- To accelerate the translation of cancer research discovery into improved cancer patient care.
- To develop standardized procedures to enable routine linking of molecular profiling with clinical decision to deliver precision therapy and improve cancer patients’ care.
Molecular Analysis Unit:
- DNA/RNA/miRNA extraction (fresh and FFPE material)
- NGS library preparation and QC
- Genomic sequencing (Illumina Next Seq 500 and Ion S5 XL)
- Digital PCR analysis (rare allele detection)
- Single cell sequencing
- NanoString nCounter (RNA/miRNA expression, copy number analysis)
Genomic Studies Provided:
Whole exome sequencing, whole transcriptomic sequencing, targeted SNV and fusion gene sequencing panels (Oncomine Comprehensive Assay, Oncomine Childhood Cancer Assay, Oncomine TMB Assay), digital PCR for rare mutation profiling, single cell RNASeq/ATAC Seq and gene expression profiling.
Bioinformatic Analysis Provided:
DNA-based analysis: single nucleotide variants (SNV) calling, tumor mutational burden (TMB), copy number variants (CNV), structural variant (SV), microsatellite instability (MSI) and DNA-based fusion detection for DNA-seq. RNA-based analysis: RNA expression, RNA based fusion detection, RNA variation detection for RNA-seq.
Functional Tissue Imaging:
- Sample processing:
- Collection of FFPE samples from Alberta Precision Laboratories and other repositories
- Generation of clinical outcome databases
- Construction of tissue microarrays
- Processing of FFPE for various downstream applications
- Tissue staining and scanning:
- Creation of customize biomarker expression cell lines as immunohistochemistry (IHC) controls
- Antibody optimization and validation for brightfield and immunofluorescent IHC for up to 9-color multiplex immunofluorescence assay
- Brightfield and immmunofluorescent whole-slide scanning
- Basic biochemical IHC stains including H&E
- Digital Image Analysis and Machine Learning:
- Clinical accredited automated Ki67 scoring and random forest analysis to predict risk of recurrence in breast cancer
- Quantitative analysis of IF/IHC-based biomarker images
- Multispectral digital image acquisition and unmixing
- Evaluation of tumor microenvironment including quantification of various immune cell, spatial analysis such as nearest neighbor, proximity to tumor cells, immune heat maps
Antibody optimization for brightfield and immunofluorescent IHC, multispectral digital image acquisition, image analysis using digital pathology software, automated Ki67 scoring for breast cancer, multiplex immunofluorescent phenotype of tumor microenvironment, customize biomarker expression using cell biology approaches, and tissue microarray construction.
- Sample Processing and Extraction:
- Purification, protein precipitation, extraction and concentration of small molecule analytes in biological matrices via solid phase extraction (SPE) and liquid-liquid organic extraction.
- Plasma protein binding studies
- Analytical Quantitative Analysis:
- Method development and analytical analysis on High performance liquid chromatography platforms (HPLC)
- Method development and analytical analysis of small drug molecules and metabolites via tandem triple quad LC/MS/MS
- Elemental analysis by Atomic Absorption Spectroscopy
- Pharmacokinetic / Pharmacodynamic Data Analysis and Modeling:
- Non-compartmental and compartmental pharmacokinetic models by Phoenix WinNonlin
- Linked pharmacokinetic and pharmacodynamic models
- Population pharmacokinetic models by Phoenix NLME
- Clinical Trial Support:
- Pharmacokinetic trial, PK sampling, and Phase I trial design
- Alberta Precision Laboratory Clinical Services:
- Therapeutic drug monitoring and dose adjustment of Busulfan
- Thiopurine Methyl Transferase (TPMT) enzyme phenotype assay
- Vitamin B1 and B6 in whole blood