Genomics

The mandate of the genomics core facility at Sunnybrook Research Institute (SRI) is to provide cutting-edge genomics services to scientists and clinicians, as well as to academic and clinical collaborators. The facility supports research by clinical departments at Sunnybrook and other major hospitals as they embrace genomic approaches to cancer screening and diagnostics.

The genomics facility is a centralized resource equipped with next-generation instrumentation designed to provide timely support for genomics research and clinical practice. We have extensive experience in innovative genomics research, providing expert services and consultation for whole genome sequencing, exome sequencing, RNA sequencing and targeted next-generation sequencing of cancer genes, as well as quantitative PCR and quantification of CRISPR/Cas9-mediated genome editing events using droplet digital PCR technology. We also provide gene expression analysis using NanoString’s nCounter Analysis system for Biomarker validation and Biomarker Development.

Our services require unique expertise and training not routinely available at research hospitals and clinical departments of hospitals. Furthermore, most research groups lack the capital investment provided to the centre.

The facility remains competitive and relevant by continually updating and expanding services and equipment in parallel with keeping up with advances in technology and applications. Few centres have networks that include direct access to both pathologists and academic researchers. For Sunnybrook researchers and clinicians, the genomics facility provides face-to-face consultation and the fastest turnaround time possible.

We also provide opportunities for SRI research fellows, graduate students and residents to gain experience and training. We encourage collaborative opportunities with investigators on research projects and support investigators’ grant applications.

Equipment

Ion Torrent DNA Sequencing Systems

Ion Chef and Ion S5XL DNA sequencer
Ion Reporter

Ion Reporter

System specifications

  • Ion Torrent semiconductor sequencing employs natural nucleotides, a highly efficient DNA polymerase that readily incorporates the nucleotides within a buffer-free environment and requires no optics to result in quality data.

  • Ion Chef System fully automates AmpliSeq library and template preparation, including clonal amplification of final library pools and reproducible chip loading to minimize variability of sequencing result.
  • Ion Reporter Software provides an optimized suite of data analysis tools that support the analysis of data from Ion S5XL and Ion PGM Systems, covering a growing number of research applications, from human variant detection to microbial diversity.

Amplicon based targeted Exome and RNA sequencing

Ion AmpliSeq technology provides exome and RNA sequencing with ultra-high-multiplex PCR primer pools designed for fast and simple production of thousands of targeted amplicons from formalin-fixed, paraffin-­embedded, fine needle biopsy and cell-free DNA research samples.

Ion AmpliSeq Cancer Panel Sequencing

Amplicon-based targeted gene sequencing panels are helpful tools for analyzing specific mutations in a given sample. Ion AmpliSeq Cancer Hotspot Panel v2 (PDF) can be used as a reliable diagnostic assay for the detection of somatic mutations in tumours. Our facility is seeing tremendous success with sample types, such as formalin-fixed paraffin-embedded tissue and circulating cell-free DNA extracted from blood.

Oncomine Cancer Assays

Oncomine assays are multi-biomarker targeted assays designed for cancer research. Enabling next-generation sequencing analysis of multiple biomarker types—fusions, insertion/deletions, single nucleotide variants, and copy number variations from genomic DNA, RNA and cell-free DNA—Oncomine assays are part of an end-to-end workflow that includes simple, scalable sequencing with Ion PGM and Ion S5 Series sequencers, and optimized bioinformatics and reporting with the Oncomine knowledge base.

Whole transcriptome and miRNome analysis by sequencing

The Ion Total RNA-Seq Kit v2 provides a rapid method for preparing representative circulating DNA libraries for strand-specific sequencing of whole transcriptome or small-RNA libraries.

Please contact Dr. Arun Seth or Dr. Yutaka Amemiya for more information on sample requirements, scheduling, data analysis options and pricing.

Droplet Digital Polymerase Chain Reaction

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The QX200 Droplet Digital PCR System

Droplet digital polymerase chain reaction (PCR) technology provides ultrasensitive and absolute nucleic acid quantification. It is useful for low-abundance targets, targets in complex backgrounds and allelic variants. This technology is also approved for in vitro diagnostic assays.

Real-Time Polymerase Chain Reaction System

StepOnePlus Real-Time PCR System

The StepOnePlus Real-Time polymerase chain reaction (PCR) system is a 96-well, real-time PCR instrument. This system can be set up in a variety of configurations and is designed to deliver precise, quantitative real-time PCR results for a variety of genomic research applications.

