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

Benoit Prevost-Potvin

Software Developer

Post-Docs

Yangguang (Sunny) Li

Post-Doctoral Fellow

Students/Trainees

Open Positions

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

Breast Pathology Fellowship

Breast Pathology Fellowship
Providence Health Care, Department of Pathology and Laboratory Medicine

One Year Term (with potential extension)

This unique fellowship is comprised of both clinical and research components in equal parts and provides an opportunity to gain research experience as a fellow. Fellows will divide their time between BC Cancer Agency, Mount Saint Joseph and St. Paul’s Hospitals and rotate through the clinical pathology laboratory and the research laboratory at BC Cancer. Fellows work closely with the breast multidisciplinary team, actively participating in rounds and providing service and consultation to clinicians in matter relating to breast diseases. It is expected that the fellow participates in collaborative research, with an option to conduct individual research, all under the guidance of a faculty member and/or pathologist]. This includes research proposals, submitting abstracts to scientific meetings and preparing manuscripts for publication in peer-reviewed journals.

Candidates with the following qualifications/experience are preferred:

  • Canadian citizenship or permanent residency.
  • MSc or PhD.
  • Research experience, especially molecular biology.

Salary will be commensurate with qualifications and experience.

To apply for this rewarding career development opportunity, please forward (1) a letter of application outlining your areas of interest, (2) a copy of your current CV, and (3) names and contact information of three references, to:

PHSA Talent Acquisition
careers@phsa.ca

Post-doctoral fellow in the Biochemistry and Chemical Biology of Spliceosome Regulation

The Genome Sciences Centre Department within the British Columbia Cancer Agency in Vancouver, British Columbia, Canada has an opening for a post-doctoral fellow in the laboratory of Dr. Gregg Morin, to study the mechanisms-of-action of pharmacological inhibition of proteins that regulate pre-mRNA splicing. The scientist will join a collaboration with Drs. Samuel Aparicio and Sohrab Shah that is using global genomic technologies to identify changes in alternative splicing due to inhibition of several classes of enzymes that regulate spliceosome function. The objective is to investigate how these enzymes regulate genome-wide spliceosomal function and splice site choice.

The position will perform laboratory research to design and interpret experiments using biochemical, proteomic, molecular and genomic tools to investigate the functional mechanisms of enzyme inhibition on the spliceosome and its regulatory proteins in human cancer cells. The candidate should have experience in ribonucleoprotein biochemistry, mammalian tissue culture, enzymatic assays, recombinant protein purification, molecular biology, and RNAi. Experience in the structure/function analysis of RNPs or enzymes and a comprehensive understanding of splicing and spliceosome function are essential.

The successful scientist will join the laboratory of Dr. Gregg Morin in the Michael Smith Genome Sciences Centre at the BC Cancer Agency. In collaboration with the laboratories of Dr. Samuel Aparicio and Dr. Sohrab Shah, the team has access to exceptional tools for next generation sequencing, bioinformatics, and advanced proteomics.

The Genome Sciences Centre provides a stimulating working environment and is located at the new British Columbia Cancer Research Centre in Vancouver, one of the world’s most livable and attractive cities.

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

Additional information can be obtained at www.bcgsc.ca.

Applicants should send a cover letter, curriculum vitae, and names of three referees by email, fax or mail to:

Dr. Gregg B. Morin
Genome Sciences Centre, BC Cancer
675 West 10th Avenue
Vancouver, BC, V6S 1L3, Canada
Email: bcgscjobs@bcgsc.ca
Fax: 604-675-8178

Selected Publications

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

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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