McMaster University

Population Genomics
Program

Scope of Search

 

Genetic and Molecular Epidemiology Laboratory (GMEL)

The Genetic and Molecular Epidemiology Laboratory (GMEL) provides a broad range of genomics  and proteomics solutions from high-throughput DNA/RNA extraction to sample quantitation and quality assessment, microarray-based experiments (genotyping, gene expression, methylation), next-generation sequencing (exome, RNA, custom target, low-pass whole-genome), multiplexed protein biomarker assays, and many other services. Our laboratory specializes in large-scale population genetic studies, and as such, is capable of handling project sizes ranging from single samples to > 10,000 samples. Additionally, we provide support for experimental design considerations, bioinformatics and statistical analyses, and interpretation/ reporting of results.

Located in the core of downtown Hamilton at the David Braley Cardiovascular and Stroke Research Institute, the GMEL directed by Dr. Guillaume Paré is fully equipped to perform cutting-edge genomics experiments. The GMEL possesses a broad variety of instrumentation (QIAsymphony, BioAnalyzer, Fragment Analyzer, Gene Titan array scanner, Illumina iScan, 2 Ion Torrent S5XL Sequencers, BioNano Genomics Irys System, Thermofisher ViiA7 RT-PCR System, QuantStudio 3D Digital PCR System, Pyromark Q24 instrument, BioMark HD System, Bio-Plex Luminex Multiplex assays, Olink panel assays, SomaLogic SOMAscan assay) as well as the necessary bioinformatics infrastructure (10 dedicated servers) to process large genomics projects at reasonable turnaround times.

Services Available

Nucleic Acid Isolation and Preparation

DNA and RNA extraction from a wide variety of materials including: buffy coat, whole blood, dried blood spots, FFPE, saliva, tissue samples and dried blood spots.  Quantitation using Nanodrop, Picogreen, or Qubit assay.  Fragment analysis using Bioanalyzer or Fragment Analyzer instruments.

Genotyping

Full complement of Thermofisher (formerly Affymetrix) genotyping arrays including: Precision Medicine Research Array and UK Biobank Array

Custom Axiom (formerly Affymetrix) genotyping – 300-200,000 marker density

Genotyping (1-96 SNPs) - Taqman and SNPtype assays using ViiA7 and BioMark instruments.

 

Full complement of Illumina genotyping arrays including: Global Screening Array, CoreExome, Omni2.5 arrays with semi-custom (add-on) content available for most arrays

Custom Infinium genotyping - 3-90K or 90,001-700K marker density

DNA Methylation

Array based methylation using Illumina MethylationEPIC Array

Targeted methylation using Qiagen Pyromark Q24

qPCR based methylation profiling

Gene Expression

Full complement of array based gene level expression profiling and whole transcriptome analysis including ClariomS and Clariom D microarrays by Thermofisher (Affymetrix). 

qPCR based gene expression analysis.

See “Next-Generation Sequencing” section for sequencing based options.

Next-Generation Sequencing

Ion Torrent sequencing using S5XL instruments:

Pre-designed and custom panel development for targeted sequencing using Ampliseq technology

Whole Exome Sequencing using Ion Ampliseq Exome library preparation and Ion Torrent sequencing technology

Low pass Whole Genome Sequencing

Sequencing based gene level expression profiling using Ion Ampliseq Transcriptome and whole transcriptome analysis using Ion Total RNAseq

See “Expression” section for array based options.

Copy Number Detection and Genomix Assembly

Whole Molecule Sequencing, long range genomic mapping, structural variations

GeneChips Thermofisher (formerly Affymetrix) including: Genome-Wide Human SNP Array 6.0 and OncoScan CNV Assay

Digital PCR for rare allele detection, precise copy number variation and low‐level fold change of gene expression

Biomarker Testing

Certified service provider of Olink assay - 92 biomarkers per panel with 12 panels covering all major disease areas including the following:  Cardiometabolic, Neurology, Oncology, and Inflammation.  Validated for EDTA serum and plasma.  Other sample types possible.  <1µl of sample per panel required for testing.

 

Certified service provider of SOMAscan assay - 1,310 biomarkers per sample with protocols for human EDTA serum and plasma, CSF, heparin plasma, cell lysates, cell conditioned media.  Other sample types and species possible.  ~150µl of sample required for testing.

 

Luminex multiplex biomarker testing – 1-96 analytes

Bioinformatics Services

We offer flexible bioinformatics support for all genomics services with regards to:

  • Experimental design and planning considerations
  • Quality control assurance
  • Statistical analysis 
  • Results interpretation and reporting 
  • Methodological / analytical tool development and optimization

 

www.thermofisher.com

www.illumina.com/

www.olink.com/

http://somalogic.com/

 


 

Contact: 

Laboratory Director, Dr. Guillaume Paré, pareg@mcmaster.ca
Laboratory Manager, Reina Ditta, reina.ditta@phri.ca Tel. 905-521-2100 ext. 40612

David Braley Cardiac, Vascular and Stroke Research Institute
30 Birge Street, Room 1-10 C4 North 207
Hamilton ON L8L 0A6