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

Project Manager - Bioinformatics

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

Project Manager - Clinical Studies

Daniel Lai

Senior Bioinformatics Scientist

Nathan Liu

Research Assistant/Tech 3

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

Elena Zaikova

Bioinformatics Scientist

Post-Docs

Gurdeep Singh

Postdoctoral Fellow

Hoa Tran

Post-doctoral Fellow

Students/Trainees

Daniel Aghda

Co-op Student

Alissa Gama

Co-op Student

Yi Fei (Eric) Liu

Directed studies student

Rizzek Narang

Co-op Student

Isaac von Riedemann

Co-op Student

Kelly Zhang

Co-op Student

Open Positions

Postdoctoral Research Fellow, Bioinformatics

Job Summary:

The candidate would work within a dynamic and vibrant lab with a proven track record of outstanding achievements and contributions in breast oncology research. This position allows the candidate to contribute bold and innovative research that can be translated to new understanding in the evolutionary processes that drive cancers.

This position's primary focus in the lab will be to lead and to participate in projects based on candidate's desire concentrated on investigating genetics of breast oncology, cancer evolutionary, and development of novel therapeutics. Using the wide network of connections and collaborations of the principal investigator, and extensive biomedical resources at the institution, candidates will be able to build on the existing research of the lab to quickly start up their own research projects.

The position will provide a unique opportunity for mentoring trainees, supervising analysts and interacting with industry. This is an excellent platform to receive outstanding training to gain the important skills for a successful medical research career in academia or industry.

This funded position with the University of British Columbia, at the BC Cancer Research Centre allows the candidate to flourish under the guidance of an experienced mentor.

Organizational Status:

The Postdoctoral Fellow will play a leadership role in the Aparicio lab, and will be reporting directly to Dr. Samuel Aparicio who is the primary investigator of the laboratory. More information on the lab, please visit https://aparicio.molonc.ca

The Department of Pathology and Laboratory Medicine at UBC is a hybrid, academically intensive Department within the UBC Faculty of Medicine whose activities span a broad spectrum of teaching, research, and academic service, often performed in the milieu of clinical practice, and are ultimately devoted to improving the care, treatment, and well-being of patients.  The Department offers academic degrees at the bachelor’s (Bachelor of Medical Laboratory Science (BMLSc)) and graduate (MSc, PhD) levels with the graduate program, one of the largest in the Faculty of Medicine, which has been recognized by UBC for its quality. The Department plays a major role in the MD undergraduate program and offers an accredited residency-training program. Faculty members participate across a spectrum of research from basic investigative to translational to clinical applied research and are recognized locally, nationally and internationally for their excellence.

Work Performed:

  • Management and supervision of trainees;
  • May be involved in recruitment and training of trainees;
  • Performing regular reviews of the relevant literature;
  • Planning and designing of experiments;
  • Analyzing, interpreting and compiling data in study reports, presenting results, and participating in the preparation of scientific manuscripts and grant application packages;
  • Updating Dr. Aparicio and the group on the status of projects during lab meetings, in email correspondence and phone conferences;
  • Managing projects with key academic and industry partners.

Minimum Qualifications:

  • PhD degree in the computer science, bioinformatics or equivalent
  • At least 4 years experience in bioinformatics research
  • Experience in genomics and next-generation sequencing
  • Extensive knowledge of cellular and molecular biology, biochemistry and genetics
  • Experience with cancer research a plus
  • Proven ability to multi-task in a deadline oriented environment with minimal supervision
  • Effective oral and written communication, analytical, and interpersonal skills
  • Excellent organizational skill and ability to learn new skills quickly
  • Ability to work independently and within a team environment.
  • Accuracy and attention to detail required
  • Candidates should demonstrate the ability to work in a highly interdisciplinary environment.

Supervision Received:

  • Works independently under direction of PI, Dr. Samuel Aparicio
  • Opportunities to work collaboratively with Industry partners and other researchers at UBC and globally

Supervision Given:

  • Assists and oversees research assistants and students as required
  • Assists and provides guidelines to other research members, as required

How to Apply:

Exceptional candidates should submit a cover letter outlining your research interests and fit with the laboratory's research, curriculum vitae, and the names of three referees willing to provide letters of reference.

Due to the number of resumes we receive, we are unable to confirm receipt of submissions over the phone, or provide the status of the competition. Only shortlisted candidates will be contacted.

This position is located within a health-care facility. Therefore, this positions requires successful verification of full vaccination against Covid-19 provided prior to the start date, as required by the provincial health mandate.

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.

Email to apply: careersmolonc@bccrc.ca

Please put Bioinformatics PDF in the subject line.

Research Assistant 2

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. You will become an integral part of the animal research team, providing technical support on animal research for multiple core projects within the lab.

DUTIES/ACCOUNTABILITIES

  • Perform a variety of established technical procedures according to written protocols.
  • Perform experiments by following established laboratory procedures according to written protocols.
  • Record results, including computer data entry.
  • Provide input regarding modification of procedures as requested by the Department Head, Principal Investigator, or designate.
  • Maintain and store cell lines and primary cultures.
  • Maintain and store test materials and products.
  • Maintain inventory of laboratory supplies and equipment.
  • May demonstrate work methods or procedures to less experienced assistants as designated.

QUALIFICATIONS

  • A level of education, training, and experience equivalent to graduation from a recognized Bachelor’s program in an appropriate discipline (e.g. Bachelor of Science)
  • Two (2) years of recent related experience in a research laboratory
  • As this role will be spending the majority of the time in an animal research facility working with mice – mice handling experience is preferred.

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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