Real-time PCR is a technique that allows for the quantification of DNA molecules in samples. Amplicons from DNA are measured as a relative value normalized to an endogenous control gene or DNA input.

RNA/DNA quantity and quality analysis

Agilent 2100 Bioanalyzer

Agilent 2100 Bioanalyzer is used for sizing, quantitation and purity assessments for DNA, RNA and protein samples.

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Qubit 3.0 Fluorometer

Qubit 3.0 Fluorometer is the next generation of the benchtop fluorometer that accurately measures DNA, RNA and protein using the highly sensitive Qubit quantitation assays.

nanoString nCounter FLEX Analysis System
NanoString nCounter FLEX Analysis System

Fully automated and easy-to-use, the nCounter FLEX Analysis System with optional Dx enablement is a platform optimized for translational research. This instrument provides a sensitive, reproducible, and highly multiplexed method for detecting multiple mRNAs/miRNAs isolated from any source, including fresh or frozen cells and tissues, formalin-fixed paraffin-embedded tumor samples and biological fluids such as blood, plasma, serum and urine samples. The assay utilizes NanoString’s nCounter platform to offer direct, digital counts of each RNA without the use of reverse transcription or amplification. It is a unique, targeted discovery and validation tool that enables collection of expression data for coding and noncoding RNA in a short amount of time with minimal hands-on manipulation.

Please contact Dr. Arun Seth or Dr. Yutaka Amemiya for more information on sample requirements, scheduling, data analysis options and pricing.

For ­pricing information, please contact Dr. Arun Seth  or Dr. Yutaka Amemiya .

At the genomics core facility, we are happy to offer a variety of services beyond the use of equipment to aid in research needs.

  • Amplicon-based exome and RNA sequencing
  • Ion Ampliseq targeted panel sequencing
  • Nucleic acid quantification by droplet digital PCR and qPCR technologies
  • Consultation on experimental design
  • Consultation on data analysis and management strategies
  • Test development for molecular diagnostics

Recent publications

Hodgson A, Amemiya Y, Seth A, Djordjevic B, Parra-Herran C. High-grade müllerian adenosarcoma: genomic and clinicopathologic characterization of a distinct neoplasm with prevalent TP53 pathway alterations and aggressive behavior. Am J Surg Pathol. 2017 Aug 22.

Hodgson A, Amemiya Y, Seth A, Cesari M, Djordjevic B, Parra-Herran C. Genomic abnormalities in invasive endocervical adenocarcinoma correlate with pattern ofinvasion: biologic and clinical implications. Mod Pathol. 2017 Jul 21.

Aguilar OA, Berry R, Rahim MM, Reichel JJ, Popović B, Tanaka M, Fu Z, Balaji GR, Lau TN, Tu MM, Kirkham CL, Mahmoud AB, Mesci A, Krmpotić A, Allan DS, Makrigiannis AP, Jonjić S, Rossjohn J, Carlyle JR. A viral immunoevasin controls innate immunity by targeting the prototypical natural killer cell receptor family. Cell. 2017 Mar 23;169(1):58–71.

Abdul-Wahid A, Cydzik M, Prodeus A, Alwash M, Stanojcic M, Thompson M, Huang EH, Shively JE, Gray-Owen SD, Gariépy J. Induction of antigen-specific TH 9 immunity accompanied by mast cell activation blocks tumor cell engraftment. Int J Cancer. 2016 Aug 15;139(4):841–53.

Nam RK, Benatar T, Wallis CJ, Amemiya Y, Yang W, Garbens A, Naeim M, Sherman C, Sugar L, Seth A. MiR-301a regulates E-cadherin expression and is predictive of prostate cancer recurrence. Prostate. 2016 Jul;76(10):869–84.

Klenov A, Neller KC, Burns LA, Krivdova G, Hudak KA. A small RNA targets pokeweed antiviral protein transcript. Physiol Plant. 2016 Mar;156(3):241–51.

Wallis CJ, Gordanpour A, Bendavid JS, Sugar L, Nam RK, Seth A. MiR-182 Is Associated with Growth, Migration and Invasion in Prostate Cancer via Suppression of FOXO1. J Cancer. 2015 Oct 25;6(12):1295–305.

