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.

For more information about our teams and projects, please visit our lab website.

Members

Faculty/Leaders

Staff

Husain Akbar

RESEARCH ADMINISTRATIVE COORDINATOR

Shadi Ansari

Microscopy Engineer

Vinci Au

Research Assistant/Technician

Cherie Bates

Research Project Manager

Sean Beatty

Bioinformatics Scientist

Viviana Cerda Llanos

Research Assistant

Shuyu Fan

Senior Biostatistician

Cynthia Ferguson

Research Projects and Operations Leader

Cristina Flores

Research Assistant/Technician

BaRun Kim

RA/Technician

Esther Kong

Research Assistant

Daniel Lai

Senior Bioinformatics Scientist

Joseph Micla

Front-end Web Developer

Ciara O'Flanagan, PhD

Research Associate

Benoit Prevost-Potvin

Software Architect

Robert Reinert

Data Manager

Yukta Thapliyal

Programmer

Michael Van Vliet

Research Assistant / Technician

Adrian Wan

Laboratory Research and Operations Manager

Jecy (Beixi) Wang

Research Assistant

Elena Zaikova

Bioinformatics Scientist

Post-Docs

Gurdeep Singh

Postdoctoral Fellow

Hoa Tran

Post-doctoral Fellow

Students/Trainees

Karen Ip

Rotation Student

Jenna Liebe

Co-op Student

Yi Fei (Eric) Liu

Directed studies student

Isaac von Riedemann

Co-op Student

Chun Hei Yiu

Co-op Student

Open Positions

Research Assistant/Tech 3 – Animal Research Technician

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 ages, tables, graphs and charts.
  • Maintains both laboratory and laboratory records of both animal data and experimental data; when require summarize results in research reports and lab presentations.
  • 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 innoculation, 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
  • 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. Noncompliance with ARC regulations may result in closure of facility. Noncompliance 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 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 and cytotoxic drugs is essential.
  • Experience in the monitoring and management of human tumour bearing animals.
  • A working knowledge of the CCAC guidelines and compassion and sensitivity for animals.
  • 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.

Finance Coordinator, Research Funds Services

We are looking for a highly motivated finance coordinator to oversee and manage grant funding, supporting a multi-institutional and multidisciplinary team of cancer scientists and leading-edge cancer research across the province. If you are detail oriented, enjoy working in a fast-paced and dynamic environment, please apply! The successful candidate will have the opportunity to learn and work within the financial systems at the University of British Columbia, BC Cancer Research Institute, Provincial Health Services Authority, and Vancouver Coastal Health Research Institute. Our finance and administration staff ensure everything flows smoothly in research projects and play an important role in cancer research. Vacation starts at 20 days a year and the position is eligible for a mix of onsite and remote work. The role is for a one year term with possibility of extension. Come join our team and be part of incredible cancer discoveries!

Job Summary

The Finance Coordinator, Research Funds Services provides research financial reporting and administration on assigned grant funded programs. The Finance Coordinator, Research Funds Services monitors research projects and researches grant budgets, coordinates the development and submission of research financial reports, liaises with PHSA restricted funds finance team to ensure grants financial information is accurately maintained, monitors and tracks receipts and disbursements and assists with the management, allocation and coordination of  research funds among Partners and Stakeholders.                                 

Duties/Accountablilties

  • Monitors research expenditures and reviews and analyzes research financial information of assigned grant funded programs for the Administrator,  Research Business Operations, and Research Project Managers to assist with planning budgets. This includes pulling appropriate research general ledger accounting information, performing review of research accounts and classifying financial information for reporting, invoicing and budgeting purposes. Ensures research budgets remain within allowable spending limits by tracking and monitoring receipts, disbursements and expenses of general accounts. Investigates and identifies errors/discrepancies and creates journal entries to correct accounting records and maintain research financial information integrity.
  • Prepares and reviews research purchase orders and expense claims to ensure applicability and correct expense coding. Verifies appropriate back-up provided and ensures compliance with PHSA policy as well as external funding agency policies. Identifies/determines if expense claim is allowable and makes suggestions on alternative options, if necessary. Follows up with vendors on outstanding credits or erroneous billing as well as cheque payment requests and facilitates payment options by ensuring that required information is obtained (cheque payment, wire transfer, credit card, etc.)
  • Performs periodic reconciliation of the research general ledger, research corporate card purchases, research capital expenditures, research payroll reports and receivables to ensure accuracy and timely follow-up.
  • Prepares research billing invoices based on the general ledger on a weekly, quarterly and ad-hoc basis to ensure timely collection of revenue from external funding agencies. Ensures research payments are received in full and follows-up on outstanding bad debt accounts.
  • Communicates internally with Accounts Payable, Accounts Receivable and PHSA Finance and provides direction on account coding to accurately reflect nature of research financial transaction. Monitors and reconciles research shadow accounts held at UBC and SFU by pulling the general ledger held at these institutions to ensure accurate and complete yearly reporting of funding received. Communicates with the universities regarding accounting discrepancies and generates journal entries and/or invoices to reflect accurate research financial information.
  • Monitors research reporting/invoicing due dates and coordinates timelines to ensure that deadlines are met. Compiles and prepares research financial reports/invoices as needed (quarterly, yearly, etc.) and ensures that expenditures reported are in compliance with spending guidelines and GAAP (generally accepted accounting principles). Identifies under/over-expenditures and recommends options to ensure that the research project stays within budget.
  • Provides support during annual and interim audits by compiling research general ledger information and ensuring proper documentation is kept on file. Provides analysis to identify/explain journal entries as required by the auditor. Coordinates periodic research financial and annual reports as required by granting agencies, PHSA , partner universities and stakeholders to ensure information is summarized according to guidelines.

                                                               

Qualifications

A level of education, training and experience equivalent to a Diploma in Accounting/Financial Management or pursuing a professional designation program and preferably three (3) years of recent related experience in a multi government institutional setting, including experience working with national and international granting and funding bodies.

Knowledge and experience in working with General Accepted Accounting Principles (GAAP) in a university/life science environment. Knowledge of grant management and familiarity with granting agencies and their guidelines and policies. Working knowledge of the university/health care funding process and procurement practices is an asset. Demonstrated ability to conduct oneself in a professional and confidential manner.  Demonstrated administrative and organizational skills.  Demonstrated ability to productively use word processing, excel spreadsheets, financial reporting and project/budget management applications.  Demonstrated ability to communicate effectively both verbally and in writing.  Ability to work independently with minimal direction. Ability to handle workload pressures and demonstrated ability to prioritize.  Ability to supervise junior staff.

Equity and diversity are essential to academic excellence. An open and diverse community fosters the inclusion of voices that have been underrepresented or discouraged.   We encourage applications from members of groups that have been marginalized on any grounds enumerated under the B.C. Human Rights Code, including sex, sexual orientation, gender identity or expression, racialization, disability, political belief, religion, marital or family status, age, and/or status as a First Nation, Metis, Inuit, or Indigenous person.

All qualified candidates are encouraged to apply; however Canadians and permanent residents will be given priority.

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

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

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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