scientist

Flora Liu

Data Manager

Lauren Merritt

Research Assistant

Ciara O'Flanagan, PhD

Research Associate

Jenifer Pham

Software Developer

Benoit Prevost-Potvin

Software Developer

Jerome Ting

Research Assistant

Jecy (Beixi) Wang

Research Assistant

Elena Zaikova

Bioinformatics Scientist

Ismat Zerin

Research Assistant

Post-Docs

Vincent Briane

Post-doctoral Fellow

Yangguang (Sunny) Li

Post-Doctoral Fellow

Hoa Tran

Post-doctoral Fellow

Students/Trainees

Ken Chu

Co-op Student

David Gee

Co-op student

Hak Woo Lee

Graduate Student

Guo Yu (Gordon) Wu

Co-op Student

Open Positions

Research Assistant/Tech 3

JOB SUMMARY

Researchers in the Department of Molecular Oncology at the BC Cancer Research Centre use the latest technologies to rapidly identify genes that are involved in the development of cancer. This position will be involved in performing research in drug pharmacology directed at human tumours, with assays in immunodeficient mice (xenotransplants).

ORGANIZATIONAL STATUS

The successful applicant will report to the Principal Investigator or his/her delegate and may assist in overseeing technical work of students and trainees.

WORK PERFORMED

- Plans and performs experiments utilizing complex procedures and/or techniques.

- Processes tissue samples and carries out primary cell isolation as instructed.

- Carries out laboratory techniques following standard operating protocols.

- Maintains laboratory records of both animal data and experimental data; when require summarize results in research reports and lab presentations.

- Assists senior level staff with writing and updating Standard Operating Procedures (SOPs) and Animal Ethics Certificates.

– Assists in the daily care of transgenic animals and maintains colonies of human tumour bearing immunodeficient animals.

- Carries out and oversees procedures involving immunization, oral gavage, injections, tumour inoculation, tumour volume measurements, blood and tissue collection, surgical procedures, necropsy, and post-operative care.

- Daily health monitoring and care of laboratory animals.

- Be able to recognize and resolve behavioral and/or housing issues; may provide technical instruction and training for other staff and/or trainees for those activities.

- Performs other related duties as assigned.

– On a rotation basis, must be available for emergency calls 24/7 and respond appropriately.

CONSEQUENCE OF ERROR

The work is of a complex nature, tasks are assigned and the incumbent exercises a considerable amount of responsibility, initiative and judgment in determining own work schedule to achieve those tasks. Non compliance with ARC regulations may result in closure of facility. Non compliance with animal protocols may result in loss of grant funding.

SUPERVISION RECEIVED

The successful applicant will report to the Principal Investigator or designate.

SUPERVISION GIVEN

The successful applicant will assist in training graduate students/trainees including instruction in use of lab equipment and procedures and will troubleshoot experiments in their area of expertise.

QUALIFICATIONS

Undergraduate degree in a relevant discipline or Graduation from a technical college or institute. A postgraduate degree in Science is preferred. CALAS certification (e.g. RLAT) is an asset. Minimum of 3 years related experience or the equivalent combination of education and experience. Experience in the monitoring and management of human tumour bearing animals is essential and central to the role. A working knowledge of the CCAC guidelines and compassion and sensitivity for animals required. Experience with cell culture and aseptic technique preferred, involving both isolation and maintenance of rodent primary cultures and cell lines. Experience in the use and handling of hazardous materials such as biological agents, radioactive substances and/or cytotoxic drugs is essential. Ability to perform and troubleshoot a wide variety of molecular and cellular biology techniques including the following: RNNDNA isolation, quantitative PCR, transfection, flow cytometry, immunohistochemistry, ELISA, protein isolation and western blotting. Demonstrated understanding of experimental design and assay optimization. Strong interpersonal skills and the ability to interact positively and productively with other team members are essential. Ability to communicate effectively both orally and in writing. The successful candidate must be well-organized, conscientious, understand the importance of detail, and be able to multi-task and prioritize duties effectively

APPLICATION INSTRUCTIONS

To apply please send your CV and cover letter to careersmolonc@bccrc.ca with subject line: RA/Tech 3.

Post-doctoral Fellow Single Cell Genomics, Molecular Biology

A postdoctoral fellowship position is available in the Aparicio lab based at the BC Cancer Research Centre in Vancouver, Canada, collaborating on an exciting project mapping clonal dynamics in human cancers with new single cell methods. 

The Aparicio lab is developing new single cell genome and transcriptome methods for tracking clonal trajectories at single cell level in patients and patient-derived xenografts. The post holder will have the opportunity to interact as part of the international CRUK Grand Challenge IMAXT project, bringing new measurement methods and computational techniques to the 3D reconstruction of tumour and mapping drug sensitivity and drug combinations using sgRNA/CRISPR methods in vivo. The program works closely with the Shah lab computational biology program on the development of new models for single cell data and cancer evolution. Some experience with bioinformatics approaches to biological data and familiarity with handling of genomics data will be an advantage.

How to Apply: Please send the following documents to careersmolonc@bccrc.ca and put “Single Cell Genomics, Aparicio Lab – PDF Position” and your family name in the subject line.

  • Cover Letter
  • Resume
  • Transcript
  • Work Sample

Post-doctoral Fellow

Posting is available immediately for a postdoctoral fellow with experience in cancer bioinformatics to work on an exciting new program developing non-invasive patient genomic monitoring. The successful candidate will have a degree and postgraduate training in bioinformatics, computer science, statistics, or allied subjects, with experience applying modern computational genome analysis methods. The post holder will work jointly with the groups of Dr Samuel Aparicio (UBC and BC Cancer) &  Dr Andrew Roth (UBC Computer Science and BC Cancer) on developing and implementing methods for analysis of genomic sequencing information from plasma and other fluids to monitor tumour burden and provide information for screening of high risk patients. This will be in conjunction with existing work on single cell genome analysis pioneered by the Aparicio and Shah labs in the last 5 years.

How to Apply:
Please send the following documents to careersmolonc@bccrc.ca and put "Post-doctoral Fellow – Aparicio Lab, family name) in the subject line

  • Cover Letter
  • Resume
  • Transcript
  • Work Sample

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

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

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

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

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

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

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

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

Sponsors

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