Nam RK, Amemiya Y, Benatar T, Wallis CJ, Stojcic-Bendavid J, Bacopulos S, Sherman C, Sugar L, Naeim M, Yang W, Zhang A, Klotz LH, Narod SA, Seth A. Identification and validation of a five microRNA signature predictive of prostate cancer recurrence and metastasis: a cohort study. J Cancer. 2015 Sep 15;6(11):1160­–71.

Cydzik M, Abdul-Wahid A, Park S, Bourdeau A, Bowden K, Prodeus A, Kollara A, Brown TJ, Ringuette MJ, Gariépy J. Slow binding kinetics of secreted protein, acidic, rich in cysteine-VEGF interaction limit VEGF activation of VEGF receptor 2 and attenuate angiogenesis. FASEB J. 2015 Aug;29(8):3493–505.

Amemiya Y, Bacopulos S, Al-Shawarby M, Al-Tamimi D, Naser W, Ahmed A, Khalifa M, Slodkowska E, Seth A. A comparative analysis of breast and ovarian cancer-related gene mutations in Canadian and Saudi Arabian patients with breast cancer. Anticancer Res. 2015 May;35(5):2601–10.

Prodeus A, Abdul-Wahid A, Fischer NW, Huang EH, Cydzik M, Gariépy J. Targeting the PD-1/PD-L1 immune evasion axis with DNA aptamers as a novel therapeutic strategy for the treatment of disseminated cancers. Mol Ther Nucleic Acids. 2015 Apr 28;4:e237.

Allan DS, Kirkham CL, Aguilar OA, Qu LC, Chen P, Fine JH, Serra P, Awong G, Gommerman JL, Zúñiga-Pflücker JC, Carlyle JR. An in vitro model of innate lymphoid cell function and differentiation. Mucosal Immunol. 2015 Mar;8(2):340–51.

Wang T, Amemiya Y, Henry P, Seth A, Hanna W, Hsieh ET. Multiplex ligation-dependent probe amplification can clarify HER2 status in gastric cancers with “Polysomy 17”. J Cancer. 2015 Feb 26;6(5):403–8.

Mulvaney JF, Amemiya Y, Freeman SD, Ladher RK, Dabdoub A. Molecular cloning and functional characterisation of chicken Atonal homologue 1: a comparison with human Atoh1. Biol Cell. 2015 Feb;107(2):41–60.

Sivanathan L, Chow A, Wong A, Hoang VC, Emmenegger U. In vivo passage of human prostate cancer cells in mice results in stable gene expression changes affecting numerous cancer-associated biological processes. Prostate. 2014 May;74(5):537–46.

Chatterjee S, Bacopulos S, Yang W, Amemiya Y, Spyropoulos D, Raouf A, Seth A. Loss of Igfbp7 causes precocious involution in lactating mouse mammary gland. PLoS One. 2014 Feb 4;9(2):e87858.

Huang X, Taeb S, Jahangiri S, Emmenegger U, Tran E, Bruce J, Mesci A, Korpela E, Vesprini D, Wong CS, Bristow RG, Liu FF, Liu SK. miRNA-95 mediates radioresistance in tumors by targeting the sphingolipid phosphatase SGPP1. Cancer Res. 2013 Dec 1;73(23):6972–86.

Deng Z, Yang X, Fang L, Rutnam ZJ, Yang BB. Misprocessing and functional arrest of microRNAs by miR-Pirate: roles of miR-378 and miR-17. Biochem J. 2013 Mar 1;450(2):375­86.

Shan SW, Fang L, Shatseva T, Rutnam ZJ, Yang X, Du W, Lu WY, Xuan JW, Deng Z, Yang BB. Mature miR-17-5p and passenger miR-17-3p induce hepatocellular carcinoma by targeting PTEN, GalNT7 and vimentin in different signal pathways. J Cell Sci. 2013 Mar 15;126(Pt 6):1517­–30.

Chow A, Amemiya Y, Sugar L, Nam R, Seth A. Whole-transcriptome analysis reveals established and novel associations with TMPRSS2:ERG fusion in prostate cancer. Anticancer Res. 2012 Sep;32(9):3629–41.

Buckley KM, Rast JP. Dynamic evolution of toll-like receptor multigene families in echinoderms. Front Immunol. 2012 Jun 5;3:136.


Contact

Professor Arun Seth, PhD Academic director 416-480-6100 ext. 63537, Room S2 38
Yutaka Amemiya, PhD Manager 416-480-6100 ext. 63108, Room C7 50b