Genomic Analysis

The Laboratory for Advanced Genome Analysis (LAGA) occupies 3,600 square feet of laboratories and offices and houses state-of-the-art equipment. LAGA specializes in the acquisition, processing, statistical analysis, integration, and visualization of next-generation sequencing (NGS) and microarray data to enable and advance basic and translational research.

LAGA offers economically priced services based on a cost-recovery, not-for-profit model. The facility provides researchers with the highest quality results; manages research projects from experimental design to interpretation of data; and supports the researchers’ grant applications and publications.

From 2011 to 2017, LAGA has produced >20 peer-reviewed publications on the characterization of the neuroendocrine phenotype in prostate cancer (1-3), cancer heterogeneity (4), characterization patient-derived xenografts for better in vitro models (5-7), integrative analysis of genomic and transcriptomic data for the discovery of patient’s prostate cancer (8), development of new methods for the detection of structural variants (9), ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA (10), RNA editing (11), detection of fusions (12) and alternative splicing (13,14), analysis of clonality (15,16), pathway and subnetwork (17), identification of clinical variants (18-20), identification of a gene expression signature (21) and drivers for therapeutic targeting (17,22).

References

  1. From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. Lapuk AV et al. (2012). J Pathol. 227(3):286-97. PMID: 22553170.
  2. Identification of DEK as a potential therapeutic target for neuroendocrine prostate cancer. Lin D et al. (2015) Oncotarget. Jan 30;6(3):1806-20. PMID: 25544761.
  3. The Placental Gene PEG10 Promotes Progression of Neuroendocrine Prostate. Akamatsu S et al. (2015) Cancer. Cell Report. 2015 Aug 11;12(6):922-36. PMID: 26235627.
  4. The inter-tumor transcriptome heterogeneity of high-risk primary prostate cancer Wyatt A et al (2014). Genome Biology 2014 Aug 26;15(8):426. PMID: 25155515.
  5. Lessons from patient-derived xenografts for better in vitro modeling of human cancer. Choi SY et al. (2014) Adv Drug Deliv Rev. Dec 15;79-80:222-37. PMID: 2530533
  6. Next generation patient-derived prostate cancer xenograft models. Lin D et al. (2014) Asian J Androl. May-Jun;16(3):407-12. PMID: 24589467
  7. High fidelity patient-derived xenografts for accelerating prostate cancer discovery and drug development. Lin D et al. (2014) Cancer Res. Feb 15;74(4):1272-83. PMID: 24356420
  8. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. Wu C, Wyatt AW et al. (2012). J Pathol. 2012 May;227(1):53-61. PMID: 22294438
  9. Nfuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing. McPherson A et al. (2012). Genome Research. 22: 2250-2261. PMID: 22745232
  10. SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA. Can Kockan et al. (2017) Bioinformatics Jan 1;33(1):26-34. PMID: 27531099
  11. Systematic identification and characterization of RNA editing in prostate tumors. Mo F. et al. (2014). PLoS One. Jul 18;9(7):e101431. PMID: 25036877
  12. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Wu C et al. (2012) Genes Chromosomes Cancer. Dec;51(12):1144-53. PMID: 22927308.
  13. ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Dao P et al. (2014) Bioinformatics. Mar 1;30(5):644-51. PMID: 24130305.
  14. The role of mRNA splicing in prostate cancer. Lapuk AV et al., (2014) Asian Journal of Andrology. 2014 July-Aug; 16(4):515-21. PMID: 24830689.
  15. Clonality inference in multiple tumor samples using phylogeny. Malikic S et al. (2015) Bioinformatics. May 1;31(9):1349-56. PMID: 25568283.
  16. Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. Donmez Net al. (2017) J Comput Biol. Jun;24(6):515-523. PMID: 28056180
  17. HIT'nDRIVE: patient-specific multi-driver gene prioritization for precision oncology. Shrestha R et al. (2017) Genome Res. Sep;27(9):1573-1588. PMID: 28768687
  18. Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target. Collins CC et al. (2012): Mol Cancer Ther 11(3): 775-83. PMID: 22252602
  19. Androgen receptor gene aberrations in circulating cell-free DNA: biomarkers of therapeutic resistance and response in castration-resistant prostate cancer. Azad AA et al., (2015). Clinical Cancer Research. 21:2315-24. PMID: 25712683
  20. Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer. Wyatt AW et al., (2016) JAMA Oncol. Dec 1;2(12):1598-1606. PMID: 27148695
  21. Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer. Mo F. Eur Urol. 2017 Mar 19. doi: 10.1016/j.eururo.2017.02.038. [Epub ahead of print] PMID: 28330676
  22. A meta-analysis approach for characterizing pan-cancer mechanisms of drug sensitivity in cell lines. Wang K et al (2014). PLosOne 2014 july 18;9(7):e103050. PMID: 25036042.

A World Class Centre

The Vancouver Prostate Centre (VPC) has a track record of success that has earned it a reputation as one of the world’s most respected cancer facilities. It is a National Centre of Excellence and a designated Centre of Excellence for Commercialization and Research.

Events

VPC Terry Fox team 2016

Terry Fox Run: Sunday September 16, 2018

On Sunday September 16, the fundraising Terry Fox walk/run/ride is taking place across Canada.  We are grateful for our  grant support provided by The Terry Fox Foundation and Terry Fox Research Institute continously since 1998 - click here to donate to our team (opens in new window)

 

Vancouver

18th Annual Pacific Northwest Prostate Cancer Conference: Sat Sept 22, 2018

The 18th Annual Pacific Northwest Prostate Cancer Conference for patients, their families and health care professionals will be held in Vancouver on Saturday September 22, from 8 AM to 4 PM.  Click here for further details and to purchase tickets ($30, includes lunch). (Opens in new window)

 

Employment

Work at the Vancouver Prostate Centre

Thursday, July 26, 2018

Dr. Gleave awarded the 2018 Dr. Chew Wei Memorial Prize in Cancer Research

Dr. Gleave
Tuesday, May 29, 2018

Three VPC trainees receive 2018 VCHRI Rising Star Awards

2018 Rising Star Awardees
DNA

Make A Difference

Help the Vancouver Prostate Centre fund research to find better treatments and a cure.